The Stuff of Life

A break from blogging

2011-07-19T06:32:00.001+01:00

The Stuff of Life is taking the rest of the summer off to spend time with the kids, but will be back!

Huntington’s disease – genetic testing, children and hope

2011-07-08T06:14:00.001+01:00

Undergoing a genetic test can be a blurry game of statistics. The results may provide an estimate of your disease risk, but certainties are few and far between. For Huntington’s disease the numbers are painfully simple. The gene has a high penetrance so, without further medical advances, if you’ve got the gene then you’ll get the disease.

I spoke to Angela, whose mother has Huntington’s, as did her mother before her. Angela blogs about her experiences and was kind enough to answer my questions about genetic testing and trying for a baby with Huntington’s in the family.

How did you decide whether to test for the HD gene?

I found out about HD being in the family when I was 16 or so. From the second I found out, I never wanted to know whether I carried the gene. I couldn’t see what good would come with it, but literally one day something changed inside me and all of a sudden I wanted to know. It wasn’t for one reason specifically, it was everything. I was starting to settle down – I’d met my husband, I’d started my career, I’d bought a house... Everything was falling into place and I just wanted to know whether or not I carried the disease. The change was so sudden and so complete, it was not a difficult decision. But I did sit on it for a year before I approached anyone about arranging a test so that I was sure that it was what I wanted.

How did you feel when you found out you have the gene?

When we walked out of the clinic, I was devastated and could barely hold myself up. I felt utterly defeated and I just could not imagine how life would continue. But it did. I was back at work the next day, we started planning our future, a big holiday, our wedding, our house together, our plans for children… I started reading lots of websites trying to find answers. I got hooked in with research projects at the hospital and through the HDA. I did a few fundraising events for the HDA. I wrote my blog and met new people. I threw myself back into our lives and our future, and each day, it got easier. There were bad days for a long while but not really anymore. Now, I think sometimes we do push ourselves maybe more than we had before in case we don’t have as long as other couples but generally we just get on with things. And other than the struggles we have had with starting our family, we have a good life. We are happy. And I don’t see it as being inevitable that I will get the disease even though I carry the gene. I am ever hopeful for a cure, that’s why I do everything I can to raise awareness via interviews and the blog, and take part in research projects.

Can you understand people who don’t want to find out?

I can totally understand. That was me for a long time. People need to work out their own routes and what works best for one person may not be the answer for someone else.

What about trying for children?

We chatted through all the options. Preimplantation genetic diagnosis (PGD) IVF offered us the route to have a child that was genetically related to both of us, without passing on the risk of HD. We both wanted to protect our children and our future descendants from a disease that can have such a devastating effect on health and family lives. PGD IVF works for one fifth of couples and we hoped to be one of the lucky ones.

PDG is often blithely referred to as the answer to genetic disease, but your experience has not been straightforward.

We tried PGD IVF twice. It didn’t work for us. My body was excellent at producing numerous eggs but they just didn’t cope well with the IVF process. We’d start off with almost 20 eggs and one by one, they’d fall by the wayside, struggling to fertilise, to develop or to live through the biopsy. At the end of both cycles, we had one egg left that was HD-free and suitable for transfer although for both cycles. However, both of these eggs were poor quality and did not become a pregnancy.

Talking to the embryologist at our first clinic, and our doctors at the next clinic, my eggs just weren’t responding as they should. There was nothing they could do to boost their quality, and considering how poorly they had responded, we were lucky to have got as far as the transfer on both cycles. One of our doctors at the first clinic said we should just continue with the PGD, but we needed something different.

We were acutely aware that I wasn’t getting any younger and that HD may shorten how much time we have. Egg donation offered us new hope. Keeping me out of the initial process meant no risk of HD, better quality eggs, and a 50/50 chance of success. Yes, it would have been lovely to have been genetically related to our children but this way I still get to be involved almost from the very beginning. Genetics didn’t seem to matter anymore.

It may become routine in the future for the entire DNA sequence of every newborn baby to be determined. What do you think we should do with the information about HD status?

I would hope that it could be kept for the child to decide – after all they might not want their parents to know or they might not want to know themselves. I guess if it could affect their health before they were 18 years old and something could be done to help, they could find out when they were younger.

Do you think PDG IVF should be restricted to diseases such as HD that are serious, due to a single gene and have high penetrance (ie if you’ve got the gene you get the disease)? Or should it become more widely available in cases where having the gene does not mean the disease is certain?

I don’t think anyone can make that decision except the people involved themselves. All the options should be made available to people so they can make their own choices. But I do think that egg/sperm/embryo donation should be more widely discussed and encouraged - our first clinic was very dismissive of egg donation and advised us against going down this route. But it gives people a chance to have their own child and minimise the risk of genetic diseases, with a much higher chance of success.

Would you want to have your own DNA sequenced to learn about other disease susceptibilities?

I don’t know. It would depend on what support was available once I had the sequence. If there were ways we could prevent diseases occurring or research programmes to get involved in then I can see there are advantages of finding out.

What are your hopes for the future?

I hope for a cure for HD. I hope for a happy and healthy life with my family. I hope our children will understand the decisions that we made on their behalves, and I hope they too will lead happy and healthy lives, free from HD.

On 14^th February of this year Angela announced on her blog that the egg donation had succeeded and she was pregnant. Two days later she wrote:

We can look at each and say "We've stopped it. We've stopped Huntington's." And that thought alone is so powerful it consumes me. Our children, their children, their children, their children, their children... Descendants who we will never meet, but people whose lives won't be affected by Huntington's.

Many congratulations Angela!

The power and influence of newborn genetic testing

Role Models in Science

2011-06-15T07:01:00.003+01:00

As a 15-year-old I could have specialised in either science or humanities. It was immersion in the words of science writing greats, combined with first-rate maths teaching, which tipped the balance. Richard Dawkins, Stephen Jay Gould*, Mr Stanbrook the head of maths: none were women, but that didn’t matter.

My ambitions were not dampened by my gender; I was inspired to do science by extraordinary scientists. I had been brought up to believe that being female was irrelevant to career choice. (Maybe my mother was a role model due to my gender neutral childhood – I grazed my knees and hated pink). On the brink of science A-levels I owned my future and had no need for role models that were particularly like me.

I went on to a science career – a PhD followed by work in the biotech industry. I don’t remember being hugely disadvantaged by being female. I do recall feeling uncomfortable by my clear minority status at bioinformatics conferences, but sticking out in a crowd has its advantages too.

And then I had kids. Suddenly my gender mattered very much. Neither my husband nor I wanted to battle with two full time jobs, day-long childcare and weekends spent catching up with household chores. So I gave up my science job. It was heartbreaking. I cried. A lot.

I was offered part-time work but didn’t feel I could do my job (and commute) in the hours my baby would be happy in childcare. He may well have thrived in nursery, but my resistance was belly-deep and frustratingly refused to submit to feminist reason. (And this is not to imply that working mothers are insensitive to their children’s needs – we must each do what feels right for us). It was the best decision for the family as a whole, and because I am now based at home we enjoy a relatively relaxed, spacious existence.

I still needed to work, so I started my own business, working locally and intensely for about 12 hours a week. I choose my working hours (term-time only) and the job does not overspill into the rest of my life. The downside is that I no longer work in science. Scientific careers do not easily lend themselves to such plasticity and school based schedules.

Despite women’s progress, the well worn roles of woman=caregiver man=breadwinner remain too easy to slip into. Although I could “choose” whether to stay in science or leave, it didn’t feel much of a choice. Science careers (along with other interesting and challenging jobs) reward long hours, and those with caring responsibilities are marginalised as a result. There is still the inbuilt assumption that scientists have someone else taking care of their children. The workplace needs serious restructuring - both men and women should to be freed to share the joys, rewards and challenges of science and the home.

In order to soften the blow I have been telling myself I am on a career break. And now, five years down the line, the kids need me less and small windows are appearing in which I can start thinking science. The online world is a wonderful opportunity for those outside the scientific establishment to participate whilst the kids are asleep upstairs. I’m enjoying riding the wave of excitement in personal genomics, once again part of an intellectual bubble, this time from my sofa.

In two years time both my children will be at school and I may even work out a way to earn money from science. By then I will be approaching 40 and I’m aware there will be afterschool care and holidays to contend with for many more years.

So at this stage in my life I need role models. I need women to show me that being older does not mean you can no longer achieve. I don’t need free-range young women unencumbered by children. Nor am I inspired by peers who have managed to combine family and career in a way I have not, although hats off to them.

I need trail-blazing birds with a few wrinkles who are singing louder than ever. I want those who have the maturity, wisdom and breadth that come from living. I need to feel that the scientist inside me has not died forever and there is plenty of time to fulfil her teenage dreams.

Here are my role models. Ladies, I salute you all.

Do you use social media to stay up to date whilst on a career break from science? I am contributing a chapter to the book “Surviving as a women in science” and would love to hear your experiences - elaine dot westwick at googlemail dot com.

*Breaking news: it looks like as well as writing beautifully he may have made things up

Children, science and the perpetual why
Diversity in science blogging - a call for action
Wilma - women's science blogging database

This is a post for the June Scientiae Carnival

Cambridge BioResource - donating your DNA to science

2011-06-05T20:33:00.000+01:00

Last week I contributed a finger of blood to the Cambridge BioResource project. The DNA extracted from my sample will live in a 96 well plate alongside the genetic material from 10 000 other local donors. Together, we form a smorgasbord of genetically distinct volunteers from which researchers investigating human health can pick and choose. In this post I will explore science behind the resource, discuss the ethics of returning data to participants and reveal what bit of my DNA I'd really like sequenced.

With the needle in my arm I spoke to the resource coordinator, Sarah Nutland, who has been involved since the resource was conceived six years ago. My initial questions concerned the nature of the data that would be derived from my sample. In particular, I was keen to find out if my full genome sequence would be determined, or if analysis was restricted to more sparse genetic regions (genotyping). Until recently, full sequencing would not have been financially viable, but technological advances now make it a question worth asking.

I was surprised to learn that no genetic information is initially extracted from the volunteers’ DNA. Instead, sequencing is driven by each scientific project. If a research team are studying a particular region of DNA, then that region is genotyped across the panel of samples. The resulting genetic data is used to pool individuals, along with criteria such as gender, age and disease history. Scientists then have the luxury of choosing research subjects who fit their experimental design perfectly.

The power of the resource comes not from the high number of volunteers in each study (typically fewer than 100 people are involved), but from the diversity of the genetic potpourri from which participants can be picked. The bigger the resource, the more likely there will be enough people with the genetic makeup and characteristics required for each investigation.

There is a plan to double the number of volunteers, in part by recruiting patients suffering from a range of long term conditions. Links are being made with disease specialists and a recruitment bus will soon swing into action visiting GP surgeries to harvest donations. It is hoped that the involvement of patients will also inspire donations from their healthy acquaintances, keen to help out.

I have always been wary of taking part in clinical trials, valuing my fully functioning biology too much to risk ingesting pharmacological unknowns. But the types of experiments run by the resource are at a much more basal level. They examine the nuts and bolts of molecular biology, acting more as a prelude to the drug discovery process rather than an investigation of nascent drugs themselves. As a result, volunteer participation tends to be straightforward – in many cases blood and a signature are the only requirements. There are experiments which involve a bigger chunk of time, but participation is always optional. Sarah says that once a volunteer has completed their first study and realise how little is required they are likely to return for another, flush with the glow of donating to a good cause.

At this stage in the conversation the needle had been removed and my two-year-old had fallen asleep on my lap. He had been fussed over by the nurses and was now sleeping off a three-pack of custard creams and a beaker of orange juice the size of his daily fluid intake. As he snoozed, Sarah told me how the resource had been set up.

The lab she was working in, headed by John Todd, was using genetics to probe the biology of Type 1 Diabetes. The experiments needed human DNA, so lab members and clinical staff rolled up their sleeves. When they needed more they asked colleagues in neighbouring labs. Soon it became clear that collection needed a formal footing and BioResource was born.

Ethical considerations underpin the design of the resource and determine which individual studies gain approval. Volunteers are not given any details about their DNA sequence, and only studies where it is ethical to withhold this information are sanctioned. Even the project researchers can only access data tied to their research subjects, rather than across the whole panel of volunteers.

Although no information crucial to the health of each individual is generated, the studies still output genetic data I’d be very interested to learn. For example, a recent paper in Neuropsychologia used the resource to study how differences in the serotonin transporter gene affect the brain’s response to emotionally laden pictures. There are two flavours of the gene’s controller, short and long, your personal combination seems likely to influence how you respond to stress, including your predisposition to depression. Having been touched by the black dog in the past, I’d love to know my serotonin uptake inhibitor type (and I’m not the only one interested). As a rational scientist, I understand that the genetic association is swimming is in caveats and uncertainties, but, on an emotional level, I’d still like to know.

According to the paper’s lead author, Elisabeth von dem Hagen, no volunteers requested the information, and she points out that the pseudo-anonymisation procedure means that the scientists themselves were ignorant. “As researchers, we were blind to an individual’s genotype. It was only once we had completed data collection for the study that the BioResource panel released genotype information to enable us to complete the analysis. At that stage, participants have been anonymised by number so the genotype never gets released together with a name. This procedure also ensures that our data collection and analysis is blind to genotype and can’t be biased in any way.”

As the cost of sequencing falls, I wonder if a point will be reached when it will make financial, logistical and scientific sense to read full genome sequences, rather than running genotyping each time a study is initiated. However, the ethical issues that the resource now neatly side steps will then be unavoidable – what to do with actionable genetic liabilities uncovered along the way. Perhaps by then there will be parallel advances in clinical genetics and everyone, not just those volunteering for studies, will be having their DNA sequenced.

The project has a very Cambridge focus – you need to live near the city not only to donate but also to exploit the resource, physical proximity of subject and researcher being key. (Although if you can’t face battling with hospital parking spaces they will send a nurse to you). The metropolis that is Addenbrookes is very much the beating heart of the resource. DNA sequencing takes place on the site, many of the research groups are based there and Addenbrooke’s staff still make up a significant fraction of volunteers.

Due to the project’s success, bioresource envy is widespread, and Oxford and London are looking to start similar banks. Each would encompass volunteers and researchers from their immediate locality and the three centres could pool samples to enable work on rarer genetic variants.

If you live in the Cambridge area then take the time to visit the BioResource website and browse the wonderful science it sustains. Consider supporting basic medical research yourself - the commitment is small and, at some future point, you may benefit from discoveries made possible by your own unique contribution.

von dem Hagen EA, Passamonti L, Nutland S, Sambrook J, & Calder AJ (2011). The serotonin transporter gene polymorphism and the effect of baseline on amygdala response to emotional faces. Neuropsychologia, 49 (4), 674-80 PMID: 21167188

Related posts:

The impact of a genetic diagnosis
Finding out you are a cystic fibrosis carrier

The power and influence of newborn genetic testing

The impact of a genetic diagnosis

2011-05-22T20:38:00.001+01:00

Deciphering developmental disorders (DDD) is an exciting new project run by the Sanger Institute in partnership with NHS genetics clinics. It aims to use sequencing and microarray analysis to diagnose children with developmental problems.

I was struck by the impact a diagnosis has on the families involved and was drawn to a quote on the project’s home page from Beverly Searle, CEO of Unique (Rare Chromosome Disorder Group):

Over many years I have witnessed the frustration and heartache of many families for whom a reason for their child's developmental delay has not been found....more recently I have been delighted to see the relief and joy of other families on receiving a diagnosis

I asked Beverly if she could suggest someone to talk to and she put me in touch with Jane Gregory, whose daughter Chrissy was diagnosed using microarray analysis. Here is our conversation:

Tell me about Chrissy

We didn’t know anything was wrong at first but in hindsight the signs were there at the start. Chrissy’s suck was weak, she vomited up all her feeds and did not gain a healthy amount of weight. Her head was floppy and her developmental milestones were late. She started having epileptic seizures at about ten months and terrible head-banging screaming outbursts.

There was a gradual realisation that something was wrong, I kept badgering our doctors but they treated me like a neurotic first-time mum. My fears intensified when I compared Chrissy to other babies of the same age, and realised how far behind she was. However no one took my fears seriously until I was pregnant with my son when Chrissy was about a year and had started having epileptic seizures. Initially I thought the long difficult birth had caused Chrissy’s problems then I wondered if the whooping cough vaccine had contributed.

Chrissy is now 27 and has moderate/severe learning disabilities, epilepsy, severe autism (only diagnosed five years ago, coincidentally - the same year as the chromosome abnormality was found) and challenging behaviour. She also has days where she is absolutely adorable, funny, affectionate and compliant. She is in an independent hospital funded by the NHS for assessment and treatment to try to stabilise her moods and find a better treatment regime. She comes home every weekend.

How did the array analysis happen and what did you learn?

The array analysis came out of the blue. Chrissy had been seen regularly by geneticists at Great Ormond Street and when she was 14 they asked if we wanted to take part in a research study looking at the ends of chromosomes in people with unexplained learning disabilities. Nothing was found and we forgot all about it. I tried to come to terms with the fact that we would probably never know the cause of Chrissy’s problems.

When Chrissy was 22 I received a letter out of the blue from Great Ormond Street. It said that our DNA had been tested for another research project, also looking at unexplained learning disability, this time using different technology – microarray analysis. An anomaly was found (1q21.1 microdeletion) and it was thought to be significant enough to be the cause of Chrissy’s problems.

How did you feel when you found out?

At first I was thrilled because I had been searching for answers for years. Then, when the implications sunk in, I was concerned that it may be hereditary and wanted to know if future generations were at risk. It turns out that the microdeletion was de novo – spontaneous. Mine and Chrissy’s dad’s DNA were normal.

What has been the impact of the results?

The results and the autism diagnosis have changed the way that I see the future. The two are interchangeable in some ways. Now I can finally tell people why Chrissy is like she is – “She has autism and a rare chromosome disorder”. It helps me to be able to explain it and people ‘get it.’

I think it has given us more leverage to get the services Chrissy needs. Health professionals accept that people with a rare chromosome disorder can be very complex but we have had a huge battle to get Chrissy into hospital. I have battled for services throughout Chrissy’s life and it is exhausting and demoralising at times. Three local authorities have been rowing over funding for Chrissy’s care for about three years now and I have recently made a formal complaint.

Knowing that Chrissy has autism has helped us to support her more effectively. We know that 1q21.1 can be associated with heart and other organ defects. We were able to get Chrissy checked and, thankfully, she is fine.

It is hard not to dwell on how much easier our lives would have been if the cause of her problems had been found when she was little. I had a book published about our experiences ‘Bringing Up a Challenging Child at Home’ and had articles published about different issues we’ve faced over the years in the Daily Mail, Woman’s Weekly and Woman among others.

Have you made any connections with other families with similar disorders?

I have made lots of connections through Unique and on Facebook. There is a Facebook group for 1q21.1 microdeletion. I have also made connections with other families affected by different rare chromosome disorders.

It would have been such a relief to have been able to do that when Chrissy was little. There is a particularly wide range of effects for people with 1q21.1 microdeletion – some people present with no problems at all, others, like Chrissy are more severe, but there are some characteristics shared by many - neuro-psychiatric and behavioural problems, autism and feeding problems in infancy.

Why do you think these kinds of studies are important?

These studies are important because a diagnosis or cause for a child’s problems can make a big difference for families. I felt terribly isolated when Chrissy was a child and even felt out on a limb among other families that had learning disabled children. Some of them were judgemental about Chrissy’s challenging behaviour.

I felt stigmatised, as if I were to blame, and felt that I’d failed as a parent. I didn’t get the support I needed until I had a breakdown when Chrissy was six, and thereafter services were patchy, particularly when we moved to different areas. Having a medical label or a cause for your child’s problems helps families to access support and health services much earlier.

Psychologically, if I had known what was wrong, I wouldn’t have felt like such a bad parent or devoted so much time and energy searching for answers or cures. (An example is the gluten and casein free diet that caused Chrissy to become anorexic.) I believe that I would have enjoyed Chrissy and her siblings more and the effects on the family may have been less drastic. Chrissy’s siblings had to grow up too quickly and saw their older sister have prolonged violent self-harming outbursts that their distressed mum didn’t have enough anything like enough support to cope with.

Also, very importantly, if parents are carriers of a chromosome abnormality, they need to know, as it has huge implications for the health of their other children and wider family. I believe that in situations like ours everything needs to be done to pinpoint a cause. I remember Chrissy’s GP saying “a diagnosis wouldn’t change anything.” I hope GPs and other health professionals are educated in the importance of a diagnosis these days!

Is there anything else you would like to add?

After years of searching for answers, to the point of obsession, the results of the microarray test changed our lives. Further research into these rare conditions continues and I hope that we will eventually gain more insight into Chrissy’s genetic disorder and be able to offer more effective support and interventions. She is the oldest person diagnosed with 1q21.1 micro-deletion as far as I know, and the more we learn about Chrissy the more info, help and support we can offer families with younger children who face similar problems.

Mefford, H. et al (2008). Recurrent Rearrangements of Chromosome 1q21.1 and Variable Pediatric Phenotypes New England Journal of Medicine, 359 (16), 1685-1699 DOI: 10.1056/NEJMoa0805384

Related posts:

Finding out you are a cystic fibrosis carrier
The power and influence of newborn genetic testing

Finding out you are a cystic fibrosis carrier

2011-05-09T06:57:00.001+01:00

A couple of weeks ago I had the pleasure of chatting the Genomes Unzippped bloggers on the sunny terrace of the Sanger Institute. Luke Jostins let slip that his personal genomics results held a few surprises, not least that he was a carrier for cystic fibrosis (CF). He has yet to write about the results in detail, so I took the opportunity to interview him about his CF carrier status.

Had you any prior indication that you may be a CF carrier?

No, I have no family history of CF at all.

What was your reaction to finding out?

At first, I overestimated how common this level of risk is. My initial reaction was "well, everyone has something wrong with them". It was only when I started talk to other people, and then to my clinician, that I realised that this was a relatively serious situation.

In retrospect, I am relieved that I know. The chance of my children or other family members developing CF is still relatively low, but at least now we can be aware of the possibility.

What particular mutation do you carry?

The mutation is G551D. There is some evidence that this mutation has a slightly less severe a phenotype then the more common F508del [1], but it is still one of the most severe CF mutations. One positive about the G551D mutation is that there is a specific drug in development, Vx-770, which is specifically designed for CF patients with this mutation, and has showed strong promise in trials so far [2].

Has anyone else in your family been tested as a result?

My parents have been, so we know which side of the family it comes from. My brother has yet to decide.

Are you pleased to have found out at this stage in your life?

I am certainly pleased to have discovered this before I started a family, and it is certainly preferable to only finding out when your child develops CF. If and when I decide to have children, I will be in a good position to decide what to do next (and, as I mentioned before, the chance of a partner being a CF carrier as well is still relatively low).

How do you feel about publically sharing this information?

I am very committed to the idea that genetic information is not something to be scared of, and definitely not something to be ashamed of. If other people want to know about my genetic risks, or can learn something from my DNA, I would be delighted.

The only issue is whether this would impact my family, but I have discussed the Genomes Unzipped data release in detail with them, and they are very happy for me to share my information.

Do you think CF carrier status should be routinely tested in newborns?

I think carrier screening for a host of Mendelian genetic diseases should become routine as soon as the cost falls enough to make it feasible.

Many thanks Luke!

[1] McKone, E., Emerson, S., Edwards, K., & Aitken, M. (2003). Effect of genotype on phenotype and mortality in cystic fibrosis: a retrospective cohort study The Lancet, 361 (9370), 1671-1676 DOI: 10.1016/S0140-6736(03)13368-5

[2] Dolgin E (2011). Mutation-specific cystic fibrosis treatments on verge of approval. Nature medicine, 17 (4), 396-7 PMID: 21475213

Related posts:
Does having children affect views on genetic testing? - An analysis of GUZ survey data
My cancer scan results
Genotyping journalists
Questions to ask before buying an internet genetics test

Genetic kinship

2011-04-27T06:03:00.007+01:00

As I run through the fields I feel a profound connection with the earth. I concentrate on my form: lengthening forward and up, striking with my midfoot so my bent knee transmits the force of each stride. My feet drum the hardened mud, kicking up puffs of dust.

I settle into the rhythm of the run and sense my ancestors treading the same paths. They ran to communicate messages and, in distant savannas, to hunt down prey, while I run for pleasure and fitness. Their lives were very different from mine but their bodies, minds and thoughts felt the same.

I am tied to my ancestors by our genetic past. The differences between us are a sniff in the sweeping plains of evolutionary history. While running, they too would have been calmed by the green brown blush of grass and trees. They would have heard the lark, smelt the mud and been shocked by the sudden white of spring blossom.

The connections run deeper still. My muscles are powered by the breakdown of sugars, a primeval metabolic pathway shared by many life forms. A key step is the reaction catalysed by GAPDH in which a sugar derivative is loaded with a high energy phosphate group.

Plants, fungi and yeast contain GAPDH, not to drive their legs but to fuel their growth. The GAPDH in the wheat of the fields I run through is around 80% similar to my own, the malarial parasite that has so plagued my ancestors shares 59% identity, the mosquito 71%.

Genomes weave a story through all life; pointing to shared origins, the inconsequence of our own brief identities and the continuity of DNA. Running is a celebration of biology, my cells are alive and my mind freewheels. I feel a connection with the twists of evolutionary past that define my present and with the living things I pass on my way.

The pictures are the Cambridgeshire fields where I run.

Introducing Wilma (Women science bloggers database)

2011-04-18T07:27:00.005+01:00

Go to database

In life BC (before children) I managed a scientific database group, so when I saw Martin Robbins’ list of women science bloggers I had an urge to organise it.

The database format allows the list to be kept up to date and enables searching. I’ve taken the opportunity to add two new fields – geographical location and scientific subject area. Please enter this information if you are already on the list. Add yourself if you were missed off the first time.

The new fields include a broad subject area category (e.g. biological sciences, physical sciences) and a free text box for more specialist subject area (e.g. genomics, geology). I plan to turn the free text box into a drop down menu by using the entries to build a controlled vocabulary, this should make searching easier.

I hope having a current and comprehensive list of women science bloggers will be useful:

1. For science bloggers – to find others in your subject area/location, particularly if you blog about an unusual topic or are from a poorly represented country

2. For readers to find new bloggers

3. For the media to contact specialists

4. Finally, as Martin said, as a celebration of women science writers

I welcome feedback – please use the comment box below.

Go to database

Why is the database called “Wilma”? Because “women science bloggers database” is a Twitter mouthful and "FemSciBlogDB" is too geeky. Wilma is from Wilma Flintstone, one of the names I used to test the database. I’m sure it could be used to make an acronym....

An idea for a future project – include all science bloggers in the database and a field for gender. The search function could then be used to recreate the women’s science bloggers database.

A special thank you to Martin for entering the data in standard format that made it easy to parse.

Diversity in science blogging: a call for action

2011-04-05T13:47:00.029+01:00

Getting to last night's science blogging talkfest was a struggle (kids to a neighbour at 5pm, passed to a childminder at 6pm), but it was worth it. I wrote this post on the train back to Cambridge.

The topic was diversity in science blogging and this is my take on the evening.

The problem: the science blogging community is not representative of society. There is a disporportionately high number of bloggers who are male, young, well educated, middle classed, London centered, white, atheist, left wing....

Why this is a problem: all types of people need to be part of science conversations - tax payers fund research and the results effect everyone.

The discussion revolved around gender, so this is my focus, but that is not to say that other types of inequality do not need to be addressed.

The problem can be split into two areas:

1. There are not enough women science bloggers
2. Women that do blog are not as celebrated as their male counterparts

Many reasons for these imbalances were discussed:

Aggressive blogging environment
Unconscious biases against promoting women
Women less likely to promote themselves
Women tending to blog less frequently than men, maybe because of lack of time - high profile blog networks require frequent posting
Less women in science careers

I certainly associate with low frequency posting. I currently blog every one to two weeks, which is the right balance for me and my family. There was a brief discussion of how women tend to spend less time socialising online, which was countered by the mention of huge communities such as mumsnet and British Mummy Bloggers. I'd just like to add, as someone with a toe in the mummy bloggers pond, that writing a science blog post is much more time consuming that writing a mummy one, mainly in terms of the research and fact checking.

What can we do about it?

Some things, such as increasing the number of women in science careers, equal sharing of childcare and domestic tasks and the bias against promoting women, will involve long-term shifts in society. They need discussion, but I want to think here about more immediate solutions.

Improving the profile of existing bloggers

Existing high profile bloggers and blog networks could offer a platform to less well known bloggers
Creation of new blog networks to gather together up and coming bloggers
Job sharing - if blogging frequency is a problem then recruit two bloggers rather than one. I like the way blog posts are scheduled on the Last Word on Nothing network.

Encouraging more scientists to blog

Give space on existing blogs for scientists that don't normally blog. For example, Body in Mind feature one off posts from a range of academics (often recently graduated PhDs)
Introduce new bloggers on twitter (there was a nice comment from someone at the Science Online 2011 women bloggers session where a higher profile blogger was thanked for a valuable introduction)

What I plan to do

I'm currently in the process of building a database to store Martin Robbins' women science bloggers list - this will make it easier to search, update and add new entries (update - it is here)
I will invite people from the database who blog on the same topic as me, and scientists who don't normally blog to guest post on my blog.
As database administrator I will send out a tweet to welcome any new bloggers. Please pass it on.

Any other ideas?

Update - other blog posts on the evening:
Podcast
Confessions of a (former) Lab Rat Richard P Grant
Contagions - Michelle Ziegler
I Science Andrew Purcell
ABSW Andrew Purcell
The Guardian Martin Robbins
Wilma - Womens science bloggers database

Flash fiction - overturning stereotypes

2011-04-03T18:22:00.003+01:00

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This week my blogging mojo has been directed towards entering a flash fiction competition in a local magazine, the Cambridgeshire Agenda. Each day there's been a different picture to write about in under 100 words. My entries are follow the picture below, but first, a little on what made me cross about the images chosen. Read the stories first if you don't want them spoilt.

I'm tired of seeing women portrayed as beautiful objects, sadly the competition perpetuated this view. Two pictures of women, two pictures of floaty young things in pretty dresses.

I didn't want to write about passive victims, so my women are powerful – an unrepentant murderess and an inspirational scientist. I hope the story about the experiment on the grass will confront automatic assumptions that professors are male.

My other stories reflect somewhat my current interests. The little boy story comes from my recent enjoyment of the books of Dorothy Rowe, who talks about “finding the person you know yourself to be”, which is often hidden by voices from the past.

And I’ve also been intrigued by mindfulness. My dolly story took inspiration from the practise of really being present with an object – thinking about who made it and where it has come from.

Exhausted, ecstatic, fulfilled, she lay back against the bank. Her lips were still warm and moist, she savoured the release that flooded her body.

In her mouth was the lingering taste of blood, from where a flash of tension had seeped into her otherwise cool demeanour. Her jaw had clenched as she squeezed the trigger, catching the edge of her tongue and piercing the flesh.

Behind her the hot butt of the discarded gun rested in the small of her back.

He had gone. She was free.

Professor Walden set the observation equipment out on the grass.

An audience of local children gathered at a distance, drawn by the stranger.

The professor smiled, offering stickers and football cards, encouraging the children closer, trying to explain the experiment. The crowd became bolder reaching out to take whatever could be spared.

She returned to the jeep with the empty equipment case, the children swarming around noisily, comparing their gifts. One had her pen, another her shoes.

As dust from the jeep’s tyres settled a girl lingered longer than the others. That night she would dream of changing the world.

“There’s a good boy” said Granny.

“Enjoy yourself while you are young” said Barbara next door.

“You can do anything if you work hard enough” said Mr Hugo.

“Go away” said little Jake.

“Listen to me” said Mrs Montgomery.

“No” said Mum.

“This is our little secret” said Mr Masters.

He blocked out the voices and looked.

Inside was the person he knew himself to be.

“Here, drink it”, she pushed the vial into her brother’s hand.

He glanced up, “At least tell me what I can expect”.

“10 million years” she replied. “Plus or minus the odd decade”.

“Location?”

“Wherever you are at the time that the compound is activated. That spot, 10 million years into the past”.

Looking into her eyes he knocked it back, not flinching at the taste.

“Just no more embarrassing disappearances, alright. How long until activation?”

“You have a good few hours yet”.

He pushed past her, grabbing his bag for orchestra practise, slamming the door as he went.

It was 23 years since Carol found out where all the money had gone.

Every day she sat in line, the roughness of her hands scratching against soft new plastic. Sometimes she was on heads – pushing glass eyes into sockets, other days it was bodies – limbs clicking into torsos.

Their chubby faces had changed over the years. When she started they were all pink and pretty, now there were more boys and coloured ones.

Some days she would laugh with the others, other days he would occupy her thoughts. She knew she would never forgive.

Genetic poetry

2011-03-22T19:37:00.001Z

To widen the debate on genetics I believe we need to be creative. Genetics says things about personal identity that go beyond science. Sequence data tell stories, contain riddles and make promises– perfect fodder for artists of all sorts.

I had a go myself: I wrote a poem for chromosome 18 of the Human Genre Project.

SMAD4

I was making love at the time.
The slice of time when G tripped to A
Deep inside,
Just once.
Silently.

The single A tottered and tipped the balance.
Go go go!
Grow grow grow!

As I slid and murmured the altered protein expressed
Itself, folding into shape, caressing its partner.
Struggling here, slipping there.
The fit was gone!
The seed was sown.
Go go go.

Over the years my pancreas peddled the cycle of life
Without brakes.
Gradually speeding up until I was overrun.

SMAD4 is a tumour suppressor gene on chromosome 18 involved in regulating the cell cycle. Mutations in this gene can cause unchecked cell growth and are present in 50% of pancreatic cancers.

Maybe an example of sci-porn?

If you want to flex your creative muscles, there is still a chance to contribute.

The power and influence of newborn genetic testing

2011-03-14T11:43:00.004Z

I remember my newborn son’s heel prick test as an emotional blur. His screams added to the din of the tightly packed ward as the doctor struggled to extract sufficient blood. He must have wondered what sort of world he had been born into.

The short term discomfort was in his best interests as the heel prick test saves lives. Many metabolic diseases can be managed by diet and lifestyle changes but are fatal if left undetected. The benefits seem clear cut – disruption to a single gene cause quantifiable alterations in metabolism which can be corrected by environmental modifications.

A paper in January 2011 issue of Medical Anthropology makes it all appear a little more messy.

The study followed 60 newborns diagnosed with metabolic diseases in a Californian paediatric genetics clinic. The authors observed interactions between the families and geneticists and documented the emotional world of parents.

The main thrust of the paper is loss of the dream of a perfect baby after a positive screening result. Here I will focus on what struck me most about the findings: the power and influence of genetic knowledge on those whose lives it touches.

Many of the observed diagnoses in the study were ambiguous, combinations of mutations whose significance weren’t fully understood. The children appeared healthy but the parents were forever fearful of disease emergence and its serious consequences.

The research captured how parents responded and the indirect effect on their babies’ early childhood experiences. The following quotes are from parents whose children were diagnosed with MCADD, a disease of fat metabolism in which sufferers cannot metabolise fat when blood sugar levels drop.

The mother of a 2-year-old boy with MCADD described her son as a ‘‘special case’’ because only one mutation was identified through DNA testing, yet his metabolite levels were high enough to warrant close clinical monitoring. Although the laboratory’s failure to detect a second mutation left unresolved questions about whether the child actually had MCADD, as opposed to being a carrier, the boy’s father refused to leave the child alone with anyone other than his wife.

Maria, the mother of a 6-month-old boy with MCADD, noted that her son seemed as normal as her two older children, yet that she worried ‘‘all the time’’: when he slept 6 hours ratherthan 3 or 4, or when she gave him vegetables—even though the dietician said this was okay. An ear infection at 4 months of age provoked grave fears about metabolic crisis, while online research made Maria concerned about the possibility that routine immunizations could lead to metabolic problems in children with MCADD. She told us that she worries constantly that she will do something wrong.

Dan, father to Molly who has MCADD suggested she was ‘‘progressing maybe at an 80 percent level compared to other kids’’ on motor development and Kim [mother] recognized that Molly was ‘‘not as verbal as maybe someone else her age.’’ But because Kim had ‘‘taken her to sign language since she was about like seven or eight months old,’’ she exceeded other children in her ability to communicate her needs. Thus, Kim concluded, ‘‘We want her to speak more. But, I mean, other than that, she seems just like an average normal kid, I mean, we think.’’

I would not argue that parental conflict should lead to questioning the value of the test itself, and the authors do not pass judgement either way. The children have a fatal disease and knowledge is lifesaving. However, it is clear that genetic data have power and reach far beyond the disease information they pertain to.

Much potential damage can be abated by a deep comprehension of the subtleties of the test results. Genetics and disease are untidy and will get more so as further layers of knowledge are acquired. The communication challenges are great - the science is tangled and forever shifting, moral sensibilities are individual and subjective, and the implications of getting it wrong cut deep.

The key is to transmit a nuanced understanding of the complexity to parents – the unknowns, the range of possible outcomes, how mutations influence the child and what is normal developmental variation, how childhoods can be overshadowed by understandable parental fear.

Future discoveries mean the lines between established illness and normal human variation will be continually redrawn. This research shows that we should consider not only false positives and negatives but also the psychological burden on the families who are told they are genetically ill.

Before we reach the stage of obligatory newborn genome sequencing we need a wider acknowledgement of the power of the data at the level of the individual family. The depth of understanding of the parents, and later of the child, could arguably have more of an influence on the life of the child than any genetic mutations.

Buchbinder, M., & Timmermans, S. (2011). Medical Technologies and the Dream of the Perfect Newborn Medical Anthropology, 30 (1), 56-80 DOI: 10.1080/01459740.2010.531065

Children, science and the perpetual why

2011-03-03T07:48:00.001Z

The school half term holidays have just finished and we did very little. To steal a line from Damon Alburn, we mostly “put our trousers on, had a cup of tea and thought about leaving the house”. When we finally ventured out we didn’t do anything very structured.

What has this got to do with science?

Kids are natural born experimenters. They excel at exploring, observing, testing and retesting. They have wild imaginations and aren’t limited by rational grown-up thinking. They discover so much if left to follow their own crazy ideas: with mud and sticks or with the contents of a recycling box.

So, wherever possible, I try to give my kids that freedom. I aim to make the house a place where they can play without fear of breaking adult stuff. I move anything I find I am nagging them to leave alone, and our grotty carpets and sofa are staying until they are old enough to understand.

Much of what we classify as naughty behaviour is simply experimentation. We encourage babies to post and poke and push the buttons on their flashy toys but we get cross if they transfer these skills to our stereo system. It’s quite a lot to expect little ones to understand the difference.

I must admit that my parenting style has evolved in part to make my own life easier. Back to back children’s activities becomes a little dull (especially as a passive observer) and I’d rather get jobs done at home whilst being available to assist with free range play. (I should also point out that this half term, my boys went to a childminder for a few hours every morning so I could do some work. I’m not sure we could have spent all day doing nothing much.)

The benefit of such a hands off approach is that kids can explore under their own steam rather than being straight jacketed by someone else’s ideas. The downside is the mess. But it can be liberating to learn to ignore the chaos for as long as possible and just clear up when it gets too much.

One day during half term my two year old said “Why?” for the first time, reminding me of his brother’s iterative questioning at the same age. “Why” is such a brilliant question – one little word and adults tell you all sorts of interesting things. I remember long conversations along the following lines:

“Mummy, why is it that fruit called an orange?”

“Because its coloured orange I suppose”

“Why?”

“Why is it coloured orange? (1. mummy in good mood) Well because there are things called photons that are either reflect or absorbed from the surface of the orange ...... (2. mummy having a bad day) Because it just is...”.

The problem with answering as option 1 is that the response will always be another:

“Why?”

And you end up struggling to talk about waves and subatomic particles, knowing that more “whys” will follow and wondering how long it will be before you finally lose your rag.

This kind of questioning reminds me of laddering – a psychotherapy tool used to uncover hidden core values. It certainly pushes all sorts of buttons when used to extreme by kids.

The best way to keep your sanity is to pretend that instead of asking “why?” the child has said “tell me more about that”. This is really what they mean, and it is a much more pleasant to respond to.

There is one question my kids ask that I do my best not to answer:

“How do I...”

I say things like “hmmm”, “I see what your trying to do...” , “that’s a tricky one...” for a bit and encourage them to think of their own response, which is normally much more creative than my own.

Later in the week, my eldest found a ruler with multiplication tables on the back. After studying it for some time he came and told me the equations were wrong. He’s just started school and has been taught about addition and subtraction but not multiplication and division. He’d looked at the multiplication signs and thought they were for adding up.

We sat down with a piece of paper and I explained about multiplication and division and the moment the penny dropped his response was to jiggle and giggle with delight.

We often complain when children display negative emotions in their bodies (temper tantrums, sibling attacks) but it was heart warming to see a show of pleasure in such a visual way.

In order to encourage your child’s scientific side it doesn’t seem necessary to do anything special – just be around to answer their questions (not being afraid to give them technical answers) and encourage them to think of solutions themselves. Then put your feet up amongst the disorder and let them loose....all in the name of science.

My genetic counselling appointment

2011-02-23T06:24:00.002Z

I started this blog to compare my experiences of taking a genetic test on the internet and having NHS genetic counselling. I have previously written about my cancer scan with deCODEme and I have outlined my family history of breast cancer which led me to request a genetic counselling appointment. I have yet to write about the counselling itself.

So here is what happened: what I learnt, whether I was offered a BRCA test and why it turns out breast cancer isn’t what I should be worrying about.

Prior to the appointment, I filled in a family tree, fleshing out the cancer cases in my relatives. The two that concerned me were on my dad’s side of the family – his sister was diagnosed with breast cancer in her 40s and his mother had a double mastectomy at age 31.

At the appointment I was given background information on the differences between hereditary cancers which tend to strike younger people and those due to the lottery of aging, which are more common after age 60. Each case of early onset cancer in my family was given a score (based on things like the age it was diagnosed, the type of cancer) and the cumulative score provided my individual risk.

Given the two cases in my family, I was assigned a lifetime risk of 17-30%. This is “moderate”, and should be compared to the average of 11%. BRCA tests on the NHS are given when the likelihood of testing positive is greater than 10%: the chance of finding such a mutation in me was estimated at 1.5% (and 7% in my aunt), so I was not offered the test.

The family tree information I had provided extended to my grandparents, but I had no information about their siblings. If it was indeed the case that my paternal grandmother was a BRCA mutation carrier and that she passed the gene to her daughter then there would be other cases of breast or ovarian cancer in her family (BRCA mutations tend not to hide their phenotypes shyly in the corner). Any new cases would increase my personal score.

I went away from the counselling session and spoke to my mum. She told me that my paternal grandmother’s parents and her siblings (a sister and brother) had all died in their 60’s, but not from cancer. My paternal grandmother had two female aunts that both lived well into their 80s.

This is not a typical BRCA mutation carrying family. I found such extra information hugely reassuring, it gives me no reason to believe that I am carrying a nasty ontological time bomb.

How do the results compare with my deCODEme DNA profiling? It is important to note that the deCODEme test did not look at BRCA itself but at other short regions of DNA that are statistically associated with breast cancer. The deCODEme result gave me a lifetime risk of 11% - significantly lower than that from my counselling and slightly below the deCODEme lifetime average of 12.5%.

It is a bit unfair to compare the internet and NHS results as they are measuring two very different things, and both in very crude ways. The NHS number was based on two occurrences of early onset breast cancer in my family, the deCODE number was a sum how associated the sequence of a handful of base pairs in my DNA are with breast cancer.

Although both came out with answers in the form of numerical values, I don’t put much value on either of the figures. The most worthwhile part of the exercise was the follow up - the lack of breast/ovarian cancer in my more distant relatives makes my odds of catching the disease seem pretty much average.

The two procedures were very different - family tree building means taking time to talk to people and hunt down information, whereas genotyping involves a click, a credit card and a consumer buzz. For those impatient, affluent and not a fan of family conversations, the computer wins hands down, but, for me, old fashioned tree building felt more meaningful. This result wasn’t as precise as a number, but it was a much more valuable in terms of personal knowledge and understanding.

There is, however, a small sting in the tail. I found my paternal grandmother’s parents and two siblings all died in their 60s. They were all killed by high blood pressure related illnesses - strokes, heart attacks - even the women. A dispassionate look at my extended family tree suggests I should not be worried about cancer, but that I should get my blood pressure checked regularly.....

How it all started

My cancer scan results

Genetics and Pain

2011-02-10T06:05:00.002Z

Last year there was a post on Body in Mind in response to an article published on the genetics of chronic pain. With refreshing honesty the author admitted he “was going to write a blog-post on it and then I read it and I was too intimidated by it.”

I had a look at the paper, with my molecular biology background, it wasn’t too scary. I was interested in the original blog post as it intersects many parts of my life. First my original training as a biochemist, second my current kiddie friendly employment as a movement teacher (which is why I follow Body in Mind) and third the long term nerve pain I have suffered since the birth of my first child.

So here is a non-geneticists run through the paper, plus some thoughts on the implications of knowing about the genetics of chronic pain.

The researchers (an international collaboration from Israel, Canada, Germany and Sweden) first studied mice. Nerves were removed from the paw of the animals in order to model the type of pain that follows nerve damage. Some mice seem to be annoyed by the numb paw which they scratch and bite. This behaviour is used as a measure of their pain.

Individual mice and mice within a strain vary in how much pain they feel, suggesting there may be a genetic component to their response. The behaviour of many mice was compared using standard genetic techniques involving inbreeding and database searches which lead to the identification of a clutch of potentially influential genes.

The researchers also looked at expression of genes in mouse paw ganglions from different strains, either from those having undergone nerve removal or a sham operation, and narrowed down the search to a gene called CACNG2. The expression of CACNG2 was turned down in mice that seemed to have more pain, and mice with mutated CACNG2 genes were shown to have different responses to nerve removal.

The corresponding gene in humans was investigated by using a group of mastectomy patients, some of whom suffered chronic pain following their operations. The researchers looked at naturally occurring differences in gene sequence in the women and found statistically significant associations between changes in two areas of the gene and chronic pain.

CACNG2 turns out to code for a protein of just the type you might expect to be involved in the control of pain response. The protein modulates AMPA receptors (ion channels gated by the neurotransmitter glutamate) by influencing their transport and probably by effecting channel gating. CACNG2 is already known to play a role in epilepsy.

The authors say their finding may be of immediate social benefit – “patients who report more pain than might be expected given the extent of their injuries are frequently stigmatised, with the suspicion that they are exaggerating their symptoms in the hope of obtaining secondary gains....knowledge of the existence of genetic factors controlling pain susceptibility....ought to reduce unwarranted stigmatization of patients with severe pain due to no fault of their own”.

I will finish with some of my thoughts on the implications of the role of genetics in chronic pain.

It doesn’t surprise me that genetics plays some part in susceptibility to long term pain, so the results in themselves do not make me feel any better about my pain. But could these findings reassure sufferers who are unaware of possible genetic vulnerabilities or even help shift the views of those who don’t believe the pain of others?

I am afraid to say that am not hopeful. Education about genetics tends to come through care providers, and I suspect only doctors who are already doing a good job communicating chronic pain knowledge would pass on new genetic findings such as these. Nothing is likely to change for patients who are currently given the impression the pain is their own fault.

Longer term, what if our DNA sequences were stored in a hospital database and we could learn of our personal genetic liabilities? Would it be helpful to know that you had a higher than average likelihood of suffering chronic pain? Or would this just create a self fulfilling prophecy?

As with genetic knowledge in other disease areas it partly depends on the type of treatment available. If stratified care for your particular genotype was offered, then you would want to know. If nothing different could be done then perhaps you wouldn’t.

And what if the genetic basis of long term pain were understood, what form would it take? It’s a fairly safe bet to say that it wouldn’t be neat and tidy. Because of the role of the sufferers’ attitudes and beliefs, their social environment and their pain escape behaviours, the genetics of chronic pain is likely to be a hodgepodge of small gene effects interwoven with environmental influences. Chronic pain also casts a wide etiological net (there are many many different causes of pain) so the underlying genetic backgrounds are likely to be similarly disparate across the population.

To my knowledge, no genome wide association studies (GWAS - large scale systematic genetic study of hundreds or thousands of individuals) have been carried out to look at chronic pain, but many psychiatric disorders have been studied this way and the results have been disappointing. Because of the shared role of the mind in both mental illness and pain any patterns emerging from GWAS of long term pain are likely to be deeply hidden too.

I’m sure in the future we will know more about the genetic basis of chronic pain and I suspect that the inherent complexity revealed will be a little intimidating to everyone.

Nissenbaum J, Devor M, Seltzer Z, Gebauer M, Michaelis M, Tal M, Dorfman R, Abitbul-Yarkoni M, Lu Y, Elahipanah T, delCanho S, Minert A, Fried K, Persson AK, Shpigler H, Shabo E, Yakir B, Pisanté A, & Darvasi A (2010). Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2. Genome research, 20 (9), 1180-90 PMID: 20688780

For further information on genetics

Genetic Future

Genomes Unzipped

Does having children affect views on genetic testing?

2011-01-30T17:02:00.007Z

Fellow Cantabrigians down the road at Genomes Unzipped held a reader survey at the tail end of last year. I’ve just got round to delving into the raw data.

I’m interested in the differences in opinion between men and women, and how having children affects those views. The GUZ team noticed that no female research geneticists would be willing to donate their full genome data without strings attached – I’ll comment on this later.

I’ve also done some digging of my own and found that becoming parents seems to affect the views of men but not women.

First, a look at qualifications and children. 32% of the female respondents have a PhD, compared with 47% of men. I wondered if, in this sample of women, having a PhD effects whether or not you have children. There turn out to be a clear difference between the sexes: 41% of female PhDs don’t have children and don’t plan to, compared to 19% of men. I also looked at what jobs the 10 women with PhDs who had children were doing – nine of them were working in science.

So far the data are both encouraging and depressing. Depressing in that it seems less possible for women to have both a PhD and a family, and encouraging because those that do combine the two can stay in science (or perhaps return to science). And the one person that has a PhD and kids and isn’t working in science – that’s me (although I blog about genetics when I’m not wiping sticky fingers or jamming toys back into small spaces, but science is not currently my main occupation).

There are loads of caveats here – having kids doesn’t mean they are still living at home and so directly influencing career choice; the sample size for women is small; I answered the employment question based on what I am currently doing, but some may have answered with their pre-kids job; and overall less women in the survey than men have children regardless of education – 46% of women compared with 55% of men.

The sample is clearly biased. I wonder if scientifically trained women with children don’t have time to fill in internet surveys. And perhaps women with PhDs who fill in internet surveys don’t have time for children.

Then I looked at how having children changes your views about sharing genetic data. First the question “should newborn babies routinely have their genomes sequenced once the technology to do so becomes affordable?”. I started with women, suspecting that they may become more cautious after becoming mothers, but there was no difference between those with and without kids – 43% of those answering yes to the question have children compared with 47% of those saying no.

However, the men’s data gave a different picture. Those answering yes had a similar family profile to the women – 49% with children. But 65% of those answering no had kids. It seems that men are more likely to reject the sequencing of newborns if they are fathers themselves. The GUZ team had commented on the overall difference between men and women in their views on sequencing newborns, the analysis here shows that family circumstances may play a part.

I wondered if this relationship was present for any of the other hot potato questions on the survey. I looked at “should parents/guardians should be able to consent minors for direct-to-consumer genetic testing?”. A similar pattern was evident, although not as clear cut. 47% of women answering yes have children, as do 42% answering no. For men, 52% of those consenting have kids, compared to 62% who would refuse. Interestingly, for both questions, women become less cautious after becoming parents – the opposite to men.

I had a quick peak at respondents’ views on sharing their own genetic data. In the interest of speed I including only the extreme answers – either “Not under any circumstances” and “Yes, and I would be happy with the data to be publicly associated with my name” for whole genome sequencing (rather than genome scan data).

Here, rather surprisingly, for both sexes, those with children are more likely to agree to no holds barred data release (71% of consenting women have kids, and 64% of consenting men). This compares the “no under any circumstance” people – 43% of the women and 58% of the men having children. Note that the sample size for the consenting women is small so the results may not be meaningful.

The obvious caveat for these investigations is that the survey did not look at the views of the same people before and after they had kids. And there are many confounding variables – for example parents tend to be older than non-parents and views change with age; plus those who have children tend to be less worried about scaring off potential genetic recombination partners.

And finally, what of the intriguing result that no women research geneticists agreed to wholehearted release of their data. Firstly, the sample size is small so it is not clear if this result is real. Secondly, I am one of the six non-geneticist fully consenting women and so cannot shed much personal light on those more wary.

I can say I answered the question instinctively based on gut reaction and without detailed introspection. On reflection I have no reservations about people knowing my personal data. This may be because I am self-employed and knee deep in family so not concerned about alarming potential employers or breeding partners. I do admit to ambivalence about how the data release would affect my relatives, any major genetic diseases in my family would probably be a show stopper.

Here ends my analysis. It’s been done swiftly by spreadsheet hacking (coloured by entrenched feminist views) but I hope offers some food for thought.

Women in science article

2011-01-09T20:15:00.007Z

I've just had an article published by People and Science magazine - "Can women out of science be good for society".

Although the headline has been edited to read:

"Can women out of science be good for society? - Elaine Westwick thinks not".

But Elaine Westwick does think so!

Its supposed to be provocative and feminist - I'm actually saying that scientists taking a few years to bring up kids may not be catastrophic for science. Having a break from the scientific establishment can be good for society because parents bring their scientific mindset to other walks of life.

Read the article and you decide....

I've not disappeared...

2010-10-04T12:25:00.003+01:00

Blogging currently on hold whilst I concentrate on my two other full time projects.

My cancer scan results

2010-08-15T20:36:00.009+01:00

There has been a recent proliferation of DNA profiling write ups (a list of eight reports at end of this page), here’s mine to add to the pot.

I can claim a degree of novelty – my test was carried out by the Icelandic genomics giant deCODEme, rather than the more ubiquitous 23andMe. I also promise to keep nothing back, I have copied every shred of my raw data directly into this post.

Given my DNA is in part owned by my family, I was not planning to divulge all the results. But investigating the raw data has made me comfortable that what lies underneath holds no great secrets.

I took the cancer scan, which generates risk assessments for seven common cancers. The results are revealed one at a time, like flipping cards in a hand of morbid poker.

Here is the first one:

The 1.0 in the middle of the bar is average risk, anything lower and greener is good, to the right and red is bad. So this is good, and as I click through the list my heart rate increases and my palms become clammy.

I feel like I’m on a roll now, how long will the luck last?

A great result as I have a family history of breast cancer.

I’m now aiming for a full house, so the next one is a letdown:

I hadn’t picked up that being female I would only get six and not seven results. I had even spent time thinking through how a high risk prostate cancer value could affect my close male relatives.

The rush of luck is over - the remaining three results sit close to the centre line (although I struggle to gain any extra insight from the numbers being quoted to two decimal places):

Each result was preceded by a critical health information page which I dismissed without reading (the first time guiltily, subsequently with abandon). My brain was viscerally primed to uncover my cancer risks and I was too impatient to digest details.

Later, when I had calmed down, I had to hunt around to trace the information again, and the option of accessing it straight after the results would have been useful. This illustrates a key dilemma in dispensing genetic information direct to consumers – how do you ensure they read the small print?

I was keen to download my raw data to see what was behind the headlines. After spotting a warning that scan results could contain one million lines of data, I pressed the download button and went to make a cup of tea. The file downloaded instantly, here it all is:

Unlike the more extensive complete scan offered by deCODEme, the targeted scan is highly focussed on the individual DNA base pairs proven to influence cancer risk. The table shows that 33 positions (SNPs) were examined in my DNA. Each individual cancer prediction is compiled from between 2 and 12 of these data points.

In terms of base pairs for your buck, the test does not score highly, and it won’t be long before the $500 USD price tag will buy me all my 3 billion bases rather than just 33 select ones.

The test's real value comes from areas in which deCODEme excel: the painstaking discovery of meaning hidden in sequence muddle and the careful communication of the resulting risk factors.

Finding even a handful of SNPs that reproducibly effect cancer risk is a tour de force of genetics. When I drill down to the peer reviewed papers behind each data point I can see that deCODE genetics have carried out the bulk of this work. The scientific details reveal a mountain of research, with data from tens of thousands of people used to define each SNP.

To understand the significance of my lower risk results I need to take the population frequency of each cancer into account. For both bladder and breast cancer my lovely green arrows translate to only a small decrease in absolute risk. Combined with the three results clustered around 1.0, this makes me a resounding Mrs Average for five out of six of the cancer types.

Only basal cell carcinoma is left. This gave my biggest risk swing and is the most prevalent of the cancers tested, affecting 25% of the population. The results reduce my personal risk to 16.5% – the only number in the whole test that stands out.

The decreased risk is reassuring but will not make me lax about using sunscreen. If anything the numbers have made me more vigilant – I didn’t realise that basal cell carcinoma was so prevalent. And despite this being is my lowest relative risk, the high background level means it is still my highest absolute risk.

However, even for the basal cell result, any sense of deviation from the mean disappears as I drill down to the three constituent SNPs. All are pretty average too – each present in more than 40% of the population. Individually they confer a slight decrease in risk, and it is only their combination by multiplication that gives an overall risk well below average.

By exploring my data I feel like I’ve descended from the heightened emotion of the headline results to a baseline of bog standard DNA. It is the very ordinary nature of the data that makes me happy to share everything here.

Although it is boring to be average, this is one time I’m thankful to be part of the crowd. Middling results are by no means guaranteed – you could learn you have 2.3 times the background risk of breast cancer (giving a lifetime risk of 28%) or over four times that of prostate cancer (lifetime risk of 66%). For a minority of customers, the results could be far from mundane.

For me, the process of taking the test has been much more educational than the test results themselves. The deCODEme website is full of well presented pre- and post-test information, and their email support has been prompt and factual. The scan has made me mull over ownership of my DNA and I’ve been inspired to look into my family history.

Even if genomic fatigue sets in and we tire of hearing about other people’s genotyping results I don’t believe we will ever stop being fascinated by our own, even the bits that are rather bland.

Related posts:

A review of the Association of British Science Writers genetics testing conference session

Questions to ask before buying an internet genetics test

The test was donated by deCODE to the Association of British Science Writers for their annual conference.

Genotyping journalists

2010-07-25T20:03:00.010+01:00

Take a bunch of journalists and ask them to undergo genetic testing - the outcome was always going to be entertaining. This was the part of Friday’s inaugural UK Conference of Science Journalists, held in the opulent surroundings of London’s Royal Society, that I was most looking forward to.

The public testing was part of the Future of Genomics session, organised by Zoe McDougall from the sequencing technology company Oxford Nanopore Technologies who provided sponsorship.

The testees to be paraded as genomic curiosities were Ed Yong, Martin Robbins, Claire Ainsworth and Mark Henderson. Three broad themes emerged from the resulting spectacle.

Firstly genotyping is confusing, no matter how impressive your scientific credentials. Claire Ainsworth has a PhD in fly genetics, Ed Yong writes a renowned biology based science blog, and Mark Henderson knows at least 50 genetic ideas that you really should too. Yet the panellists were all bemused or overwhelmed by at least some of their data. This is not criticism of their expertise but an indication of the complexity of the information involved.

Mark was genotyped by 23andMe, deCODEme and Pathway and has written in detail about his experience (subscribers to Times online content can read his three blog posts). The tests identified an increased risk of exfoliation glaucoma, which he knew from family history, but the companies differed in their estimate of background risk, leaving Mark perplexed:

How prevalent is exfoliation glaucoma, and how much do I need to worry about it? If 23andMe is correct, then even though I have a high risk genetic variant, my overall risk of this condition remains low. If deCODEme is right, I have a one in three lifetime risk. And if Pathway is right, the population risk is low, but the peculiarities of my genome dramatically enhance my chances of getting it.... I am now a confused customer!

Ed, who took the 23andMe test, has also blogged about the experience. He initially took his cystic fibrosis big fat negative at face value, but a genetic councillor quickly got in touch to explain the results were less clear cut. The test was for the most common cystic fibrosis variants, but over 1000 have been identified giving the potential for false reassurance. You can follow the discussion in Ed’s post comments, and there was a swift response from 23andMe.

That Mark and Ed were willing to share their results gave them the opportunity to receive input from experts. Mark sent his data to be analysed by Daniel MacArthur, researcher from the Sanger Centre, author of the influential blog Genetic Future, and presenter of the opening talk at the session.

Daniel’s analysis (further details in Mark’s second post) showed that out of the 554,618 variants called by both 23andMe and deCODEme, there were differences in only 77, giving an error rate of 0.007%, far lower than conventional diagnostic kits on the market.

This open-access sharing and caring model is just what 23andMe encourage with their community membership and genotype comparison technology. And, as Mark and Ed found, this is a productive way of navigating the information tangle.

But the testees’ own genetic knowledge and their ready access to experts are not shared by every consumer. As Ed pointed out, you cannot fault the information that 23andMe provide, but you need time and knowledge to take it on board.

My second theme is that genotyping generates emotions as well as information.

Testee Martin Robbins, who doesn’t possess a genetics background, was more illustrative of your standard genomic punter. He described the impersonal result screen as like facing a “wall of death” and said he found the whole testing procedure uncomfortable.

His test, carried out by Navigenics, identified an increased risk of Alzheimer’s, which as Martin pointed out will be shared by at least one of his parents, neither of whom consented to be screened.

Martin also highlighted fears about data ownership and protection from hackers and third parties such as future employers and dating sites. This was raised later in the session by Alison Hall from the PHG Foundation, who discussed the conflict between consumers ~~posting their haplotypes on Facebook~~ sharing their data online and the fundamental principles of data security and confidentiality.

Claire was the most circumspect about the test, phoning her parents in advance to gauge their thoughts on being indirectly genotyped. She also choose not to disclose all the data, feeling the information was not hers alone to share and pointing out that today’s innocuous variants could be tomorrow’s risk magnets.

Although the testing provoked a range of emotions and there was much talk of hypothetical dangers, no one seemed to regret having taking the plunge. This is in line with the general lack of concrete evidence for damage caused by consumer genetic tests.

My final point is that the tests provided more fodder for jokes than they did undercover meaningful clinical insights. Ed’s blog post is full of smart gags (a hypothetical love child with Mark, science writer disease risk top trumps and too much talk of wet earwax). My favourite wisecracks from the session were Claire’s disappointment that her phenotype was less sexy than the dark-eyed curvy genotype prediction and Martin’s dismissal of his increased prostate cancer risk given his expected Alzheimer’s oblivion.

Ed’s results gave the starkest illustration of the insignificance of much of the potentially non-trivial information. Most genetic studies have been carried out on Europeans, so his Asian ancestry meant that his risk predictions are currently very unreliable and practically useless. But Ed now owns a copy of his genotype so will be able to uncover future associations as research becomes more geographically widespread.

There was also a genetic councillor, Christine Patch, on the panel who outlined the differences between the targeted clinical tests provided by the NHS and those of low predictive value available direct to consumers. For example, the NHS do not screen for the Alzheimer’s variants flagged in Martin’s results as the tests are not deemed clinically useful.

My only criticism of the session was that there wasn’t room on the agenda to explore the implications of full genome sequencing. James Brenton, from Cancer Research UK, hinted at the future complexity in his presentation on cancer genomics. He described research showing genetically distinct populations of cancers cells present in different locations of the same tumour, and how the populations evolve and shift in response to therapy.

Neither was their time to discuss the previous day’s US hearing on regulation of the direct-to-consumer genetic test industry. If Daniel MacArthur was tired from staying up to post his analysis of the events on Genomes Unzipped, he didn’t show it.

The rest of the day was equally stimulating, a raft of expert speakers and bubbling discussion. There was much talk about the role of bloggers, social networks and cyberspace review. If the web provides an audience for newcomers typing from their kitchen table then this conference was equally inclusive. The day was made accessible by the efforts of British Association of Science Writers members and sponsorship from Elsevier and others.

Other conference attendees received genotyping kits, not all could present on the day. I am waiting for the results of a deCODEme cancer scan which will go in a separate post, and I will update this post with any links to others who share their experiences.

For me, it was a full, blissfully child-free, day immersed in science and new communication technologies. I left with a humming mind and a curiosity about what story my DNA would tell.

Children and genomics - the underworld of DNA talent testing

2010-07-12T14:26:00.001+01:00

My last post looked at how direct-to-consumer genetic testing companies promote the testing of children. Here I explore the shadowy underworld of genetic talent tests.

There is a clutch of companies who market DNA tests to children without the backing of real science. They hail mainly from Singapore and China and their marketing machines are getting slicker.

My Gene Profile has now created a reputable looking front-end which contrasts to their original flaky website featuring a mohican baby. They are based in Singapore, but list offices in the UK (Haslemere) and US (Connecticut).

Their newer homepage has an amusing picture of two scientists looking gobsmacked by a cyclohexane molecule (which I presume is meant to be a nucleotide). The rest of the site would also be hilarious if it wasn’t for real. They offer an “Inborn Talent Genetic Test” and a “Disease Susceptibility Genetic Test”. Drilling down to the talent test gives a list of 40 genes (2/3 of the way down this sprawling page), including such gems as:

Propensity for Teenage Romance Gene
Drawing Gene
Self Detoxifying Gene

The new URL still hides links to scam-like behaviour, for example add /vip to bring up information sent to targeted individuals last year:

Make Biggest Commission Paycheck by Riding On World’s Fastest Growing Industry: DNA and Genetic Market!

Another Singaporean offering, Map My Gene, sells the same two tests. Francis Collins and Robert Plomin (Professor, Kings College London), are quoted as offering their support. The company ask for a copy of your passport or identity papers to be submitted along with your DNA sample – a frightening combination to part with.

Again from Singapore, Magic Fidler is a company running children’s music classes with a sideline in DNA testing to determine musical ability. The number of tests offered is a familiar sounding 40:

For $2,000 the scientific results can pinpoint your child’s strengths and weaknesses in 40 areas, including IQ, EQ, memory as well as artistic and athletic abilities. For $2,800, you can get the DNA Test plus 12 weekly music classes.

The music teaching may well be wonderful, but the science is not. The site testimonials summarise all that is wrong with this approach (based on children tested in January 2010):

“My first reaction was: ‘Are you sure this is my child?’ Kiran (aged 7) scored very high in intelligence and creativity, but I always thought he was just average....While he likes singing to pop songs, he’s never expressed an interest in music lessons. So I was surprised that he has a good sense of rhythm and is supposedly good at learning different instruments."

“What surprised me was that it didn’t show up in his DNA that he has a flair in maths. I always thought that he is quick at understanding concepts, which even the elder sister has difficulty understanding.”

“Since we received the results, my husband and I had many interesting discussions about our girl (aged 2). Isn’t she supposed to be talented in arts? (She’s always doodling!) Well, it’s not in her DNA. Didn’t she learn to walk only after 15 months old? (A friend’s kid of the same age was already running around.) Yet, the results showed she has a natural flair for sports, with high endurance gene."

The music school act on the spurious DNA results:

“If the child’s DNA results show that he has strong genetic propensity for music and creativity, for instance, he might be put in a more intensive class, which teaches composition skills.”

The tragedy is that such results (which may as well come from a random number generator) lead parents to dismiss the best way of finding out about their children’s talents – their own observations.

Finally, a couple more quotes to further illustrate the potential influence of such information. Firstly from The Genetic Center who sell a “Child Talent Gene test”:

"This child is very thoughtful and focused," Shanghai Biochip's Healthcare Director Huang Xinhua explained while looking over a girl's test results. "I suggest she go into management."

Secondly, the American Atlas Sports Genetics who sell a test based on the ACTN3 gene:

“Although, my daughter is only 9 she now knows that she had a the Sprint, Power, & Strength advantage which we can use to market her Athletic Career and hopefully a wonderful scholarship from this process.”

Note that the parent wants to market the child – has genetic testing turned her into a commodity?

For now, such websites will only affect those credulous enough to believe the manufactured science. But the genomics juggernaut is on a roll, bringing with it more robust links between personality traits and DNA sequence. When predictive testing finally comes of age, should we allow children to be tested? And if so, how will we ensure that eager parents are aware of the caveats, subtleties and statistics that hang off each data point?

Marketing direct to consumer genetic tests to children

2010-07-07T05:29:00.010+01:00

I’ve been looking at the websites of main-player consumer genetics companies to see if they promote testing of children. I’m driven primarily by curiosity, rather than the belief that such testing is necessarily wrong.

A quick survey of the type of people used in promotional website photos is a good way to gauge intended audience. Staid lab-coated researchers, trustworthy medics and wealthy, aging Caucasians feature most often (e.g. deCODEme, Navigenics). 23andme breaks rank by featuring a non-white girl, father and baby. Knome is light on the photos (but if you can afford the price tag you are probably not motivated by identifying with a target consumer group).

The official Pathway Genomics site has a scientist at the bench, along with a picture of a young couple presumably undergoing prenatal counselling. In addition, they sponsor a separate site, called My Genes My Child, that has a very different focus. It contains a fairly balanced discussion of the risks and benefits of testing children, with prominent, unbranded adverts taking you direct to Pathway. My Genes My Child is managed by an organisation called morefocus, who claim not to accept editorial from their sponsors.

In fact, there is a list of similarly sponsored Pathway sites, each with a slightly different twist:

Genetic Health
Nature and Nurture
Adoption DNA
Family Helix
Ancestor DNA

The genetic testing of children can touch a raw ethical nerve, which is maybe why children don't feature on many corporate websites. Even those who are liberally minded about adults exploring their DNA may feel a little uncomfortable where children are concerned.

Adults can choose to test, whereas children may not be mature enough to deal with the consequences. The availability of direct to consumer, rather than physician mediated testing sharpens such concerns. There is the real fear that labelling a child with some sort of “DNA destiny”, especially in these early days of scientific unknowns, has the potential to be detrimental to their upbringing.

23andme seem to have ridden roughshod over any such hesitations. They have no concerns about featuring children on their corporate site, and indeed they encourage the testing of extended families to uncover generational DNA interplay. And they seem to be selling something that people want to buy.

Babies always exert a stronger pull on the ethical heart strings than older children. Although 23andme have a cutesy baby on their homepage, an FAQ warns of the difficulty of collecting sufficient saliva from under threes (and so sidestepping any ethical concerns for this age group).

But there are other ways to get DNA: I have just sent off a DNA sample to deCODEme, and rather than spitting I had to scrape a stick inside my cheek. I reckon I could collect my 20-month-old son’s DNA this way (yes, it would be a struggle, but no more than the twice daily teeth brushing battle).

So, it seems like most genetic testing companies are not overtly promoting testing to children, with the exception of 23andme (who do not appeared to have suffered as a result), and Pathway whose anonymous approach may have slipped under the radar.

Regardless of your views on the promotion of direct to consumer genetic tests to children, it is happening. At least the main players are backed up by sound science and peer reviewed research, which cannot be said by the proliferation of more disturbing child talent sites – more on these in the next post.

Questions to ask before buying an internet genetics test

2010-06-29T20:15:00.034+01:00

The Human Genetics Commission has produced a list of questions to ask if you are thinking of buying a health related genetic test over the internet.

I will run through the questions while I am waiting for my deCODE cancer scan and my NHS BRCA test. There are two sets, I’ll answer the first in this post.

1. Why am I considering taking this test?
I'm taking the test because I'm interested in consumer genetic testing and in sharing the experience, I'm also intrigued to know what my cancer markers have in store. DeCODE do not test for BRCA genes but for common variants (SNP markers) that can increase risk three fold from average (that is up to 37% lifetime risk, compared to the more dramatic 55-85% risk for BRCA). The deCODE information is to some extent complementary to BRCA testing, all be it less clear cut.

I have no immediate medical motivation to find out about risks for cancers other than breast, given that I am under 40, have a reasonably healthy lifestyle and no untoward family history. I am, however, very excited about being part of the consumer DNA experiment and fascinated by the implications for society. I would love to have my complete DNA sequence but I’m happy to wait until sequencing costs come down and science fills in some of the gaps.

I have been researching the rival screens sold by 23and me, which I admit to finding tempting, the full list of tests is here. The trivial stuff (such as memory, pain sensitivity, avoidance of errors etc) is alluring in a pop psychology kind of way, the drug response information would be useful, the ancestry tracking looks enticing and now I’ve had my kids I could cope with the carrier status data. It does all seems slightly shallow, and drilling down to the disease information details reveals fewer markers than deCODE, which would explain the cheaper price. But overall it gives me that tingly hover-over-the-buy-it-now button feeling that precedes the desire to purchase something expensive online.

2. What do I hope the test will tell me?
I hope that I will have a low or average risk profile for breast cancer, and a low risk for the other cancers.

3. How important is it to know what the test may tell me?
Taking breast cancer separately, the outcomes could be crudely divided into 4:

a. Low deCODE marker risk - High BRCA risk
b. Low deCODE marker risk - Low BRCA risk
c. High deCODE marker risk - High BRCA risk
d. High deCODE marker risk - Low BRCA risk

[Although for the deCODE markers I’m unlikely to get results as clear cut as high/low risk, but numbers in between]

Using this to answer the question:

Scenarios a and c – deCODE test not that important compared to positive BRCA
Scenario b – deCODE test adds some extra reassurance
Scenario d – despite not having BRCA, a high deCODE score would reinforce my family risk

I’ve crudely defined “importance” as how much I’d change my behaviour. Based just on my family history I’m already trying to lower my risk (diet, exercise, self-examination), but I’m not hyper-vigilant - a high risk for either BRCA or deCODE markers would lead me to investigate early scans and preventative medicine. However, the whole hog mastectomy/ovary removal option could not be justified on the basis of profiling SNP markers. Would the NHS offer me breast scans at a younger age if I am low risk BRCA but high risk according to deCODE?

4. Will the test be able to answer my question?
The tests will give me more information on my cancer risks, but I'll wait to find out if they will add much more to my risk profile over and above that already in my family history.

5. What do I hope to be able to do after getting the test result that I can’t do now?
If I have high risk deCODE markers then I will take action (but perhaps I should be suitably motivated by my family history). In terms of the other cancer types, having a higher risk of skin cancer would make me more away of the amount of time I spend in the sun.

6. What if I get a result that I am not expecting?
I am expecting to be moderately high risk for the deCODE breast cancer scan, but not to be in the top risk band (that would involve markers from both sides of my family, and my mother’s relations have no history of early onset breast cancer). Being in the top band would take some getting used to.
It would be a shock to be higher risk for the other cancers for which I have no family history – I have the mindset that I am low risk for these.

7. Would it be a good idea to get professional advice (e.g. from my doctor) before buying the test and if so how can I get it?
I saw my GP to get referred for the BRCA test. I didn’t ask about the deCODE test but I doubt he would have recommended it or even been particularly familiar with the genetic markers involved.

8. Will the information the test provides have implications for my relatives?
The BRCA test will have more implications than the deCODE markers for my children and sibling, plus the children of my affected aunt. But the SNP risks will still be relevant to my immediate family, especially if there are any increased risks.

9. Am I going to tell them? If so, how?
I’m hoping the results are low risk so I won’t have to deal with this – if they are high then I would tell my brother (but would he want to know?). My sons are too young now which postpones the decision. They are likely to have access to their own DNA sequence by the time they are old enough to understand. If they were older now? I'm not sure I would say anything until they were adults, and I worry about the scope for nagging refrains such as “with your DNA your really must eat your broccoli”.

10. Will they want to know?
I can ask my brother if he wants to know, but I will only ask if there is a high risk, so the act asking may change his answer. Although, of course, I am blogging about the results...although I don’t have to blog ALL the results. Thankfully kids too young to read the blog...

11. Ought I to discuss this with them beforehand?
Hmm, too late now. Buying the test was very much like buying anything else on the internet, an individual consumer decision: it's my DNA and I can do what I want with it. This is even embedded in the company brands – 23andme, deCODEme. But buying a DNA test is actually one of the few consumer decisions that is not me me me.

12. Do I need to take the test now?
I could wait for the price to come down and the science to progress, although the BRCA test is urgent as I’m older than my grandmother was when she was diagnosed.

13. Is there another way of finding this information out?
Arguable my family history gives as much information as the deCODE markers are likely to. There are swathes of studies correlating the SNP markers to disease sufferers, but are there any correlations between markers and the family history of healthy individuals – i.e. which is more predictive of disease outcome – looking at common SNPs or looking at family history? It somewhat depends on the size of your family – expansive extended families contain much more data.

14. Would the result of the test have any impact for my work or my insurance prospects now or in the future?
There is currently an insurance moratorium regarding use of genetic information in the UK. I’m self-employed but don’t see that an employer would need to know.

Posting answers to these questions has forced me to think about the test in more detail than had I worked through the responses in my head. I suppose this has been a DIY genetic counselling session. Nothing similar was pushed at me when I ordered by kit from deCODE, which makes sense from a commercial point of view, but I wonder if some families have struggled with nasty genetic shocks that they weren’t expecting.

Going Private

2010-06-17T15:08:00.003+01:00

Today I am in possession of a promotion code to order a free DNA testing kit from the Icelandic company deCODEme. Six kits are being given out by the Association of British Science Writers for the “Future of Genomics” strand of their forthcoming London conference.

I choose the cancer screen, clicking past the $500 price tag. Ordering is easier than Amazon – no family trees or consent forms. Given the recent sample mix up at rivals 23andMe I wonder if I will be asked any questions (such as gender) to enable a simple cross-check, but the online form is minimal.

I tick the “sign your life away” boxes and open the Service Agreement (which I normally ignore). It includes the confirmation that the sample is mine or belongs to someone who has agreed to have it taken, plus a few interesting bits:

“Users’ Settings, public or private, will be used by deCODE to gather statistical aggregate information about the users...such analysis may include, but is not limited to...associating genetic variants with any of the self reported user attributes.”In other words, I am providing data to help deCODE’s research projects.

“You acknowledge your understanding of genetic risk as a statistical measure that has implications derived from a large group of people with characteristics equivalent to yours but does not determine your chances for getting the corresponding disease, the disease severity, or the disease outcome.”I’m hoping this will be pointed out again further down the line, in a place where it is actually likely to be read.

“The Genetic Scan product is for informational purposes only, is not medical advice, and is not a substitute for professional medical advice, genetic counseling, diagnosis, or treatment.”It’s a fine line....

I click through to the final page. DeCODE has been slowly sliding down into the commercial cesspit of precariously regulated direct-to-consumer genomic testing companies, and with Iceland’s economy as turbulent as their volcanoes I wonder if I will hear anything back.

How it all started

2010-03-04T14:45:00.009Z

Today I went to the GP to discuss genetic testing for breast cancer. Requesting a test has been floating around my mind for a few years, but now I’ve finished my family (my husband and myself have replaced ourselves, two is plenty), I’ve done my breastfeeding and I’m approaching 36, it’s time to make an appointment. The science behind genetic testing for familial breast cancer has been around a while now, but until recently I wouldn’t have wanted to know my risk. A positive test can mean an oophorectomy (a playful sounding word for the not-so-fun procedure of ovary removal), something I would not have been willing to go through prophylactically before having children.

My family history is quite simple. My father’s sister had breast cancer at the age of 45 and her mother (my paternal grandmother) had her breasts removed at 31 or 32. My grandmother never thought she had cancer, and there is no proof – at the time double mastcetomy was the standard, brutal treatment for any ominous looking growth. My aunt however, thinks her mother’s lump was similar in location to her own and the early onset in both cases makes a genetic link worth following up. There are no other cases, but then I have few female relatives (my sibling and cousins are all male, my father only has the one sister). On my mother’s side, there is the odd late-onset cancer, but nothing unusual.

The GP listened to my family history. He was unsure and had to check the guidelines – do I need a first degree relative suffering from early onset disease to be referred? I explain that this is impossible, seeing as any genetic predisposition is on my father’s side of the family and I do not have a sister. It turns out second degree relatives will suffice and he agrees to refer me.