dgmacarthur | April 13, 2009Mark Henderson has a great piece in the Times exploring the impact of personal genomics on the practice of medicine.
The basic theme should be familiar to anyone who has been following the emergence of the personal genomics industry: doctors are currently almost completely unprepared for the onslaught of genetic information they are about to experience. Here's the situation:
At present, genetic training focuses on Mendelian diseases - rare mutations in
single genes, which usually have severe effects. People who inherit the
Huntington's mutation, for example, will invariably develop the…
dgmacarthur | April 13, 2009This BBC video is worth checking out - it's a nice visual display of the processes used by genome sequencing provider Complete Genomics to smash apart and resequence a human genome.
I can't help but wonder if Complete built the blue-lit, monitor-lined hallway (screen shot below) purely for this video; it makes for great cinematics.
It must be personal genomics week here in the UK - the BBC also ran a generally favourable story on 23andMe a few days ago.
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dgmacarthur | April 12, 2009Razib points me to a great plain-language article reviewing our current scientific understanding of human genetic variation.
The major focus is on copy-number variants (CNVs) - genetic variants involving the insertion or deletion of large chunks of DNA, sometimes spanning over a million bases. These large-scale variants lurked essentially unknown within the human genome until the recent advent of chip-based platforms, which make it possible to very rapidly assay almost the entire genome for their presence. Such surveys have revealed that large-scale CNVs are far more common than anyone…
dgmacarthur | April 12, 2009Razib has crunched the numbers from the General Social Survey (a massive longitudinal study of societal trends) to explore the variables associated with response to this question:
Some people say that genetic testing may cause trouble. Others think it
is a wonderful medical advance. Based on what you know, do you think
genetic testing will do more harm than good or more good than harm? [my emphasis]
The major finding: by far the strongest correlation is with attitude towards the Bible (those who regard it as the Word of God are more skeptical of testing), with position on the political…
dgmacarthur | April 12, 2009GenomeWeb News reports that genome sequencing company Complete Genomics is cutting costs in the lead-up to the commercial launch of its whole-genome sequencing service in June:
In order to save its remaining cash, the company recently
implemented "a variety of cost-saving measures," including "some
reductions" in the salaries of its employees and a trimming of
"non-essential" costs, such as discretionary spending. "We just want to
be prudent about [spending] our cash," Reid said.
The company has not had any layoffs, he added, and is "still running at full capacity."
At this time, he said,…
dgmacarthur | April 9, 2009There are a couple of things I didn't explain very well in my previous post about the strange case of the 13-year-old girl suing a sperm bank using product liability law, on the grounds that the sperm used to conceive her carried a genetic defect resulting in her mental retardation.
First and foremost, what's with a girl inheriting Fragile X Syndrome from her father? This syndrome is (as you might expect) caused by mutations in a region located on the X chromosome, and the classic pattern of inheritance of X-linked diseases is that males are affected while females are "carriers" (who may also…
dgmacarthur | April 9, 2009New Scientist reports that a 13-year-old girl with Fragile X Syndrome - a severe genetic disorder - is suing the sperm bank that provided the sperm that led to her conception.
Curiously, the legal issue hinges on "a product liability law more commonly associated with manufacturing defects, such as faulty car brakes":
Donovan does not have to show that Idant was negligent, only that the
sperm it provided was unsafe and caused injury. "It doesn't matter how
much care was taken," says Daniel Thistle,
the lawyer representing Donovan, based in Philadelphia, Pennsylvania.
Genetic tests have…
dgmacarthur | April 7, 2009Attila Csordas has a post up at Partial Immortalization explaining how to use the application MitoWheel (which Csordas helped develop) to visualise data from the new Haplogroup Tree Mutation Mapper from 23andMe. This might be a fun way for genetic genealogy afficianados to spend a few minutes getting to know their genomes better.
This reminded me about a little experiment of Csordas' that I learnt about when I met him in Cambridge a couple of weeks ago, which strikes me as a quintessential expression of the spirit of the personal genomic era - posting his genetic data from 23andMe, one base…
dgmacarthur | April 7, 2009Jeffrey Perkel at Biotechnically Speaking has a great overview of a recent paper in Nature Methods (see also coverage at GenomeWeb).
The study in question used second-generation sequencing (with the ABI SOLiD system) to peer inside a single cell isolated from a mouse embryo. By sequencing the messenger RNA (mRNA) produced by the cell's genome they were able to generate a high-resolution snapshot of the genes switched on by the cell.
Isolating and analysing RNA from a single cell is no small technical feat, and although the technique still has its limitations - for instance, the technique can…
dgmacarthur | April 3, 2009OK, so this GenomeWeb Daily News article is approximately four centuries old in internet time (i.e. around a week), but it's worth going back and reading.
I've previously argued at length that although personal genomics currently offers little in the way of useful, predictive health information, that lack of information in itself represents an important opportunity to educate consumers about the fuzzy nature of common disease genetics.
So long as personal genomics companies represent the data accurately (which the major reputable companies currently do quite well, by and large), their…
dgmacarthur | April 2, 2009GenomeWeb Daily News points to a new funding opportunity from the US National Institutes of Health (NIH) for researchers interested in studying the link between genetic variants and variation in the expression levels of genes.
This is an incredibly important area of research. Genome-wide association studies have recently uncovered vast numbers of DNA regions linked to common diseases (the latest estimate I've heard suggests around 400 common genetic variants associated with 75 different diseases or traits) - but we still don't have a clue how the majority of these regions actually alter…
dgmacarthur | April 1, 2009So I'm trying this Twitter thing all the cool kids are talking about - seems like a handy way to share interesting genetics-related stuff that doesn't quite warrant a full blog post. If you are so inclined you can follow me here. That is all.
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dgmacarthur | April 1, 2009I noted yesterday that the annual earnings report of Icelandic biotech giant deCODE Genetics, one of the major players in modern human genetics, suggested that the company is veering steadily towards financial oblivion.Â
Today the company had a crucial earnings call - anyone interested in the details of deCODE's plight, or at least a sanitised corporate version thereof, should check out the webcast. The main messages from the call have been ably dissected by articles from Kevin Davies of Bio-IT World and Mark Henderson at The Times (in which I am delighted to be quoted alongside human…
dgmacarthur | April 1, 2009Personalised medicine pioneers Helix Health have announced their intention to seize control of the assets of personal genomics company 23andMe.
Helix Health founder Steve Murphy (left) laid out his takeover plans during a press conference this morning. "It's time to seize the moral high ground!!!!" he proclaimed, physically spelling out the additional exclamation marks to the assembled reporters. "23andMe have played their BS PR games for too long, and I'm here to put that right!"
During a four hour-long monologue that was often rambling and at times completely incoherent, pausing only for…
dgmacarthur | March 31, 2009deCODE Genetics, the major Icelandic biotech company behind personal genomics outfit deCODEme, has just released its financial results for 2008. Things really aren't looking good:
At December 31, 2008, the company had liquid funds available for operating activities, comprised of cash and cash equivalents together with current investments, of $3.7 million, compared to $64.2 million at December 31, 2007. In early 2009 the company sold its auction rate securities (ARS) for $11.0 million in cash which the company has been using to finance its operating activities. The company believes it has…
dgmacarthur | March 31, 2009Personal genomics company 23andMe has just launched an online community of "mommy bloggers" - a move I can only describe as sheer marketing genius.
I'll give you a moment to let the vision sink in. Imagine a group of women hungry for information about the best way to ensure the future health and wellbeing of their unborn children. Now imagine a website packed with sincere, caring mother-types - most of them well-established bloggers with a strong existing fan base - writing about the real day-to-day issues that mothers care about (in the words of one recruit: "momming, aging, and my twenty…
dgmacarthur | March 25, 2009New Scientist has a fascinating piece in which reporters Peter Aldhous and Michael Reilly demonstrate - with a little cash, and more than a little effort - the possibility of obtaining large-scale genetic data from someone without their knowledge or permission.
The reporters started with a glass that Aldhous had drunk water from; Reilly swabbed the glass and sent the sample to an unnamed commercial lab for whole-genome amplification (a technique widely used in forensics and research applications, which allows small amounts of DNA to be converted into larger amounts). An initial attempt to…
dgmacarthur | March 25, 2009Neuroscientists Sam Wang and Sandra Aamodt have a guest post on Olivia Judson's NY Times blog discussing the complex interplay between genes and environment in the determination of personality traits. A taste:
So some of the effects that we call "genetic" (or "nature") are the
indirect result of people being drawn to particular environments
because of their personality. Or to put it another way, some
"environmental" (or "nurture") effects are actually attributable to
genetic tendencies.
It's worth noting that similar effects can occur for other traits: for instance, a genetic variant that…
dgmacarthur | March 24, 2009Pickrell, J., Coop, G., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Srinivasan, B., Barsh, G., Myers, R., Feldman, M., & Pritchard, J. (2009). Signals of recent positive selection in a worldwide sample of human populations Genome Research DOI: 10.1101/gr.087577.108I pointed yesterday to a new paper in Genome Research taking a genome-wide look at the signatures of recent natural selection in a worldwide sample of humans.
I promised a more thorough analysis of this paper today, but I see Razib at Gene Expression has already done a fine job of that. Razib's post covers the bulk of the…
dgmacarthur | March 23, 2009I'll hopefully have more time to write about this tomorrow, but for now I'll simply suggest that you go and read the free full text PDF of this advance online manuscript in Genome Research.
This is the most important recent paper in the field of human evolutionary genetics - a thorough and careful analysis of the signatures of positive natural selection left in our genome by the last 10-40,000 years of adaptation, using a population sample that is far broader than those used in previous studies (53 populations rather than 4). I covered some of the approaches used in the paper in this post on…