dgmacarthur | April 29, 2010Kai Wang is a postdoctoral fellow at the Center for Applied Genomics, Children's Hospital of Philadelphia and an author on numerous genome-wide association studies. He left this lengthy comment as a response to my recent post on this comment by McClellan and King in Cell, and I felt it warranted promotion to a full post (with Kai's permission). For more discussion of the M&K review see also two recent posts by Steve Turner at Getting Genetics Done, and an excellent post from p-ter at Gene Expression.
A similar version of this comment is also published at Getting Genetics Done. I've done…
dgmacarthur | April 28, 2010Yesterday's inaugural Genomes, Environments, Traits (GET) meeting was by all accounts a massive success, pulling together the largest number of individuals with fully sequenced genomes ever assembled in the same room for a long day of discussion about the future of personal genomics.
While I was unfortunately unable to attend myself, there was phenomenal coverage of the event on Twitter from several attendees (notably Dan Vorhaus, Jonathan Eisen, Kevin Davies, Emily Singer, and many others). To get a sense of the event yourself there are few better resources than Dan Vorhaus' compendium of…
dgmacarthur | April 26, 2010This critique of genome-wide association studies by Jon McClellan and Mary-Claire King in Cell is the latest salvo in a prolonged backlash against genome-wide association studies (GWAS).
I hope to have more on the McClellan and King paper shortly, but in the meantime I will point you to a positive take on the paper by Stephen Turner (read the comments section), and an excellent response to one of M&K's more bizarre criticisms by p-ter at Gene Expression. The claim in question is that the tendency of GWAS to find disease associations outside of protein-coding genes is somehow a problem;…
dgmacarthur | April 20, 2010It's a big week for family genomics. I wrote a couple of days ago about the West family, all four members of which recently had their entire genomes sequenced by Illumina. Now an article in the Salt Lake Tribune reveals the identity of yet another four-person nuclear family with complete genome sequences: the wife and two step-children of Utah geneticist Lynn Jorde, as well as the children's biological father.
This family were sequenced to explore the basis of the two separate rare, severe genetic diseases (Miller syndrome and primary ciliary dyskinesia) that affect the two children - that…
dgmacarthur | April 19, 2010Mark Henderson breaks the news of the first sequencing of an entire nuclear family for non-medical (read: recreational) reasons. John West, his wife and two teenage children (aged 14 and 17) apparently paid the full retail price of almost US$200,000 (update: in the comments, Mark writes that West apparently got a "small" but not "hefty" discount off this retail price) to sequencing company Illumina to generate their complete DNA sequences.
The West family members are no strangers to sequencing - John West is the former CEO of Solexa, the sequencing technology company purchased by Illumina in…
dgmacarthur | April 1, 2010My previous post on the Myriad gene patent decision has resulted in one of the most useful and enjoyable comment threads in the history of this blog.
The debate revolves around a single, central question: while it's clear that the loss of gene-based patent protection (should the current decision be upheld by the Supreme Court) will be beneficial for companies and academic labs seeking to develop multi-gene tests - extending up to whole-genome sequencing - will these benefits come at a disastrous cost to the field as a whole by eroding financial incentives for innovation?
This outcome is…
dgmacarthur | April 1, 2010If you haven't already browsed through Nature's most recent edition, do so immediately - it's packed with juicy genomic goodness.
I particularly enjoyed the brief commentaries from Francis Collins and Craig Venter, both providing retrospectives on the last decade of human genomics and predictions for the future of the field, and the neat infographic illustrating the staggering change in sequencing capacity over the last ten years - but the whole issue is well worth reading.
dgmacarthur | March 31, 2010
Wellcome Trust Case Control Consortium. (2010). Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature, 464 (7289), 713-720 DOI: 10.1038/nature08979
The Wellcome Trust Case Control Consortium has just published the results of a massive survey of common, large DNA duplications and deletions (collectively termed copy number variation, or CNVs) in 16,000 patients suffering from complex diseases and 3,000 controls. The results come as no surprise, but are nonetheless disappointing: the study identified absolutely no novel CNVs…
dgmacarthur | March 29, 2010One of the major potential stumbling blocks for the field of genome-based diagnostics - particularly as we begin to move into the whole-genome sequencing era - is the unresolved issue of gene patents.
Currently somewhere in the order of 20% of the protein-coding genes in the human genome are covered by some kind of patent protection. However, the legal status of gene patents remains contentious.
Yesterday's astonishing defeat of Myriad Genetics in an ACLU-led case before a United States District Court is unexpected, and potentially a positive outcome for companies seeking to offer large-…
dgmacarthur | March 23, 2010Earlier this month I wrote a post skewering a terrible opinion piece about personal genomics in the Sunday Times by Camilla Long. This was my conclusion:
If Long wishes to stay ignorant of her own genetic risks - just as she has managed to remain ignorant of the entire field of genetics, even while writing an op-ed piece about it - that should be her choice. But her criticism of others who choose to pursue a greater understanding of their own genetic risk is entirely, horrendously misplaced.
Dan Vorhaus from Genomics Law Report was equally disgusted by the piece. While we were unsuccessful…
dgmacarthur | March 19, 2010Nick Loman (of the University of Birmingham, and the Pathogens: Genes and Genomes blog) has a post updating us on his survey of second-generation sequencing machines around the world. Loman's results are also available in the format of a handy Google map (see left).
The take-home messages based on 669 machines in the database: Illumina continues to utterly dominate the second-gen market, with competing short-read platform SOLiD squabbling for scraps with Roche's 454. That's a pretty poor outcome for SOLiD, which has failed to gain traction in the market despite having the full force of Life…
dgmacarthur | March 18, 2010Update: Dan Vorhaus has a brilliantly thorough post outlining the implications of the registry.
NIH Director Francis Collins has announced the creation of a voluntary registry for genetic testing services, with the details of each service being made fully available in a public database.
Much depends on the details, but if this database is done right it will be good news both for consumers and for reputable genetic testing companies. The press release states that one aim of the database is to "[e]ncourage providers of genetic tests to enhance transparency by publicly sharing information…
dgmacarthur | March 14, 2010Camilla Long's appallingly bad op-ed piece about personal genomics in the Sunday Times is a true masterpiece of unsupported criticism, and an ode to willful ignorance.
I'd encourage readers to discover their own favourite errors and misconceptions (there are plenty to go around), but here are some of the more glaring flaws:
Direct-to-consumer genetic testing is not illegal in the UK.
Long claims:
Although most of these tests seem pretty harmless and are marketed as "educational" rather than "diagnostic", in the UK such over-the-counter kits are outlawed.
She's completely wrong. In fact…
dgmacarthur | March 11, 2010Nic Wade says something very strange in his most recent article on whole genome sequencing in reference to the outcomes of genome-wide association studies:
The results of this costly international exercise have been disappointing. About 2,000 sites on the human genome have been statistically linked with various diseases, but in many cases the sites are not inside working genes, suggesting there may be some conceptual flaw in the statistics.
Erm... or maybe many common variants affecting the risk of complex diseases simply aren't found in protein-coding regions? That's the (biologically…
dgmacarthur | March 11, 2010
Zoe McDougall from Oxford Nanopore points me to a press release from Illumina announcing a new era of celebrity genomics:
Illumina, Inc. (NASDAQ:ILMN) today announced that it has sequenced the DNA of American actress Glenn Close, the first publicly named female to have her DNA sequenced to full coverage. The service was completed in Illumina's CLIA certified and CAP accredited laboratory utilizing Illumina's Genome Analyzer technology and following the established process shown at http://www.everygenome.com/. Ms. Close's DNA was sequenced to an average depth greater than 30 fold, providing…
dgmacarthur | March 10, 2010Lupski, J.R., et al. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine advance online 10.1056/nejmoa0908094
Roach, J.C., & et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science : 10.1126/science.1186802
Two new papers out today - the first ever studies to employ whole-genome sequencing for disease gene discovery - neatly illustrate both the promise and the challenges lying ahead both for clinical and personal genomics.
The first paper presents the final - and successful…
dgmacarthur | March 10, 2010Dan Koboldt has a very nice recap of the various sequencing technologies presented at last week's Advances in Genome Biology and Technology meeting. I totally agree with his central point:
Something had been bothering me about the sequencing-company presentations this year, and I finally realized what it was. During AGBT 2009, every player was gunning to take over the world. This year it seems like every sequencing platform has a niche in mind.
The recent proliferation of sequencing technologies - each with their own characteristic profile of strengths and weaknesses - has been bewildering…
dgmacarthur | March 8, 2010Dan Vorhaus pointed me to this review of the recent PBS series Faces of America. I haven't seen the series myself, but I found this segment of the review hilarious:
The element of the last PBS episode I found most intriguing was Gates' interview with novelist Louise Erdrich, who declined to have her DNA tested because her identity as a descendant of the Chippewa Native American tribe is so important to her. She said that she felt her tribe and family were what made her who she was. And, as she explained to Gates, she "didn't want to add any confusion to it."
Erdrich, in other words, didn't…
dgmacarthur | March 7, 2010A colleague just pointed me to an entry on Brad Templeton's blog where Templeton reveals some bizarre connections between people he has met as distant cousins via 23andMe's Relative Finder algorithm. Nothing too spooky, but a precursor of things to come if (as I hope and expect) 23andMe manages to ride out the current troubles besetting personal genomics and continue building its genetic database.
(H/T John).
Subscribe to Genetic Future.
Follow Daniel on Twitter
dgmacarthur | March 4, 2010
Over at Gene Expression, Razib suggests that trouble lies ahead for personal genomics company 23andMe. Although I'm generally a bit of a cheerleader for the Mountain View-based startup, I must admit the signs over the past year or so haven't been good: two rounds of lay-offs, the departure of co-founder Linda Avey, and the apparent deployment of $4M from a recent funding round to pay back a loan from fellow co-founder Anne Wojcicki.
Razib also notes some anonymous employee reviews of the company on GlassDoor suggesting poor morale among 23andMe workers; it's hard to make too much of these…