Chromosome-Scale Selective Sweeps and Genomic Diversity in C. elegans
Andersen, Gerke et al., Nature Genetics
Researchers at Princeton University and elsewhere discuss the effects of chromosome-scale selective sweeps on genomic diversity in Caenorhabditis elegans. Taking a high-throughput selective sequencing approach on a collection of 200 wild C. elegans strains, the team found that the nematode's "genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases." Further, the team reports on its population genetic modeling experiments, which showed that "this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years," it writes.
Are LabCorp and Quest's Clinical-Trials Arms Missing the Next-Gen Sequencing Boat?
This post has been updated to clarify that SeqWright uses only Roche 454's next-gen sequencing platform in its clinical-trials business. It uses Illumina's and ABI's instruments in its research business. It also adds comment from a Quest spokesperson who said the company currently does use a next-gen sequencer in its clinical-trials arm.
SeqWright may force LabCorp and Quest's clinical-trials segments to work a littler harder — or smarter — for their supper.
The Houston-based company yesterday said its research service has added Illumina's HiSeq 2000 platform to its growing arsenal of next-gen sequencing systems. It already owns an ABI SOLiD 4 instrument for that portion of its business.
More importantly for clinical labs that dabble in the clinical-trials space, SeqWright has an equally strong hand: It uses Roche 454's next-gen sequencer in its clinical trials business, which caters to Phase I through Phase IV studies.
Its ownership of all three platforms could put LabCorp and Quest on notice that they should consider either investing in next-gen sequencing systems or expanding their installed base.
LabCorp currently does not employ a next-gen sequencer either in its clinical lab business or in its clinical trials arm. According to a Quest spokesperson, the company "has a next-generation sequencer which we use for clinical trials and other areas of our business." She did not elaborate.
For its part, SeqWright has gained some traction in this regard: This time last year the company penned a deal with drug maker Eli Lilly in which it will use the 454 sequencer to help identify genetic variants associated with psychiatric diseases.
By comparison, LabCorp's Esoterix Clinical Trials Services division offers flow cytometry, image analysis, immunohistochemistry, immunoassays, and PCR assays for Phase I work; while for Phase II-IV work it says it provides "solutions for clients who require different units (SI, ISO) or blood drawing systems for investigators across multiple countries or with unique needs," and that its "global capabilities provide consistent reference intervals, test methodologies and instrumentation, as well as standardized quality assurance and quality control measures."
The point about "global capabilities" was enhanced last week when LabCorp said its Esoterix business penned an international drug-testing partnership with Clearstone Central Laboratories, a central lab that provides services for late-stage clinical drug trials in several countries around the world. As I noted in that post, the deal could also have a clinical diagnostic component for LabCorp.
One bright spot for LabCorp appeared last December when CEO David King said next-generation sequencing is an “opportunit[y] that [is] out there that will have an impact over the next several years.”
However, he didn't say whether this "opportunity" would surface in the Esoterix business or in LabCorp's clinical diagnostics business, which also does not use next-gen sequencers.
Meantime, Quest's clinical trials business offers a wide array of technology platforms, including next-gen sequencing, DNA and RNA extraction, FISH, genotyping, individual and multiplex SNP analysis, molecular pathology, quantitative and qualitative PCR, custom sequencing arrays, viral load assays, flow cytometry, and immunoassays such as ELISAs, among others.
To be sure, SeqWright isn't without weaknesses. It's been around for just 15 years, has been offering next-gen sequencing services — on a single platform — for a relatively short time, and in early 2009 was granted a license by California regulators to operate as a clinical lab.
But as of now it's knee-deep in next-gen sequencing, and that's a pretty strong advantage, even for a drug-discovery services minnow like SeqWright.
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