MAQC Adds Genome-Wide Association Studies to Phase II To-Do List
CARY, NC — The MicroArray Quality Control Consortium has expanded its scope by adding a new workgroup that will identify “best practices” for genome-wide association studies.
Leming Shi, a researcher at the US Food and Drug Administration’s National Center for Toxicological Research and a coordinator of the MAQC initiative, announced the new group during the MAQC’s seventh face-to-face project meeting held here on the campus of the SAS Institute last week.
The new workgroup will be the fifth under the auspices of the second phase of the MAQC project, dubbed MAQC-II. The consortium published the results of the first phase of its study, which evaluated the reproducibility of microarray experiments across different labs and platforms, in Nature Biotechnology last fall.
In phase II, the consortium is addressing the challenges of developing and confirming predictive models that use gene-expression profiles to predict outcomes for individuals, including disease recurrence, prognosis, drug response, or the like.
Before last week’s meeting, the project comprised four workgroups: the Clinical Working Group, which is analyzing patient data from large-scale clinical studies; the Toxicogenomics Working Group, which is doing the same for toxicogenomics experiments; the Titrations Working Group, which is following up on titration samples from MAQC-I; and the Regulatory Biostatistics Working Group, which is advising the Clinical and Toxicogenomics groups on ways to evaluate the performance of predictive models and classifiers.
However, according to several speakers at last week’s meeting, the recent rise of array-based genome-wide association studies has presented a number of issues that the consortium would be better off addressing sooner rather than later.
In a presentation arguing in favor of forming the working group, Nick Xiao of SAIC Frederick said that “MAQC has successfully proven that microarray technology can be used for biomarker discovery,” and noted that the group can apply many of the lessons learned from MAQC-I to show that “genotyping technology can be just as trusted and just as robust.”
In a similar presentation, Federico Goodsaid, senior staff scientist in the genomics group at FDA’s Office of Clinical Pharmacology, said that the FDA has been getting “a number” of genome-wide association studies under its Voluntary Exploratory Data Submissions guidelines. These GWAS experiments have “enormous sources of variability at each analysis step,” Goodsaid said, yet there is currently “no framework to tell us why [submitters] are doing this or that.”
These examples are “amazingly parallel” to the issues MAQC-I explored for gene expression analysis, he said.
Goodsaid suggested that the goal of the GWAS working group would be to publish “best practices for analyzing whole-genome analysis data.”
After the discussion, Shi announced the formation of the fifth workgroup and named Goodsaid and Xiao as coordinators. The first task for the group, he said, will be to identify experts in academia, industry, and government who will be willing to assist with the project.
Shi noted that GWAS experiments present several “new challenges” for the microarray community, “but a lot of similarity with what we saw in gene expression.”
Ultimately, he said, the objectives of the new working group align with the broader goal of MAQC-II, which is to predict health outcomes based on microarray measurements of biological samples.
“For personalized medicine to be realized, we have to be able to make a prediction for each patient,” he said.
LabCorp Licenses Veridex's Gene-Methylation IP to Develop Prostate Cancer Dx
LabCorp said this week that it has licensed a gene-methylation technology developed by Veridex in order develop a qPCR assay for prostate cancer.
LabCorp said it is the first company to license the technology, which is designed to detect the methylated GST-Pi gene. The reference lab said the test may "provide a more sensitive and accurate detection of prostate cancer" when used with histology, than would histology testing alone.
According to LabCorp, the assay would be used in biopsies showing "suspicious histopathology," for patients who show elevated prostate-specific antigen values, and in patients whose biopsies are repeatedly negative.
Financial terms of the agreement were not released.
Qiagen, Epigenomics Expand Alliance to Include Molecular Dx
Qiagen this week said it has licensed exclusive worldwide rights to Epigenomics' sample-handling technologies for applied testing and in vitro diagnostics as part of an expansion of an earlier alliance.
The companies inked an OEM agreement two years ago that gave Qiagen exclusive rights to Epigenomics' bisulfite DNA treatment technology and Methylight assay technology for research uses.
Under the new agreement, Qiagen will pay Epigenomics an up-front fee, milestone payments, and royalties, Qiagen said. Financial terms of the deal were not disclosed.
Epigenomics will retain the rights to its sample technologies in its own or partnered development projects and for commercializing diagnostics through a non-exclusive back-license from Qiagen.
Qiagen said the expansion follows the launch of the EpiTect Bisulfite kit, which uses Epigenomics' DNA-methylation technology and is for research use only. Based on the results of that program, Qiagen said the companies now plan to use DNA methylation to develop and sell a complete and validated IVD pre-analytical sample technology portfolio.
Qiagen CEO Peer Schatz said the companies expect DNA methylation technology to play an important role in the molecular diagnostics market, particularly in areas such as cancer screening.
Schatz said Qiagen's epigentic testing portfolio now includes "sample technologies such as DNA sample collection, stabilization, purification, and bisulfite conversion to assay technologies such as PCR- and sequencing-based methods for DNA methylation analysis."
NIH Releases GAIN Study Data, Details Data-Access Procedure
The National Institutes of Health announced last week that it has released the first data from the Genetic Association Information Network, or GAIN, project, via the dbGAP database at the National Center for Biotechnology Information.
In a notice released on Friday, the NIH announced the availability of the data and outlined the process under which researchers can apply for access to GAIN project datasets.
GAIN is a public-private genome-wide association study project coordinated by the NIH and the Foundation for the NIH. FNIH awarded the first grants under the effort last October.
Last week, NIH released the data through GAIN dbGaP, the database of Genotype and Phenotype, which offers two levels of access: summary-level data that is available to anyone with no restrictions; and individual-level data that requires preauthorization.
Researchers can request access to the individual-level data from GAIN studies through the dbGaP data access request system. Further information about the process is available here.
Summary-level data is already available, and NIH said it expects to begin releasing individual-level data by June 9.
Philips and Organon Will Use Imaging Technology in Biomarker Research
Philips Life Sciences and Organon said last week that they are partnering to perform biomarker studies that could benefit Philips’ imaging programs and Organon's drug-development efforts.
Under the agreement, researchers from both companies will use Philips' labs and medical-imaging technologies to identify, validate, and pursue uses for novel biomarkers that Organon may use to develop drug programs for psychiatric and immune system disorders. Specifically, the companies hope to study the effects of psychiatric drugs in the brain at the molecular level.
The companies said the research will be conducted at Philips' High Tech Campus in Eindhoven, the Netherlands.
Rick Harwig, Philips’ chief technology officer, said in a statement that the project will help Philips "speed the evolution" of its imaging technology "into tools to image the body at the molecular level."
The companies said that imaging technologies can be used to monitor the effect of the therapies and customize treatment programs accordingly.
23andMe Completes Series A Financing; Google Holds Minority Stake
23andMe, a startup that describes itself as a “personal genetics” company, has closed a Series A round of financing with investments from Google, Genentech, MDV-Mohr Davidow Ventures, and New Enterprise Associates.
Terms of the financing were not disclosed.
23andMe said in a statement that it is focused on enabling individuals to “access, explore, and better understand their genetic information, making use of recent advances in DNA analysis technologies and proprietary web-based software tools.”
The company currently plans to launch at the end of the year and will provide more information at that time.
In an SEC document filed May 22, Google disclosed that it invested around $3.9 million in the firm and that it now holds a minority interest in the company as a result of this investment.
23andMe’s investors include Anne Wojcicki, who is married to Google founder Sergey Brin. Google noted in its SEC filing that its audit committee reviewed and approved the transaction “as part of Google’s procedures for entering into transactions with related parties.”
23andMe states on its website that its goal “is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits.”
The company claims on its website that it is “building on recent advances in DNA analysis technologies to enable broad, secure, and private access to trustworthy and accurate individual genetic information.”
Canadian Government Pledges $32M for Population Genomics Consortium
The Canadian government and the government of Québec plan to pump CA$34.5 million ($31.9 million) into a human genomics consortium, government officials said last week.
The Public Population Project in Genomics, or P3G, could receive as much as CA$64.5 million when funds from other partners are counted, government ministers and the head of Genome Canada said at the Human Genome Organization’s annual meeting in Montreal last week.
The primary aim of the Montreal-based P3G consortium is to foster “collaboration between researchers and projects in the field of population genomics." The group also includes the ongoing CARTaGENE project, Genome Canada said.
One of the major projects will be the creation of a large biobank that will hold data from 20,000 residents of Québec between the ages of 40 and 69.
Claude Laberge, a population genomics expert at the Laval University in Québec City who is involved in CARTaGENE, said the infrastructure “will function as a precursor for the development and testing of standards for large biobanks.”