Contact: Jane E. Rubinstein
Goal is highly scalable pharmacogenomics research
Mountain View, Calif. — 23andMe has launched a project funded by the National Institutes of Health (NIH) which is aimed at validating 23andMe’s highly-scalable platform for pharmacogenomics research. The company received $190,000 in stimulus funding from the American Recovery and Reinvestment Act of 2009 for “Web-based Phenotyping for Genome-Wide Association Studies of Drug Response” from NIH’s National Human Genome Research Institute.
“One of 23andMe’s research goals is to identify novel pharmacogenetic associations using web-based phenotyping of efficacy and toxicity,” said Anne Wojcicki. co-founder and CEO of 23andMe. “If this project is successful in yielding replications, it will set the stage for rapid, well-powered and cost-effective research on many mediations. In particular, it will facilitate research on new medications as they hit the market, serving to significantly advance personalized medicine.”
Building on 23andMe’s initial success in discovering novel genetic associations related to hair curl, asparagus anosmia (the inability to detect the scent of certain asparagus metabolites in urine), the photic sneeze reflex (the tendency to sneeze when entering bright light), and freckling, as published in PLoS Genetics this year, the research arm of 23andMe is now investigating genetic factors underlying responses to three classes of drugs: non-steroidal anti-inflammatory drugs (NSAIDs); protein-pump inhibitors (PPIs), used to treat gastroesophogeal reflux disease (GERD); and the blood thinner, Warfarin.
This project leverages 23andMe’s customized genotyping chip, which includes thousands of single nucleotide polymorphisms (SNPs) not included on standard chips. In particular, this chip tests numerous SNPs within genes known to be associated with drug metabolism, efficacy, toxicity, or other side effects.
The first phase of the study includes development and validation of web-based surveys to assess the drug side effects and drug effectiveness experienced directly by 23andMe’s customers. During the second phase, the research team will determine whether this approach enables them to replicate previously known associations between response to these three classes of drugs and variation within two genes: CYP2C9 and CYP2C19. 23andMe’s research team will also search for previously unknown genetic factors associated with response to these classes of drugs, taking into consideration a broad range of non-genetic factors such as age, sex, and body-mass index, among others.
In previous studies, 23andMe has demonstrated that self-reported information from customers yields data of quality comparable to that gathered using traditional research methods. Additional benefits of 23andMe’s web-based research model include: the ability to perform hundreds of studies in parallel; easy and efficient ways to contact individual participants multiple times and ask follow-up questions — this enables 23andMe researchers to quickly zero-in on associations that could be the building blocks for future research aimed at prevention, better treatments, and potentially cures for a multitude of diseases and conditions. A web-based research model also affords participants added flexibility, they can choose when and where to respond to surveys and may take breaks to check on answers to specific questions as needed. The geographic location of research participants and their proximity to a research center is no longer a limiting factor with a web-based approach, providing an even larger pool of potential research participants.
Ultimately, web-based data collection, parallel analysis of hundreds of traits and diseases, and highly automated genotyping lead to low cost research. 23andMe’s more than 60,000 customers are invited regularly to participate in a range of research projects; eligible and consenting customers will be invited to join this study during 2011.
The project described is supported by Award Number 1R43HG005807-01 from the National Human Genome Research Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health.
Disclosures: 23andMe is also currently conducting a study related to Parkinson’s disease that involves web-based collection of phenotypic data.
23andMe, Inc. is a leading personal genetics company dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. The company’s Personal Genome Service enables individuals to gain deeper insights into their ancestry and inherited traits. The vision for 23andMe is to personalize healthcare by making and supporting meaningful discoveries through genetic research. 23andMe, Inc., was founded in 2006, and the company is advised by a group of renowned experts in the fields of human genetics, bioinformatics and computer science. More information is available at www.23andme.com.
ScienceDaily (Dec. 8, 2010) A recent study accepted for publication in The Endocrine Society’s Journal of Clinical Endocrinology Metabolism (JCEM) has demonstrated a novel and accurate test for early diagnosis of Turner syndrome. Turner syndrome affects one in 1,500 to 2,000 female live births and early diagnosis allows for the timely management of short stature and co-morbid conditions including cardiac and renal problems.
Turner syndrome (TS) is the most common genetic problem affecting girls with short stature. Average adult height in untreated girls with TS is 4 feet, 8 inches, yet with early diagnosis and initiation of growth hormone therapy, normal or near-normal adult stature can be achieved. Unfortunately, the vast majority of girls with TS go unrecognized until after 10 years of age. This new study suggests a new way to diagnose TS to help prevent delayed recognition.
“We have developed a novel approach for diagnosing TS that can be used to practically test large numbers of girls and is much quicker and less expensive than the current methods,” said Scott Rivkees, MD, of Yale University School of Medicine in New Haven, Conn. and lead author of the study. “The new test would also provide the benefit of early detection of other health conditions associated with TS, such as potential renal and cardiac problems.”
TS occurs when an X-chromosome is completely or partially deleted. In this study, researchers developed a test based on a quantitative method of genotyping to detect X-chromosome abnormalities. Of 90 clinically-confirmed TS individuals tested, the assay correctly identified 87 (96.7 percent).
“Because of the small amount of DNA needed for the test, ample DNA can be extracted from cheek swabs or from newborn screening blood spots that are routinely collected,” said Rivkees. “If broadly used in the clinical setting at young ages, this test can prevent the delayed recognition of TS.”
Other researchers working on the study include: Anastasia Wise, Peining Li, Henry Rinder and Jeffrey Gruen of Yale University School of Medicine in New Haven, Conn.; and Karl Hager and Seiyu Hosono of JS Genetics in New Haven, Conn.
Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.
The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by The Endocrine Society, via EurekAlert!, a service of AAAS.
- Scott Rivkees et al. A Highly Sensitive, High-Throughput Assay for the Detection of Turner Syndrome. Journal of Clinical Endocrinology Metabolism, March 2011
Note: If no author is given, the source is cited instead.
Science. 2010 Oct 22;330(6003):514-7.
Neafsey DE, Lawniczak MK, Park DJ, Redmond SN, Coulibaly MB, Traoré SF, Sagnon N, Costantini C, Johnson C, Wiegand RC, Collins FH, Lander ES, Wirth DF, Kafatos FC, Besansky NJ, Christophides GK, Muskavitch MA.
Broad Institute, Cambridge, MA 02142, USA.
Mosquitoes in the Anopheles gambiae complex show rapid ecological and behavioral diversification, traits that promote malaria transmission and complicate vector control efforts. A high-density, genome-wide mosquito SNP-genotyping array allowed mapping of genomic differentiation between populations and species that exhibit varying levels of reproductive isolation. Regions near centromeres or within polymorphic inversions exhibited the greatest genetic divergence, but divergence was also observed elsewhere in the genomes. Signals of natural selection within populations were overrepresented among genomic regions that are differentiated between populations, implying that differentiation is often driven by population-specific selective events. Complex genomic differentiation among speciating vector mosquito populations implies that tools for genome-wide monitoring of population structure will prove useful for the advancement of malaria eradication.
PMID: 20966254 [PubMed - in process]
ScienceDaily (Oct. 20, 2010) Two strains of the type of mosquito responsible for the majority of malaria transmission in Africa have evolved such substantial genetic differences that they are becoming different species, according to researchers behind two new studies published in the journal Science.
Over 200 million people globally are infected with malaria, according to the World Health Organisation, and the majority of these people are in Africa. Malaria kills one child every 30 seconds.
The international research effort, co-led by scientists from Imperial College London, looks at two strains of the Anopheles gambiae mosquito, the type of mosquito primarily responsible for transmitting malaria in sub-Saharan Africa. These strains, known as M and S, are physically identical. However, the new research shows that their genetic differences are such that they appear to be becoming different species, so efforts to control mosquito populations may be effective against one strain of mosquito but not the other.
The scientists argue that when researchers are developing new ways of controlling malarial mosquitoes, for example by creating new insecticides or trying to interfere with their ability to reproduce, they need to make sure that they are effective in both strains.
The authors also suggest that mosquitoes are evolving more quickly than previously thought, meaning that researchers need to continue to monitor the genetic makeup of different strains of mosquitoes very closely, in order to watch for changes that might enable the mosquitoes to evade control measures in the future.
Professor George Christophides, one of the lead researchers behind the work from the Division of Cell and Molecular Biology at Imperial College London, said: “Malaria is a deadly disease that affects millions of people across the world and amongst children in Africa, it causes one in every five deaths. We know that the best way to reduce the number of people who contract malaria is to control the mosquitoes that carry the disease. Our studies help us to understand the makeup of the mosquitoes that transmit malaria, so that we can find new ways of preventing them from infecting people.”
Dr Mara Lawniczak, another lead researcher from the Division of Cell and Molecular Biology at Imperial College London, added: “From our new studies, we can see that mosquitoes are evolving more quickly than we thought and that unfortunately, strategies that might work against one strain of mosquito might not be effective against another. It’s important to identify and monitor these hidden genetic changes in mosquitoes if we are to succeed in bringing malaria under control by targeting mosquitoes.”
The researchers reached their conclusions after carrying out the most detailed analysis so far of the genomes of the M and S strains of Anopheles gambiae mosquito, over two studies. The first study, which sequenced the genomes of both strains, revealed that M and S are genetically very different and that these genetic differences are scattered around the entire genome. Previous studies had only detected a few ‘hot spots’ of divergence between the genomes of the two strains. The work suggested that many of the genetic regions that differ between the M and S genomes are likely to affect mosquito development, feeding behaviour, and reproduction.
In the second study, the researchers looked at many individual mosquitoes from the M and S strains, as well as a strain called Bamako, and compared 400,000 different points in their genomes where genetic variations had been identified, to analyse how these mosquitoes are evolving. This showed that the strains appear to be evolving differently, probably in response to factors in their specific environments — for example, different larval habitats or different pathogens and predators. This study was the first to carry out such detailed genetic analysis of an invertebrate, using a high density genotyping array.
As a next step in their research, the Imperial researchers are now carrying out genome-wide association studies of mosquitoes, using the specially designed genotyping chip that they designed for their second study, to explore which variations in mosquito genes affect their propensity to become infected with malaria and other pathogens.
Both of the studies just published were collaborations between researchers at Imperial and international colleagues, involving researchers from institutions including the University of Notre Dame, the J. C. Venter Institute, Washington University and the Broad Institute. Funding for the projects was provided by the National Human Genome Research Institute, the National Institutes of Health, the BBSRC, and the Burroughs Wellcome Fund.
Editor’s Note: This article is not intended to provide medical advice, diagnosis or treatment.
The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Imperial College London, via AlphaGalileo.
Note: If no author is given, the source is cited instead.