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Enabled by 23andMe Customer Data, GWAS IDs New Loci for Basal Cell Carcinoma

NEW YORK (GenomeWeb) – A new GWAS, reportedly the largest to date on basal cell carcinoma, has identified 14 new susceptibility loci for the disease and confirmed 17 more discovered in earlier efforts.

The study, published today in Nature Communications, involved investigators from Stanford University and several other academic centers, as well as from the commercial testing firm 23andMe, who performed a two-stage GWAS involving more than 17,000 cases and almost about 290,000 controls.

The first stage of the study involved about 13,000 self-reported BCC cases and 275,000 controls of European ancestry recruited from genotyped 23andMe customers who have consented to contribute their results to scientific research.

The second stage evaluated an independent GWAS cohort of about 4,000 BCC cases and 12,800 controls from the Nurses’ Health Study and Health Professionals Follow-Up Study.

According to the authors, results of these two analyses confirmed 12 of 16 loci that had been found in prior smaller BCC GWAS, along with all of the five loci identified in previous candidate gene studies.

Importantly, the analysis also identified 14 novel susceptibility loci for BCC that reached genomewide significance — 10 of which only did so in the first cohort, and four that were significant in a meta-analysis of both cohorts.

The newly associated SNPs clustered into five main functional categories: telomere biology, immune regulation, tumor progression, non-coding RNA, and pigmentation, the researchers reported.

One newly identified locus appeared to be telomere-related, six were in immune-related gene regions, four were linked to areas involved in tumor progression, two were in or near long non-coding RNA genes, and one in an area that might affect pigmentation.

"Further investigation of these loci will improve our understanding of BCC pathogenesis and improve our ability to prevent these common tumors," the authors wrote.

The BCC study follows another by many of the same researchers, published in Nature Communications in July, taking the same approach to squamous cell carcinoma.

Similar studies relying on 23andMe customers who have agreed to provide their data to research have also led to discoveries in other disease areas. For example, in another study published this month researchers from Pfizer, 23andMe, and Massachusetts General Hospital found 15 genetic loci linked to the risk of major depressive disorder using data from hundreds of thousands of 23andMe customers as well as participants in published MDD studies.

Other studies have also been initiated including a collaboration between 23andMe and Genentech to enroll 3,000 Parkinson's disease patients from 23andMe's research community for a whole-genome sequencing study to inform its drug R&D efforts, and another with Pfizer studying the genetics of lupus.

More recently, 23andMe launched what it calls its Genotyping Services for Research (GSR) platform, which expands the possibilities of research collaborations beyond the existing cohort of 23andMe customers who have already been genotyped and agreed to share their data.

GSR offers researchers the opportunity to incentivize participation in studies by the public. After getting IRB approval to return genetic test results to participants, researchers can order spit kits online from 23andMe and send them to participants, who return them to 23andMe.

The company then processes samples and reports the raw SNP data to researchers through an online portal, but also allows participants to log onto its site and, like any other customer, view their genotyped results on ancestry, traits, and wellness, as well as their US Food and Drug Administration-cleared carrier status reports.

When it officially launched the service last month, 23andMe said that it was collaborating with researchers at a number of institutions, including McMaster University/St. Joseph’s Healthcare Hamilton, the University of California, San Diego, and Washington University in St. Louis.