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All of Us Genomics Working Group Recommends Genotyping, WGS for Pilot Study

NEW YORK (GenomeWeb) – The All of Us Research Programs' Genomics Working Group suggested today that the national project launch a pilot study to assess the feasibility of performing genotyping and whole-genome sequencing on all the study's participants.

The goal of the All of Us Research Program is to collect in a longitudinal fashion a variety of data, including genomic, medical, and environmental information, and use that to fuel research and advance precision medicine. The program entered beta testing over the summer.

With regard to the collection of genomic data specifically, the program aims to create both genotyping and sequencing data sets; develop workflows for generating, interpreting, and visualizing the data, as well as for returning a limited set of results before directing people to clinical care; and create a resource for researchers. 

The Genomics Working Group, which began meeting in June, discussed various platforms, including exome sequencing, WGS, and genotyping, and determined it would evaluate the latter two approaches in a subset of study participants. "In incorporating research value and potential for return of information, the group … agreed that whole-genome sequencing offers sufficient research advantages over whole-exome sequencing, at costs only incrementally greater, to warrant evaluation in a pilot phase without investment in whole-exome sequencing," the working group wrote in a report

The group estimated the cost of microarray-based genotyping to be between $30 and $100; the cost of exome sequencing in a CLIA-certified lab to be between $350 and $1,000; and the cost of WGS in a CLIA-certified lab to be between $1,000 and $2,000 per sample. "On average, the cost of WGS is currently three to four times more than WES," the working group wrote. "However, … this difference will narrow considerably in the next few years, to the point that the pricing of whole-genome sequencing per sample might approach the cost of whole-exome sequencing."

The working group estimated that 5 percent of the 1 million participant cohort, or 50,000 individuals, will have to receive testing in the pilot phase, in order to evaluate testing pipelines, assess data types and variant types across diverse groups, as well as establish strategies for return of results and have an understanding of genetic counseling needs.

"Genomic analysis is a fundamental part of our program, and we want to get it right," Eric Dishman, director of the All of Us Research Program, said in a statement. "It takes a lot of careful thought and planning not only to sequence 1 million genomes, but also to return information to participants in a meaningful way."

Based on the recommendations in the report, the All of Us staff and awardees plan to outline a comprehensive genomics plan before the program’s national launch in spring 2018.

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