NIST has led the Genome in a Bottle Consortium to develop widely-used benchmark germline variant calls for seven human cell lines [1]. Similar extensively characterized benchmark cell lines and DNA are needed to benchmark somatic variant detection in tumors. This project would involve working with a unique group of technology and informatics developers in the public-private-academic Genome in a Bottle Consortium to develop methods to integrate short-, linked-, and long-read sequencing technologies to form benchmarks for somatic variant calls. It will also be important to develop appropriate performance metrics and tools to calculate these metrics for somatic variants, similar to those NIST and the Global Alliance for Genomics and Health developed for germline variants [2].

[1] JM Zook, et al. An open resource for accurately benchmarking small variant and reference calls. Nature Biotechnology 2019, 37, 561.
[2] P Krusche, et al, JM Zook. Best practices for benchmarking germline small-variant calls in human genomes. Nature Biotechnology 2019, 37, 555.

key words

Genomics; Bioinformatics; DNA sequencing; De novo assembly; Machine learning; Reference materials; Precision medicine; Data science; Artificial intelligence

Citizenship:  Open to U.S. citizens

Level:  Open to Postdoctoral applicants