The NIST-led Genome in a Bottle Consortium has extensively characterized the genomes of several human reference cell lines to serve as benchmarks for genome sequencing methods [1]. In addition, these cell lines have been used as a well-characterized background DNA in over 50 commercial products. These cell lines, as well as induced pluripotent stem cell lines from the same individuals, could serve as reference samples for other ‘omics technologies as well. For example, this postdoc could take advantage of the extensive single molecule sequencing data and other epigenomics data available for these cell lines to develop benchmarks for methylation of DNA or other epigenetics technologies. This postdoc could also work with the transcriptomics technology development community and cell line repositories to design reference transcriptome samples, and then develop methods to integrate transcriptome sequencing data from short and long read technologies to form benchmark transcriptomes. Finally, to use these benchmark data, the postdoc could work with methods developers to develop appropriate performance metrics for other ‘omics and develop tools to use reference samples to give users these performance metrics, 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; Epigenetics; Transcriptomics; DNA methylation; Bioinformatics; Sequencing; Machine learning; Reference materials; Precision medicine; Data science; Artificial intelligence

Citizenship:  Open to U.S. citizens

Level:  Open to Postdoctoral applicants