Genetics and Genomics Program Seminar

Friday, October 7, 2016 - 4:10pm
Event Type: 

Yaniv Erlich, Ph.D., Columbia University
Professor of Computer Science
Member New York Genome Center.

Title: "The hitchhiker guide for genome hacking"

"Public sharing of sequencing datasets without identifiers has become a common practice in genomics to protect the privacy of research participants. We found that that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We further demonstrated that this information, together with other types of metadata, such as age and state, can be used to triangulate the identity of the target. We are interested in investigating strategies to protect genetic privacy while promoting data sharing."

Here is an abstract from a publication in Nature Genetics ( 48, 22–29 (2016) doi:10.1038/ng.3461 ) from the Erlich lab entitled: Abundant contribution of short tandem repeats to gene expression variation in humans by:

Abstract: The contribution of repetitive elements to quantitative human traits is largely unknown. Here we report a genome-wide survey of the contribution of short tandem repeats (STRs), which constitute one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from that of linked SNPs and indels and found that eSTRs contribute 10–15% of the cis heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, colocalize with regulatory elements and may modulate certain histone modifications. By analyzing known genome-wide association study (GWAS) signals and searching for new associations in 1,685 whole genomes from deeply phenotyped individuals, we found that eSTRs are enriched in various clinically relevant conditions. These results highlight the contribution of STRs to the genetic architecture of quantitative human traits.