In " UKB-RAP Researcher Spotlight "
The Monthly Researcher Spotlight is our new section highlighting the exciting work of the UK Biobank Research Analysis Platform user community. If you would like to be featured, email firstname.lastname@example.org.
Po-Ru Loh, PhD
Harvard Medical School
What are the focus and discovery highlights of your research?
My research group broadly seeks to develop and apply efficient computational tools for exploring genetic effects on complex traits in population cohorts. Much of our work has focused on designing new statistical algorithms to extract hidden information about genetic variation from biobank data sets. My early work in statistical genetics centered around fast methods for genome-wide association analysis and haplotype phasing. More recently, my group has studied inherited and somatic genomic structural variants and their effects on human health.
What are some of the key questions that you are looking to answer using UK Biobank data?
We are currently focused on better understanding the phenotypic impact of structural variation on health and disease. Structural variants (SVs) -- i.e., variants that affect >50bp of sequence -- have long been suspected to contribute substantially to human trait heritability, but analyzing SVs at biobank scale has not previously been possible. The UK Biobank sequencing data provides a unique opportunity to characterize the effects of both common and rare SVs.
How has the UK Biobank Research Analysis Platform (UKB-RAP) helped you perform your research?
UKB-RAP has transformed the way we interact with UKB data and the types of questions we are able to ask, especially regarding sequencing data now available for hundreds of thousands of participants. UKB-RAP has made it possible for us to run a cohort-wide analysis of sequence data at a structural variant locus in ~1 hour for ~$1, in contrast to the weeks of download time previously required -- not to mention the ~$1 million per year that data storage would otherwise cost. Additionally, the high quality of documentation, tutorials, user support, and cost transparency on UKB-RAP have greatly eased our transition from HPC to cloud computing.
Any tools or tutorials that you have developed that would be useful for the UKB-RAP community?
My group recently developed a software package for CNV-calling from large-scale SNP-array data (HI-CNV), and I continue to maintain the BOLT-LMM and Eagle software packages for association analysis and haplotype-phasing.