Analyzing repeat expansions in human genomes

Tandem repeats (TRs) have been implicated in more than 40 Mendelian diseases, such as Fragile X Syndrome and Huntington's Disease. While a variety of tools can now profile short TRs from next generation sequencing data, these approaches do not immediately expand to longer TRs that cannot be spanned by a single sequencing read. In this project, we will model properties of read alignments at long TRs in order to build a statistical framework to detect expanded repeats in the genome. We will also evaluate the ability of long read (e.g. Nanopore, PacBio) and synthetic long read technologies (e.g. 10X Genomics) to capture long repeats.