HMMSTR: A Modified Profile-HMM for Tandem Repeat Copy Number Determination in Nanopore Sequence Reads

• Known tandem repeats (TRs) make up ~3% of the human genome

• Cause over 50 human diseases

Short-read sequencing methods fail to accurately characterize TRs

• Oxford Nanopore Technologies (ONT) produce reads up to 2Mb • ONT is compatible with multiple targeted enrichment techniques

• Accurate TR copy number determination is critical for understanding TR expansion pathogenesis and diagnostics

We propose a targeted technique for TR copy number determination that combines Cas9-targeted Nanopore sequencing with a modified profile-HMM based counting algorithm

Download the PDF