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