RT Journal Article SR Electronic T1 REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.10.20.465046 DO 10.1101/2021.10.20.465046 A1 Egor Dolzhenko A1 Ben Weisburd A1 Kristina Ibanez Garikano A1 Indhu Shree Rajan Babu A1 Mark F Bennett A1 Kimberley Billingsley A1 Ashley Carroll A1 Matt C. Danzi A1 Viraj Deshpande A1 Jinhui Ding A1 Sarah Fazal A1 Andreas Halman A1 Bharati Jadhav A1 Yunjiang Qiu A1 Phillip Richmond A1 Konrad Scheffler A1 Joke J.F.A van Vugt A1 Ramona R.A.J. Zwamborn A1 Genomics England Research Consortium A1 Samuel S. Chong A1 Jan M. Friedman A1 Arianna Tucci A1 Heidi L. Rehm A1 Michael A Eberle YR 2021 UL http://biorxiv.org/content/early/2021/10/21/2021.10.20.465046.abstract AB Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely-recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads.Results We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in STR research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically-relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR.Conclusions Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions.Competing Interest StatementA subset of the authors are or were employees of Illumina, Inc., a public company that develops and markets systems for genetic analysis.REViewerRepeat expansion viewerSTRShort tandem repeatIn-repeat readRead fully contained in the repeat sequenceTP-PCRTriplet primed PCREHExpansionHunter