REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

Dolzhenko, E.; Weisburd, B.; Ibanez, K.; Rajan Babu, I. S.; Bennett, M. F.; Billingsley, K. J.; Carroll, A.; Danzi, M. C.; Deshpande, V.; Ding, J.; Fazal, S.; Halman, A.; Jadhav, B.; Qiu, Y.; Richmond, P.; Scheffler, K.; van Vugt, J. J. F. A.; Zwamborn, R. R. A. J.; Genomics England Research Consortium,; Chong, S. S.; Friedman, J. M.; Tucci, A.; Rehm, H. L.; Eberle, M. A.

doi:10.1101/2021.10.20.465046

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bioRxiv · 10.1101/2021.10.20.465046

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

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Abstract

BackgroundExpansions 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. ResultsWe 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. ConclusionsRead 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.

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Dolzhenko, E., Weisburd, B., Ibanez, K., Rajan Babu, I. S., Bennett, M. F., Billingsley, K. J., Carroll, A., Danzi, M. C., Deshpande, V., Ding, J., Fazal, S., Halman, A., Jadhav, B., Qiu, Y., Richmond, P., Scheffler, K., van Vugt, J. J. F. A., Zwamborn, R. R. A. J., Genomics England Research Consortium,, Chong, S. S., Friedman, J. M., Tucci, A., Rehm, H. L., Eberle, M. A.. 2021-10-21. REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats. https://doi.org/10.1101/2021.10.20.465046

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