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Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients

Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autos...

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Autores principales: Nakamichi, Kenji, Van Gelder, Russell N., Chao, Jennifer R., Mustafi, Debarshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10219926/
https://www.ncbi.nlm.nih.gov/pubmed/37237007
http://dx.doi.org/10.1038/s41598-023-35791-4
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author Nakamichi, Kenji
Van Gelder, Russell N.
Chao, Jennifer R.
Mustafi, Debarshi
author_facet Nakamichi, Kenji
Van Gelder, Russell N.
Chao, Jennifer R.
Mustafi, Debarshi
author_sort Nakamichi, Kenji
collection PubMed
description Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autosomal recessive IRDs, one or no disease-causing variants are identified. Furthermore, chromosomal maps cannot be reconstructed for allelic variant discovery with short-reads. Long-read genome sequencing can provide complete coverage of disease loci and a targeted approach can focus sequencing bandwidth to a genomic region of interest to provide increased depth and haplotype reconstruction to uncover cases of missing heritability. We demonstrate that targeted adaptive long-read sequencing on the Oxford Nanopore Technologies (ONT) platform of the USH2A gene from three probands in a family with the most common cause of the syndromic IRD, Usher Syndrome, resulted in greater than 12-fold target gene sequencing enrichment on average. This focused depth of sequencing allowed for haplotype reconstruction and phased variant identification. We further show that variants obtained from the haplotype-aware genotyping pipeline can be heuristically ranked to focus on potential pathogenic candidates without a priori knowledge of the disease-causing variants. Moreover, consideration of the variants unique to targeted long-read sequencing that are not covered by short-read technology demonstrated higher precision and F1 scores for variant discovery by long-read sequencing. This work establishes that targeted adaptive long-read sequencing can generate targeted, chromosome-phased data sets for identification of coding and non-coding disease-causing alleles in IRDs and can be applicable to other Mendelian diseases.
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spelling pubmed-102199262023-05-28 Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients Nakamichi, Kenji Van Gelder, Russell N. Chao, Jennifer R. Mustafi, Debarshi Sci Rep Article Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autosomal recessive IRDs, one or no disease-causing variants are identified. Furthermore, chromosomal maps cannot be reconstructed for allelic variant discovery with short-reads. Long-read genome sequencing can provide complete coverage of disease loci and a targeted approach can focus sequencing bandwidth to a genomic region of interest to provide increased depth and haplotype reconstruction to uncover cases of missing heritability. We demonstrate that targeted adaptive long-read sequencing on the Oxford Nanopore Technologies (ONT) platform of the USH2A gene from three probands in a family with the most common cause of the syndromic IRD, Usher Syndrome, resulted in greater than 12-fold target gene sequencing enrichment on average. This focused depth of sequencing allowed for haplotype reconstruction and phased variant identification. We further show that variants obtained from the haplotype-aware genotyping pipeline can be heuristically ranked to focus on potential pathogenic candidates without a priori knowledge of the disease-causing variants. Moreover, consideration of the variants unique to targeted long-read sequencing that are not covered by short-read technology demonstrated higher precision and F1 scores for variant discovery by long-read sequencing. This work establishes that targeted adaptive long-read sequencing can generate targeted, chromosome-phased data sets for identification of coding and non-coding disease-causing alleles in IRDs and can be applicable to other Mendelian diseases. Nature Publishing Group UK 2023-05-26 /pmc/articles/PMC10219926/ /pubmed/37237007 http://dx.doi.org/10.1038/s41598-023-35791-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Nakamichi, Kenji
Van Gelder, Russell N.
Chao, Jennifer R.
Mustafi, Debarshi
Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title_full Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title_fullStr Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title_full_unstemmed Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title_short Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
title_sort targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10219926/
https://www.ncbi.nlm.nih.gov/pubmed/37237007
http://dx.doi.org/10.1038/s41598-023-35791-4
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