Familial long-read sequencing increases yield of de novo mutations

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Item Type:	Article
Title:	Familial long-read sequencing increases yield of de novo mutations
Creators Name:	Noyes, M.D., Harvey, W.T., Porubsky, D., Sulovari, A., Li, R., Rose, N.R., Audano, P.A., Munson, K.M., Lewis, A.P., Hoekzema, K., Mantere, T., Graves-Lindsay, T.A., Sanders, A.D., Goodwin, S., Kramer, M., Mokrab, Y., Zody, M.C., Hoischen, A., Korbel, J.O., McCombie, W.R. and Eichler, E.E.
Abstract:	Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41 × 10(-8) substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by >25% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.
Keywords:	De Novo Mutation, Autism, Genome Sequencing, Long-Read Sequencing
Source:	American Journal of Human Genetics
ISSN:	0002-9297
Publisher:	Cell Press
Volume:	109
Number:	4
Page Range:	631-646
Date:	7 April 2022
Official Publication:	https://doi.org/10.1016/j.ajhg.2022.02.014
PubMed:	View item in PubMed

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