Leveraging the power of long reads for targeted sequencing

Iyer, Shruti V, Goodwin, Sara, McCombie, William Richard (November 2024) Leveraging the power of long reads for targeted sequencing. Genome Research, 34 (11). pp. 1701-1718. ISSN 1088-9051

PDF 10.1101.gr.279168.124.pdf - Published Version Available under License Creative Commons Attribution. Download (4MB)

Abstract

Long-read sequencing technologies have improved the contiguity and, as a result, the quality of genome assemblies by generating reads long enough to span and resolve complex or repetitive regions of the genome. Several groups have shown the power of long reads in detecting thousands of genomic and epigenomic features that were previously missed by short-read sequencing approaches. While these studies demonstrate how long reads can help resolve repetitive and complex regions of the genome, they also highlight the throughput and coverage requirements needed to accurately resolve variant alleles across large populations using these platforms. At the time of this review, whole-genome long-read sequencing is more expensive than short-read sequencing on the highest throughput short-read instruments; thus, achieving sufficient coverage to detect low-frequency variants (such as somatic variation) in heterogenous samples remains challenging. Targeted sequencing, on the other hand, provides the depth necessary to detect these low-frequency variants in heterogeneous populations. Here, we review currently used and recently developed targeted sequencing strategies that leverage existing long-read technologies to increase the resolution with which we can look at nucleic acids in a variety of biological contexts.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics organism description > animal organism description > animal > mammal > primates > hominids organism description > animal > mammal > primates > hominids > human organism description > animal > mammal organism description > animal > mammal > primates
CSHL Authors:	Iyer, Shruti Goodwin, Sara McCombie, W. Richard
Communities:	CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL labs > McCombie lab CSHL labs > Goodwin lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	20 November 2024
Date Deposited:	22 Nov 2024 20:04
Last Modified:	22 Nov 2024 20:04
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41738

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