Leveraging the power of long reads for targeted sequencing

被引:5
作者
Iyer, Shruti V. [1 ]
Goodwin, Sara [1 ]
Mccombie, William Richard [1 ]
机构
[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
ENRICHMENT; GENE; PCR; ENDONUCLEASE; SELECTION; VARIANTS; CLONING; CAPTURE;
D O I
10.1101/gr.279168.124
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1701 / 1718
页数:18
相关论文
共 139 条
[11]   Advances in clinical next-generation sequencing: target enrichment and sequencing technologies [J].
Ballester, Leomar Y. ;
Luthra, Rajyalakshmi ;
Kanagal-Shamanna, Rashmi ;
Singh, Rajesh R. .
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS, 2016, 16 (03) :357-372
[12]   CRISPR-mediated isolation of specific megabase segments of genomic DNA [J].
Bennett-Baker, Pamela E. ;
Mueller, Jacob L. .
NUCLEIC ACIDS RESEARCH, 2017, 45 (19)
[13]   Rapid Characterization of Complex Killer Cell Immunoglobulin-Like Receptor (KIR) Regions Using Cas9 Enrichment and Nanopore Sequencing [J].
Bruijnesteijn, Jesse ;
van der Wiel, Marit ;
de Groot, Natasja G. ;
Bontrop, Ronald E. .
FRONTIERS IN IMMUNOLOGY, 2021, 12
[14]   CRISPR-Cas9 Long-Read Sequencing for Mapping Transgenes in the Mouse Genome [J].
Bryant, W. Bart ;
Yang, Allison ;
Griffin, Susan H. ;
Zhang, Wei ;
Rafiq, Ashiq M. ;
Han, Weiping ;
Deak, Ferenc ;
Mills, Mary Katherine ;
Long, Xiaochun ;
Miano, Joseph M. .
CRISPR JOURNAL, 2023, 6 (02) :163-175
[15]   Automated assembly of centromeres from ultra-long error-prone reads [J].
Bzikadze, Andrey, V ;
Pevzner, Pavel A. .
NATURE BIOTECHNOLOGY, 2020, 38 (11) :1309-+
[16]   An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing [J].
Cao, Hongzhi ;
Wu, Jinghua ;
Wang, Yu ;
Jiang, Hui ;
Zhang, Tao ;
Liu, Xiao ;
Xu, Yinyin ;
Liang, Dequan ;
Gao, Peng ;
Sun, Yepeng ;
Gifford, Benjamin ;
D'Ascenzo, Mark ;
Liu, Xiaomin ;
Tellier, Laurent C. A. M. ;
Yang, Fang ;
Tong, Xin ;
Chen, Dan ;
Zheng, Jing ;
Li, Weiyang ;
Richmond, Todd ;
Xu, Xun ;
Wang, Jun ;
Li, Yingrui .
PLOS ONE, 2013, 8 (07)
[17]   PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus [J].
Charnaud, Sarah ;
Munro, Jacob E. ;
Semenec, Lucie ;
Mazhari, Ramin ;
Brewster, Jessica ;
Bourke, Caitlin ;
Ruybal-Pesantez, Shazia ;
James, Robert ;
Lautu-Gumal, Dulcie ;
Karunajeewa, Harin ;
Mueller, Ivo ;
Bahlo, Melanie .
COMMUNICATIONS BIOLOGY, 2022, 5 (01)
[18]   Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction [J].
Chiou, Chien-Shun ;
Chen, Bo-Han ;
Wang, You-Wun ;
Kuo, Nang-Ting ;
Chang, Chih-Hsiang ;
Huang, Yao-Ting .
COMMUNICATIONS BIOLOGY, 2023, 6 (01)
[19]   Approaches to Sequence the HTT CAG Repeat Expansion and Quantify Repeat Length Variation [J].
Ciosi, Marc ;
Cumming, Sarah A. ;
Chatzi, Afroditi ;
Larson, Eloise ;
Tottey, William ;
Lomeikaite, Vilija ;
Hamilton, Graham ;
Wheeler, Vanessa C. ;
Pinto, Ricardo Mouro ;
Kwak, Seung ;
Morton, A. Jennifer ;
Monckton, Darren G. .
JOURNAL OF HUNTINGTONS DISEASE, 2021, 10 (01) :53-74
[20]   Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks [J].
Clarke, Ryan ;
Heler, Robert ;
MacDougall, Matthew S. ;
Yeo, Nan Cher ;
Chavez, Alejandro ;
Regan, Maureen ;
Hanakahi, Leslyn ;
Church, George M. ;
Marraffini, Luciano A. ;
Merrill, Bradley J. .
MOLECULAR CELL, 2018, 71 (01) :42-+