Leveraging the power of long reads for targeted sequencing

被引:2
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
美国国家卫生研究院; 美国国家科学基金会;
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
[1]   Targeted Long-Read Sequencing Decodes the Transcriptional Atlas of the Founding RAS Gene Family Members [J].
Adamopoulos, Panagiotis G. ;
Tsiakanikas, Panagiotis ;
Boti, Michaela A. ;
Scorilas, Andreas .
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (24)
[2]   The CRISPR tool kit for genome editing and beyond [J].
Adli, Mazhar .
NATURE COMMUNICATIONS, 2018, 9
[3]   A complete reference genome improves analysis of human genetic variation [J].
Aganezov, Sergey ;
Yan, Stephanie M. ;
Soto, Daniela C. ;
Kirsche, Melanie ;
Zarate, Samantha ;
Avdeyev, Pavel ;
Taylor, Dylan J. ;
Shafin, Kishwar ;
Shumate, Alaina ;
Xiao, Chunlin ;
Wagner, Justin ;
McDaniel, Jennifer ;
Olson, Nathan D. ;
Sauria, Michael E. G. ;
Vollger, Mitchell R. ;
Rhie, Arang ;
Meredith, Melissa ;
Martin, Skylar ;
Lee, Joyce ;
Koren, Sergey ;
Rosenfeld, Jeffrey A. ;
Paten, Benedict ;
Layer, Ryan ;
Chin, Chen-Shan ;
Sedlazeck, Fritz J. ;
Hansen, Nancy F. ;
Miller, Danny E. ;
Phillippy, Adam M. ;
Miga, Karen H. ;
McCoy, Rajiv C. ;
Dennis, Megan Y. ;
Zook, Justin M. ;
Schatz, Michael C. .
SCIENCE, 2022, 376 (6588) :54-+
[4]   Direct selection of human genomic loci by microarray hybridization [J].
Albert, Thomas J. ;
Molla, Michael N. ;
Muzny, Donna M. ;
Nazareth, Lynne ;
Wheeler, David ;
Song, Xingzhi ;
Richmond, Todd A. ;
Middle, Chris M. ;
Rodesch, Matthew J. ;
Packard, Charles J. ;
Weinstock, George M. ;
Gibbs, Richard A. .
NATURE METHODS, 2007, 4 (11) :903-905
[5]   Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles [J].
Albrecht, V. ;
Zweiniger, C. ;
Surendranath, V. ;
Lang, K. ;
Schoefl, G. ;
Dahl, A. ;
Winkler, S. ;
Lange, V. ;
Boehme, I. ;
Schmidt, A. H. .
HLA, 2017, 90 (02) :79-87
[6]   Characterization of full-length CNBP expanded alleles in myotonic dystrophy type 2 patients by Cas9-mediated enrichment and nanopore sequencing [J].
Alfano, Massimiliano ;
De Antoni, Luca ;
Centofanti, Federica ;
Visconti, Virginia Veronica ;
Maestri, Simone ;
Degli Esposti, Chiara ;
Massa, Roberto ;
D'Apice, Maria Rosaria ;
Novelli, Giuseppe ;
Delledonne, Massimo ;
Botta, Annalisa ;
Rossato, Marzia .
ELIFE, 2022, 11
[7]   Complete genomic and epigenetic maps of human centromeres [J].
Altemose, Nicolas ;
Logsdon, Glennis A. ;
Bzikadze, Andrey, V ;
Sidhwani, Pragya ;
Langley, Sasha A. ;
Caldas, Gina, V ;
Hoyt, Savannah J. ;
Uralsky, Lev ;
Ryabov, Fedor D. ;
Shew, Colin J. ;
Sauria, Michael E. G. ;
Borchers, Matthew ;
Gershman, Ariel ;
Mikheenko, Alla ;
Shepelev, Valery A. ;
Dvorkina, Tatiana ;
Kunyavskaya, Olga ;
Vollger, Mitchell R. ;
Rhie, Arang ;
McCartney, Ann M. ;
Asri, Mobin ;
Lorig-Roach, Ryan ;
Shafin, Kishwar ;
Lucas, Julian K. ;
Aganezov, Sergey ;
Olson, Daniel ;
de Lima, Leonardo Gomes ;
Potapova, Tamara ;
Hartley, Gabrielle A. ;
Haukness, Marina ;
Kerpedjiev, Peter ;
Gusev, Fedor ;
Tigyi, Kristof ;
Brooks, Shelise ;
Young, Alice ;
Nurk, Sergey ;
Koren, Sergey ;
Salama, Sofie R. ;
Paten, Benedict ;
Rogaev, Evgeny, I ;
Streets, Aaron ;
Karpen, Gary H. ;
Dernburg, Abby F. ;
Sullivan, Beth A. ;
Straight, Aaron F. ;
Wheeler, Travis J. ;
Gerton, Jennifer L. ;
Eichler, Evan E. ;
Phillippy, Adam M. ;
Timp, Winston .
SCIENCE, 2022, 376 (6588) :56-+
[8]   Enrichment of target sequences for next-generation sequencing applications in research and diagnostics [J].
Altmueller, Janine ;
Budde, Birgit S. ;
Nuernberg, Peter .
BIOLOGICAL CHEMISTRY, 2014, 395 (02) :231-237
[9]  
Ammar Ron, 2015, F1000Res, V4, P17, DOI 10.12688/f1000research.6037.2
[10]   Characterizing the Major Structural Variant Alleles of the Human Genome [J].
Audano, Peter A. ;
Sulovari, Arvis ;
Graves-Lindsay, Tina A. ;
Cantsilieris, Stuart ;
Sorensen, Melanie ;
Welch, AnneMarie E. ;
Dougherty, Max L. ;
Nelson, Bradley J. ;
Shah, Ankeeta ;
Dutcher, Susan K. ;
Warren, Wesley C. ;
Magrini, Vincent ;
McGrath, Sean D. ;
Li, Yang I. ;
Wilson, Richard K. ;
Eichler, Evan E. .
CELL, 2019, 176 (03) :663-+