Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

被引：528

作者：

Ardui, Simon ^{[1
]}

Ameur, Adam ^{[2
,3
]}

Vermeesch, Joris R. ^{[1
]}

Hestand, Matthew S. ^{[1
,4
,5
]}

机构：

[1] Katholieke Univ Leuven, Dept Human Genet, B-3000 Leuven, Belgium

[2] Uppsala Univ, Sci Life Lab, Dept Immunol Genet & Pathol, S-75108 Uppsala, Sweden

[3] Monash Univ, Sch Publ Hlth & Prevent Med, Melbourne, Vic, Australia

[4] Vrije Univ Amsterdam, Med Ctr, Dept Clin Genet, Amsterdam, Netherlands

[5] Cincinnati Childrens Hosp Med Ctr, Div Human Genet, Cincinnati, OH 45229 USA

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / 05期

关键词：

STRUCTURAL VARIATION; DNA METHYLATION; ERROR-CORRECTION; GENOME SEQUENCE; REPEAT; ALIGNMENT; INTERRUPTIONS; DISCOVERY; MOSAICISM; GENE;

D O I：

10.1093/nar/gky066

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：

Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule realtime (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.

引用

页码：2159 / 2168

页数：10

共 97 条

[1] 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

[2] Limitations of next-generation genome sequence assembly [J].

Alkan, Can ;

Sajjadian, Saba ;

Eichler, Evan E. .

NATURE METHODS, 2011, 8 (01) :61-65

[3] Detecting AGG Interruptions in Male and Female FMR1 Premutation Carriers by Single-Molecule Sequencing [J].

Ardui, Simon ;

Race, Valerie ;

Zablotskaya, Alena ;

Hestand, Matthew S. ;

Van Esch, Hilde ;

Devriendt, Koenraad ;

Matthijs, Gert ;

Vermeesch, Joris R. .

HUMAN MUTATION, 2017, 38 (03) :324-331

[4] Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing [J].

Bergfors, Assar ;

Leenheer, Daniel ;

Bergqvist, Anders ;

Ameur, Adam ;

Lennerstrand, Johan .

ANTIVIRAL RESEARCH, 2016, 126 :81-89

[5] The Epigenomic Landscape of Prokaryotes [J].

Blow, Matthew J. ;

Clark, Tyson A. ;

Daum, Chris G. ;

Deutschbauer, Adam M. ;

Fomenkov, Alexey ;

Fries, Roxanne ;

Froula, Jeff ;

Kang, Dongwan D. ;

Malmstrom, Rex R. ;

Morgan, Richard D. ;

Posfai, Janos ;

Singh, Kanwar ;

Visel, Axel ;

Wetmore, Kelly ;

Zhao, Zhiying ;

Rubin, Edward M. ;

Korlach, Jonas ;

Pennacchio, Len A. ;

Roberts, Richard J. .

PLOS GENETICS, 2016, 12 (02)

[6] Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing [J].

Borras, Daniel M. ;

Vossen, Rolf H. A. M. ;

Liem, Michael ;

Buermans, Henk P. J. ;

Dauwerse, Hans ;

van Heusden, Dave ;

Gansevoort, Ron T. ;

den Dunnen, Johan T. ;

Janssen, Bart ;

Peters, Dorien J. M. ;

Losekoot, Monique ;

Anvar, Seyed Yahya .

HUMAN MUTATION, 2017, 38 (07) :870-879

[7] Haplotype phasing: existing methods and new developments [J].

Browning, Sharon R. ;

Browning, Brian L. .

NATURE REVIEWS GENETICS, 2011, 12 (10) :703-714

[8] Flexible and Scalable Full-Length CYP2D6 Long Amplicon PacBio Sequencing [J].

Buermans, Henk P. J. ;

Vossen, Rolf H. A. M. ;

Anvar, Seyed Yahya ;

Allard, William G. ;

Guchelaar, Henk-Jan ;

White, Stefan J. ;

den Dunnen, Johan T. ;

Swen, Jesse J. ;

van der Straaten, Tahar .

HUMAN MUTATION, 2017, 38 (03) :310-316

[9] A method for near full-length amplification and sequencing for six hepatitis C virus genotypes [J].

Bull, Rowena A. ;

Eltahla, Auda A. ;

Rodrigo, Chaturaka ;

Koekkoek, Sylvie M. ;

Walker, Melanie ;

Pirozyan, Mehdi R. ;

Betz-Stablein, Brigid ;

Toepfer, Armin ;

Laird, Melissa ;

Oh, Steve ;

Heiner, Cheryl ;

Maher, Lisa ;

Schinkel, Janke ;

Lloyd, Andrew R. ;

Luciani, Fabio .

BMC GENOMICS, 2016, 17

[10] Pacific biosciences sequencing technology for genotyping and variation discovery in human data [J].

Carneiro, Mauricio O. ;

Russ, Carsten ;

Ross, Michael G. ;

Gabriel, Stacey B. ;

Nusbaum, Chad ;

DePristo, Mark A. .

BMC GENOMICS, 2012, 13

← 1 2 3 4 5 6 7 8 9 10 →