Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

被引：36

作者：

Chiu, Readman ^{[1
]}

Rajan-Babu, Indhu-Shree ^{[2
,3
,4
]}

Friedman, Jan M. ^{[2
,3
]}

Birol, Inanc ^{[1
,2
]}

机构：

[1] BC Canc, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada

[2] Univ British Columbia, Dept Med Genet, Vancouver, BC V6T 1Z3, Canada

[3] BC Childrens Hosp Res Inst, Vancouver, BC V5Z 4H4, Canada

[4] Kings Coll London, Dept Med & Mol Genet, London WC2R 2LS, England

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

基金：

加拿大健康研究院;

关键词：

D O I：

10.1186/s13059-021-02447-3

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.

引用

页数：20

共 49 条

[31]

Paulson Henry, 2018, Handb Clin Neurol, V147, P105, DOI 10.1016/B978-0-444-63233-3.00009-9

[32] Repeat Interruptions Modify Age at Onset in Myotonic Dystrophy Type 1 by Stabilizing DMPK Expansions in Somatic Cells [J].

Pesovic, Jovan ;

Peric, Stojan ;

Brkusanin, Milos ;

Brajuskovic, Goran ;

Rakocevic-Stojanovic, Vidosava ;

Savic-Pavicevic, Dusanka .

FRONTIERS IN GENETICS, 2018, 9 :1-14

[33] Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions [J].

Rajan-Babu, Indhu-Shree ;

Pen, Junran J. ;

Chiu, Readman ;

Li, Chenkai ;

Mohajeri, Arezoo ;

Dolzhenko, Egor ;

Eberle, Michael A. ;

Birol, Inanc ;

Friedman, Jan M. .

GENOME MEDICINE, 2021, 13 (01)

[34] FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome [J].

Rajan-Babu, Indhu-Shree ;

Lian, Mulias ;

Cheah, Felicia S. H. ;

Chen, Min ;

Tan, Arnold S. C. ;

Prasath, Ethiraj B. ;

Loh, Seong Feei ;

Chong, Samuel S. .

EXPERT REVIEWS IN MOLECULAR MEDICINE, 2017, 19

[35] Tandem repeat disorders [J].

Ryan, Calen P. .

EVOLUTION MEDICINE AND PUBLIC HEALTH, 2019, (01) :17-17

[36] Haplotype threading: accurate polyploid phasing from long reads [J].

Schrinner, Sven D. ;

Mari, Rebecca Serra ;

Ebler, Jana ;

Rautiainen, Mikko ;

Seillier, Lancelot ;

Reimer, Julia J. ;

Usadel, Bjoern ;

Marschall, Tobias ;

Klau, Gunnar W. .

GENOME BIOLOGY, 2020, 21 (01)

[37] Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes [J].

Shafin, Kishwar ;

Pesout, Trevor ;

Lorig-Roach, Ryan ;

Haukness, Marina ;

Olsen, Hugh E. ;

Bosworth, Colleen ;

Armstrong, Joel ;

Tigyi, Kristof ;

Maurer, Nicholas ;

Koren, Sergey ;

Sedlazeck, Fritz J. ;

Marschall, Tobias ;

Mayes, Simon ;

Costa, Vania ;

Zook, Justin M. ;

Liu, Kelvin J. ;

Kilburn, Duncan ;

Sorensen, Melanie ;

Munson, Katy M. ;

Vollger, Mitchell R. ;

Monlong, Jean ;

Garrison, Erik ;

Eichler, Evan E. ;

Salama, Sofie ;

Haussler, David ;

Green, Richard E. ;

Akeson, Mark ;

Phillippy, Adam ;

Miga, Karen H. ;

Carnevali, Paolo ;

Jain, Miten ;

Paten, Benedict .

NATURE BIOTECHNOLOGY, 2020, 38 (09) :1044-+

[38] Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease [J].

Sone, Jun ;

Mitsuhashi, Satomi ;

Fujita, Atsushi ;

Mizuguchi, Takeshi ;

Hamanaka, Kohei ;

Mori, Keiko ;

Koike, Haruki ;

Hashiguchi, Akihiro ;

Takashima, Hiroshi ;

Sugiyama, Hiroshi ;

Kohno, Yutaka ;

Takiyama, Yoshihisa ;

Maeda, Kengo ;

Doi, Hiroshi ;

Koyano, Shigeru ;

Takeuchi, Hideyuki ;

Kawamoto, Michi ;

Kohara, Nobuo ;

Ando, Tetsuo ;

Ieda, Toshiaki ;

Kita, Yasushi ;

Kokubun, Norito ;

Tsuboi, Yoshio ;

Katoh, Kazutaka ;

Kino, Yoshihiro ;

Katsuno, Masahisa ;

Iwasaki, Yasushi ;

Yoshida, Mari ;

Tanaka, Fumiaki ;

Suzuki, Ikuo K. ;

Frith, Martin C. ;

Matsumoto, Naomichi ;

Sobue, Gen .

NATURE GENETICS, 2019, 51 (08) :1215-+

[39] Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data [J].

Tankard, Rick M. ;

Bennett, Mark E. ;

Degorski, Peter ;

Delatycki, Martin B. ;

Lockhart, Paul J. ;

Bahlo, Melanie .

AMERICAN JOURNAL OF HUMAN GENETICS, 2018, 103 (06) :858-873

[40] PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome [J].

Teng, Jade L. L. ;

Yeung, Man Lung ;

Chan, Elaine ;

Jia, Lilong ;

Lin, Chi Ho ;

Huang, Yi ;

Tse, Herman ;

Wong, Samson S. Y. ;

Sham, Pak Chung ;

Lau, Susanna K. P. ;

Woo, Patrick C. Y. .

FRONTIERS IN MICROBIOLOGY, 2017, 8

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