Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

被引：124

作者：

Giesselmann, Pay ^{[1
]}

Braendl, Bjorn ^{[1
,2
]}

Raimondeau, Etienne ^{[3
]}

Bowen, Rebecca ^{[3
]}

Rohrandt, Christian ^{[4
]}

Tandon, Rashmi ^{[2
]}

Kretzmer, Helene ^{[1
]}

Assum, Gunter ^{[5
,6
]}

Galonska, Christina ^{[1
]}

Siebert, Reiner ^{[5
,6
]}

Ammerpohl, Ole ^{[5
,6
]}

Heron, Andrew ^{[3
]}

Schneider, Susanne A. ^{[7
]}

Ladewig, Julia ^{[8
,9
,10
,11
,12
]}

Koch, Philipp ^{[8
,9
,10
,11
,12
]}

Schuldt, Bernhard M. ^{[2
]}

Graham, James E. ^{[3
]}

Meissner, Alexander ^{[1
,13
]}

Mueller, Franz-Josef ^{[1
,2
]}

机构：

[1] Max Planck Inst Mol Genet, Dept Genome Regulat, Berlin, Germany

[2] Univ Klinikum Schleswig Holstein, Zentrum Integrat Psychiat gGmbH, Campus Kiel, Kiel, Germany

[3] Oxford Nanopore Technol, Oxford, England

[4] Kiel Univ Appl Sci, Inst Commun Technol & Embedded Syst, Kiel, Germany

[5] Ulm Univ, Inst Human Genet, Ulm, Germany

[6] Ulm Univ, Med Ctr, Ulm, Germany

[7] Ludwig Maximilians Univ Munchen, Dept Neurol, Munich, Germany

[8] Heidelberg Univ, Med Fac Mannheim, Cent Inst Mental Hlth, Mannheim, Germany

[9] HITBR Hector Inst Translat Brain Res gGmbH, Mannheim, Germany

[10] German Canc Res Ctr, Heidelberg, Germany

[11] Univ Bonn, Sch Med, Inst Reconstruct Neurobiol, Bonn, Germany

[12] Univ Hosp Bonn, Bonn, Germany

[13] Harvard Univ, Dept Stem Cell & Regenerat Biol, Cambridge, MA 02138 USA

来源：

NATURE BIOTECHNOLOGY | 2019年 / 37卷 / 12期

关键词：

HEXANUCLEOTIDE REPEAT; CPG ISLAND; WEB TOOL; C9ORF72; GENOME; REGION; ALS; HYPERMETHYLATION; CHOPCHOP;

D O I：

10.1038/s41587-019-0293-x

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：

Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods(1-4). Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism. We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification. Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.

引用

页码：1478 / +

页数：8

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