Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

Xiao Dong; Lei Zhang; Brandon Milholland; Moonsook Lee; Alexander Y. Maslov; Tao Wang; Jan Vijg

doi:10.1038/nmeth.4227

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

Xiao Dong, Lei Zhang, Brandon Milholland, Moonsook Lee, Alexander Y. Maslov, Tao Wang, Jan Vijg

Research output: Contribution to journal › Article › peer-review

118 Scopus citations

Abstract

Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.

Original language	English (US)
Pages (from-to)	491-493
Number of pages	3
Journal	Nature Methods
Volume	14
Issue number	5
DOIs	https://doi.org/10.1038/nmeth.4227
State	Published - Apr 27 2017
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2017 Nature America, Inc. part of Springer Nature. All rights reserved.

Publisher link

10.1038/nmeth.4227

Find It

Find It at U of M Libraries

Cite this

@article{bd25aa96313041e68ace878b35a2ca5d,

title = "Accurate identification of single-nucleotide variants in whole-genome-amplified single cells",

abstract = "Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.",

author = "Xiao Dong and Lei Zhang and Brandon Milholland and Moonsook Lee and Maslov, {Alexander Y.} and Tao Wang and Jan Vijg",

year = "2017",

month = apr,

day = "27",

doi = "10.1038/nmeth.4227",

language = "English (US)",

volume = "14",

pages = "491--493",

journal = "Nature Methods",

issn = "1548-7091",

number = "5",

}

TY - JOUR

T1 - Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

AU - Dong, Xiao

AU - Zhang, Lei

AU - Milholland, Brandon

AU - Lee, Moonsook

AU - Maslov, Alexander Y.

AU - Wang, Tao

AU - Vijg, Jan

PY - 2017/4/27

Y1 - 2017/4/27

N2 - Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.

AB - Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.

UR - http://www.scopus.com/inward/record.url?scp=85015632028&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85015632028&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4227

DO - 10.1038/nmeth.4227

M3 - Article

C2 - 28319112

AN - SCOPUS:85015632028

SN - 1548-7091

VL - 14

SP - 491

EP - 493

JO - Nature Methods

JF - Nature Methods

IS - 5

ER -

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

Abstract

Bibliographical note

Publisher link

Find It

Other files and links

Fingerprint

Cite this