clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

被引：71

作者：

Campbell, Kieran R. ^{[1
,2
,3
]}

Steif, Adi ^{[1
,4
]}

Laks, Emma ^{[1
,4
]}

Zahn, Hans ^{[1
,7
]}

Lai, Daniel ^{[1
]}

McPherson, Andrew ^{[1
]}

Farahani, Hossein ^{[1
]}

Kabeer, Farhia ^{[1
]}

O'Flanagan, Ciara ^{[1
]}

Biele, Justina ^{[1
,6
]}

Brimhall, Jazmine ^{[1
,6
]}

Wang, Beixi ^{[1
,6
]}

Walters, Pascale ^{[1
]}

Bouchard-Cote, Alexandre ^{[2
]}

Aparicio, Samuel ^{[1
,6
]}

Shah, Sohrab P. ^{[1
,5
,6
]}

机构：

[1] British Columbia Canc Res Ctr, Dept Mol Oncol, Vancouver, BC, Canada

[2] Univ British Columbia, Dept Stat, Vancouver, BC, Canada

[3] Univ British Columbia, UBC Data Sci Inst, Vancouver, BC, Canada

[4] Univ British Columbia, Genome Sci & Technol Grad Program, Vancouver, BC, Canada

[5] Mem Sloan Kettering Canc Ctr, Dept Epidemiol & Biostat, Computat Oncol, New York, NY 10021 USA

[6] Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC, Canada

[7] Univ British Columbia, Michael Smith Labs, Vancouver, BC, Canada

[8] CRUK IMAXT Grand Challenge Consortium, Cambridge, England

来源：

GENOME BIOLOGY | 2019年 / 20卷 / 1期

基金：

加拿大健康研究院;

关键词：

COPY-NUMBER ALTERATION; MHC CLASS-I; GENOME; SEQ; EXPRESSION; INFERENCE; REVEALS;

D O I：

10.1186/s13059-019-1645-z

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：

Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association. We present clonealign, which assigns gene expression states to cancer clones using single-cell RNA and DNA sequencing independently sampled from a heterogeneous population. We apply clonealign to triple-negative breast cancer patient-derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either sequencing method alone.

引用

页数：12

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