Sequencing thousands of single-cell genomes with combinatorial indexing

Sarah A. Vitak, Kristof A. Torkenczy, Jimi L. Rosenkrantz, Andrew J. Fields, Lena Christiansen, Melissa Wong, Lucia Carbone, Frank J. Steemers, Andrew Adey

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

Single-cell genome sequencing has proven valuable for the detection of somatic variation, particularly in the context of tumor evolution. Current technologies suffer from high library construction costs, which restrict the number of cells that can be assessed and thus impose limitations on the ability to measure heterogeneity within a tissue. Here, we present single-cell combinatorial indexed sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single-cell libraries for detection of somatic copy-number variants. We constructed libraries for 16,698 single cells from a combination of cultured cell lines, primate frontal cortex tissue and two human adenocarcinomas, and obtained a detailed assessment of subclonal variation within a pancreatic tumor.

Original languageEnglish (US)
Pages (from-to)302-308
Number of pages7
JournalNature Methods
Volume14
Issue number3
DOIs
StatePublished - Feb 28 2017

Fingerprint

Genes
Genome
Tumors
Tissue
Libraries
Frontal Lobe
Cells
Primates
Cultured Cells
Neoplasms
Adenocarcinoma
Cell Count
Technology
Costs and Cost Analysis
Cell Line
Costs

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Vitak, S. A., Torkenczy, K. A., Rosenkrantz, J. L., Fields, A. J., Christiansen, L., Wong, M., ... Adey, A. (2017). Sequencing thousands of single-cell genomes with combinatorial indexing. Nature Methods, 14(3), 302-308. https://doi.org/10.1038/nmeth.4154

Sequencing thousands of single-cell genomes with combinatorial indexing. / Vitak, Sarah A.; Torkenczy, Kristof A.; Rosenkrantz, Jimi L.; Fields, Andrew J.; Christiansen, Lena; Wong, Melissa; Carbone, Lucia; Steemers, Frank J.; Adey, Andrew.

In: Nature Methods, Vol. 14, No. 3, 28.02.2017, p. 302-308.

Research output: Contribution to journalArticle

Vitak, SA, Torkenczy, KA, Rosenkrantz, JL, Fields, AJ, Christiansen, L, Wong, M, Carbone, L, Steemers, FJ & Adey, A 2017, 'Sequencing thousands of single-cell genomes with combinatorial indexing', Nature Methods, vol. 14, no. 3, pp. 302-308. https://doi.org/10.1038/nmeth.4154
Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong M et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nature Methods. 2017 Feb 28;14(3):302-308. https://doi.org/10.1038/nmeth.4154
Vitak, Sarah A. ; Torkenczy, Kristof A. ; Rosenkrantz, Jimi L. ; Fields, Andrew J. ; Christiansen, Lena ; Wong, Melissa ; Carbone, Lucia ; Steemers, Frank J. ; Adey, Andrew. / Sequencing thousands of single-cell genomes with combinatorial indexing. In: Nature Methods. 2017 ; Vol. 14, No. 3. pp. 302-308.
@article{794fbc0b09fe4fefae902b93cae7c954,
title = "Sequencing thousands of single-cell genomes with combinatorial indexing",
abstract = "Single-cell genome sequencing has proven valuable for the detection of somatic variation, particularly in the context of tumor evolution. Current technologies suffer from high library construction costs, which restrict the number of cells that can be assessed and thus impose limitations on the ability to measure heterogeneity within a tissue. Here, we present single-cell combinatorial indexed sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single-cell libraries for detection of somatic copy-number variants. We constructed libraries for 16,698 single cells from a combination of cultured cell lines, primate frontal cortex tissue and two human adenocarcinomas, and obtained a detailed assessment of subclonal variation within a pancreatic tumor.",
author = "Vitak, {Sarah A.} and Torkenczy, {Kristof A.} and Rosenkrantz, {Jimi L.} and Fields, {Andrew J.} and Lena Christiansen and Melissa Wong and Lucia Carbone and Steemers, {Frank J.} and Andrew Adey",
year = "2017",
month = "2",
day = "28",
doi = "10.1038/nmeth.4154",
language = "English (US)",
volume = "14",
pages = "302--308",
journal = "Nature Methods",
issn = "1548-7091",
publisher = "Public Library of Science",
number = "3",

}

TY - JOUR

T1 - Sequencing thousands of single-cell genomes with combinatorial indexing

AU - Vitak, Sarah A.

AU - Torkenczy, Kristof A.

AU - Rosenkrantz, Jimi L.

AU - Fields, Andrew J.

AU - Christiansen, Lena

AU - Wong, Melissa

AU - Carbone, Lucia

AU - Steemers, Frank J.

AU - Adey, Andrew

PY - 2017/2/28

Y1 - 2017/2/28

N2 - Single-cell genome sequencing has proven valuable for the detection of somatic variation, particularly in the context of tumor evolution. Current technologies suffer from high library construction costs, which restrict the number of cells that can be assessed and thus impose limitations on the ability to measure heterogeneity within a tissue. Here, we present single-cell combinatorial indexed sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single-cell libraries for detection of somatic copy-number variants. We constructed libraries for 16,698 single cells from a combination of cultured cell lines, primate frontal cortex tissue and two human adenocarcinomas, and obtained a detailed assessment of subclonal variation within a pancreatic tumor.

AB - Single-cell genome sequencing has proven valuable for the detection of somatic variation, particularly in the context of tumor evolution. Current technologies suffer from high library construction costs, which restrict the number of cells that can be assessed and thus impose limitations on the ability to measure heterogeneity within a tissue. Here, we present single-cell combinatorial indexed sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single-cell libraries for detection of somatic copy-number variants. We constructed libraries for 16,698 single cells from a combination of cultured cell lines, primate frontal cortex tissue and two human adenocarcinomas, and obtained a detailed assessment of subclonal variation within a pancreatic tumor.

UR - http://www.scopus.com/inward/record.url?scp=85010982914&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85010982914&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4154

DO - 10.1038/nmeth.4154

M3 - Article

VL - 14

SP - 302

EP - 308

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 3

ER -