publication . Article . 2017

Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

Pamela Moody; Timour Baslan; Timour Baslan; Timour Baslan; Lee Spraggon; Larry Norton; Linda Rodgers; Felipe C. Geyer; Arnaud Da Cruz Paula; Arnaud Da Cruz Paula; ...
Open Access English
  • Published: 01 Feb 2017 Journal: Nature medicine, volume 23, issue 3, pages 376-385 (issn: 1078-8956, eissn: 1546-170X, Copyright policy)
Abstract
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust an...
Subjects
free text keywords: Article, General Biochemistry, Genetics and Molecular Biology, General Medicine, Tumour heterogeneity, Genome, Genomics, Cancer cell, Computational biology, Breast cancer, medicine.disease, medicine, Genetic heterogeneity, Genetic variation, Whole genome sequencing, Pathology, medicine.medical_specialty, Biology
Funded by
NIH| CSHL CANCER CENTER SUPPORT GRANT
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA045508-08S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| MOUSE GENETICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2P30CA008748-43
  • Funding stream: NATIONAL CANCER INSTITUTE
48 references, page 1 of 4

Gerlinger, M. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012; 366: 883-892 [OpenAIRE] [PubMed]

Navin, N. Tumour evolution inferred by single-cell sequencing. Nature. 2011; 472: 90-94 [OpenAIRE] [PubMed]

Aparicio, S, Caldas, C. The implications of clonal genome evolution for cancer medicine. N Engl J Med. 2013; 368: 842-851 [PubMed]

Ng, CK. Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification. Genome Biol. 2015; 16: 107 [OpenAIRE] [PubMed]

Hernandez, L. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. J Pathol. 2012; 227: 42-52 [OpenAIRE] [PubMed]

de Bruin, EC. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014; 346: 251-256 [OpenAIRE] [PubMed]

Yates, LR. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015; 21: 751-759 [OpenAIRE] [PubMed]

Ng, CK, Schultheis, AM, Bidard, FC, Weigelt, B, Reis-Filho, JS. Breast cancer genomics from microarrays to massively parallel sequencing: paradigms and new insights. J Natl Cancer Inst. 2015; 107 [OpenAIRE]

Ding, L. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012; 481: 506-510 [OpenAIRE] [PubMed]

Nik-Zainal, S. The life history of 21 breast cancers. Cell. 2012; 149: 994-1007 [OpenAIRE] [PubMed]

Carter, SL. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012; 30: 413-421 [OpenAIRE] [PubMed]

Roth, A. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014; 11: 396-398 [OpenAIRE] [PubMed]

Wang, Y. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014; 512: 155-160 [OpenAIRE] [PubMed]

Baslan, T. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res. 2015; 25: 714-724 [OpenAIRE] [PubMed]

Baslan, T. Genome-wide copy number analysis of single cells. Nat Protoc. 2012; 7: 1024-1041 [OpenAIRE] [PubMed]

48 references, page 1 of 4
Abstract
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust an...
Subjects
free text keywords: Article, General Biochemistry, Genetics and Molecular Biology, General Medicine, Tumour heterogeneity, Genome, Genomics, Cancer cell, Computational biology, Breast cancer, medicine.disease, medicine, Genetic heterogeneity, Genetic variation, Whole genome sequencing, Pathology, medicine.medical_specialty, Biology
Funded by
NIH| CSHL CANCER CENTER SUPPORT GRANT
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA045508-08S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| MOUSE GENETICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2P30CA008748-43
  • Funding stream: NATIONAL CANCER INSTITUTE
48 references, page 1 of 4

Gerlinger, M. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012; 366: 883-892 [OpenAIRE] [PubMed]

Navin, N. Tumour evolution inferred by single-cell sequencing. Nature. 2011; 472: 90-94 [OpenAIRE] [PubMed]

Aparicio, S, Caldas, C. The implications of clonal genome evolution for cancer medicine. N Engl J Med. 2013; 368: 842-851 [PubMed]

Ng, CK. Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification. Genome Biol. 2015; 16: 107 [OpenAIRE] [PubMed]

Hernandez, L. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. J Pathol. 2012; 227: 42-52 [OpenAIRE] [PubMed]

de Bruin, EC. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014; 346: 251-256 [OpenAIRE] [PubMed]

Yates, LR. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015; 21: 751-759 [OpenAIRE] [PubMed]

Ng, CK, Schultheis, AM, Bidard, FC, Weigelt, B, Reis-Filho, JS. Breast cancer genomics from microarrays to massively parallel sequencing: paradigms and new insights. J Natl Cancer Inst. 2015; 107 [OpenAIRE]

Ding, L. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012; 481: 506-510 [OpenAIRE] [PubMed]

Nik-Zainal, S. The life history of 21 breast cancers. Cell. 2012; 149: 994-1007 [OpenAIRE] [PubMed]

Carter, SL. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012; 30: 413-421 [OpenAIRE] [PubMed]

Roth, A. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014; 11: 396-398 [OpenAIRE] [PubMed]

Wang, Y. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014; 512: 155-160 [OpenAIRE] [PubMed]

Baslan, T. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res. 2015; 25: 714-724 [OpenAIRE] [PubMed]

Baslan, T. Genome-wide copy number analysis of single cells. Nat Protoc. 2012; 7: 1024-1041 [OpenAIRE] [PubMed]

48 references, page 1 of 4
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