Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples.
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 and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes.
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Luciano G
LG
Martelotto
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.|Department of Molecular and Cellular Biology, Stony Brook University, New York, New York, USA.
Timour
T
Baslan
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Jude
J
Kendall
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Felipe C
FC
Geyer
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Kathleen A
KA
Burke
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Lee
L
Spraggon
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Salvatore
http://orcid.org/0000-0003-2686-2939
S
Piscuoglio
Molecular Cytogenetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Kalyani
K
Chadalavada
Molecular Cytogenetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Gouri
http://orcid.org/0000-0002-8547-1957
G
Nanjangud
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Charlotte K Y
CK
Ng
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Pamela
P
Moody
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Sean
S
D'Italia
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Linda
L
Rodgers
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Hilary
H
Cox
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.|Instituto Português de Oncologia, Porto, Portugal.
Arnaud
A
da Cruz Paula
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
Asya
A
Stepansky
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Michail
M
Schizas
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Hannah Y
HY
Wen
Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Tari A
TA
King
Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Larry
L
Norton
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Britta
B
Weigelt
Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.
James B
JB
Hicks
Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.
Jorge S
JS
Reis-Filho
D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000235:genetics* / Q000473:pathology; D002285:Carcinoma, Intraductal, Noninfiltrating / Q000235:genetics* / Q000473:pathology; D002467:Cell Nucleus; D056915:DNA Copy Number Variations / Q000235:genetics*; D018450:Disease Progression; D005260:Female; D005434:Flow Cytometry; D005557:Formaldehyde; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D061986:MCF-7 Cells; D018613:Microscopy, Confocal; D060885:Multiplex Polymerase Chain Reaction; D016612:Paraffin Embedding; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis; D016707:Tissue Fixation
D005557:Formaldehyde