Evidence map›Paper›PMID 39567747›Full record

ArticleNature genetics2024

Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations.

Marc J Williams, Michael U J Oliphant, Vinci Au, Cathy Liu, Caroline Baril, Ciara O'Flanagan, Daniel Lai, Sean Beatty, Michael Van Vliet, Jacky Ch Yiu and 15 more

Abstract read
In one paragraph

Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

22 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Guideline
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  4. Article
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  6. Tissue-Specific Prevalence and Clonal Architecture ofbioRxiv : the preprint server for biology · 2026
    Article
  7. Review
  8. Article
  9. Review
  10. Article
  11. Review
  12. BMI and Breast Subcutaneous Fat: Potential Indicators for Ultrasound Diagnosis of Breast Cancer?Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine · 2026
    Article
  13. Article
  14. Article
  15. Review
  16. Article
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors.

Marc J Williams *Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.ORCID http://orcid.org/0000-0001-5524-4174
Michael U J Oliphant *Department of Cell Biology, Ludwig Center at Harvard, Harvard Medical School (HMS), Boston, MA, USA.
Vinci Au *Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0002-3587-6200
Cathy LiuDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Caroline BarilDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Ciara O'FlanaganDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Daniel LaiDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0001-9203-6323
Sean BeattyDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0001-6819-7071
Michael Van VlietDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Jacky Ch YiuDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0009-0007-4273-0051
Lauren O'ConnorDepartment of Cell Biology, Ludwig Center at Harvard, Harvard Medical School (HMS), Boston, MA, USA.
Walter L GohDepartment of Cell Biology, Ludwig Center at Harvard, Harvard Medical School (HMS), Boston, MA, USA.
Alicia PollaciDepartment of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA.
Adam C WeinerComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.ORCID http://orcid.org/0000-0002-5968-3606
Diljot GrewalComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
Andrew McPhersonComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
Klarisa NortonDepartment of Cell Biology, Ludwig Center at Harvard, Harvard Medical School (HMS), Boston, MA, USA.
McKenna MooreDepartment of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA.
Vikas PrabhakarDepartment of Pathology, Brigham and Women's Hospital (BWH), Boston, MA, USA.
Shailesh AgarwalDepartment of Surgery, Brigham and Women's Hospital (BWH), Boston, MA, USA.
Judy E GarberDepartment of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA.
Deborah A DillonDepartment of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA.
Sohrab P ShahComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA. shahs3@mskcc.org.ORCID http://orcid.org/0000-0001-6402-523X
Joan S BruggeDepartment of Cell Biology, Ludwig Center at Harvard, Harvard Medical School (HMS), Boston, MA, USA. joan_brugge@hms.harvard.edu.ORCID http://orcid.org/0000-0002-2547-4814
Samuel AparicioDepartment of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. saparicio@bccrc.ca.ORCID http://orcid.org/0000-0002-0487-9599

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Tissue and Pathology CoreP50CA168504 · NCI · DANA-FARBER CANCER INST · PI LEIF W ELLISEN, NANCY U LIN · 2013 to 2026
$30.1M
Center for Integrated Cellular Analysis - Valeria A. Sanchez EstradaRM1HG011014 · NHGRI · NEW YORK GENOME CENTER · PI LANDAU, DAN, SATIJA, RAHUL · 2020 to 2025
$22.1M
Targeting Polθ to Overcome PARP Inhibitor Resistance in Homologous Recombination Deficient Breast CancerP50CA247749 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI Sarat Chandarlapaty, Simon N. Powell · 2020 to 2026
$16.3M
Tracking the evolution of breast cancer through single cell analyses of premalignant breast tissues from women at high risk for cancer developmentR35CA242428 · NCI · HARVARD MEDICAL SCHOOL · PI BRUGGE, JOAN SIEFERT · 2019 to 2025
$7.1M
Single cell quantification of genomic instability in cancer as a determinant of therapeutic responseK99CA256508 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI WILLIAMS, MARC · 2021 to 2022
$200k
NCI NIH HHS K99 CA256508NCI NIH HHS P30 CA008748NCI NIH HHS P50 CA168504NCI NIH HHS P50 CA247749NCI NIH HHS R35 CA242428NHGRI NIH HHS RM1 HG011014
6 · The paper itself

Abstract

The prevalence and nature of somatic copy number alterations (CNAs) in breast epithelium and their role in tumor initiation and evolution remain poorly understood. Using single-cell DNA sequencing (49,238 cells) of epithelium from BRCA1 and BRCA2 carriers or wild-type individuals, we identified recurrent CNAs (for example, 1q-gain and 7q, 10q, 16q and 22q-loss) that are present in a rare population of cells across almost all samples (n = 28). In BRCA1/BRCA2 carriers, these occur before loss of heterozygosity (LOH) of wild-type alleles. These CNAs, common in malignant tumors, are enriched in luminal cells but absent in basal myoepithelial cells. Allele-specific analysis of prevalent CNAs reveals that they arose by independent mutational events, consistent with convergent evolution. BRCA1/BRCA2 carriers contained a small percentage of cells with extreme aneuploidy, featuring loss of TP53, BRCA1/BRCA2 LOH and multiple breast cancer-associated CNAs. Our findings suggest that CNAs arising in normal luminal breast epithelium are precursors to clonally expanded tumor genomes.

Indexed as

BRCA1 ProteinBRCA2 ProteinBreast NeoplasmsDNA Copy Number VariationsEpithelial CellsHeterozygoteLoss of HeterozygosityMutationBreastFemaleHumansSingle-Cell AnalysisBRCA1 ProteinBRCA1 protein, humanBRCA2 ProteinBRCA2 protein, human

Identifiers

PMID39567747
PMCPMC11631757

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.