ArticleNature communications2017
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
2 registry-linked trialsOpen access · goldAbstract read
In one paragraph
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 2 registered trials, which are not on this map. Cited by 679 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
679citing papers in PubMed, 1 pooled it
21.1field-weighted citation impact, top 1% of its field
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.
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.
Phase II Trial of CAPOX, Bevacizumab and Trastuzumab for Patients With HER2-Positive Metastatic Esophagogastric Cancer
Treatment Response and microRNA Profiles in Triple Negative Breast Cancer Patients Receiving Standard Chemotherapy
Who cites it
679 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,062 citations in OpenAlex.
- Circulating Tumor DNA and Circulating Tumor Cells in Liquid Biopsy as Post-Treatment Prognostic Biomarkers in Early Breast Cancer: A Systematic Review and Meta-Analysis.International journal of molecular sciences · 2026Pooled it
- A Phase II Study of Berzosertib in Combination with Carboplatin Compared with Docetaxel with Carboplatin in Metastatic Castration-Resistant Prostate Cancer.Cancer research communications · 2026Trial
- Genome-wide variation in cell-free DNA end-motif entropy predicts immunotherapy response in head and neck cancer.The Journal of clinical investigation · 2026Trial
- Evolution of AR and Non-AR Alterations in ctDNA of Patients with Metastatic Prostate Cancer Treated in the Phase III Alliance A031201 Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Trial
- Tumor-derived cell-free DNA detected in cerebrospinal fluid enables minimally invasive profiling of pediatric brain tumors.The Journal of clinical investigation · 2026Trial
- CfDNA-based copy-number dynamics during anti-PD1 treatment in metastatic triple negative breast cancer.Cell reports. Medicine · 2025Trial
- Cell-free DNA as a complementary marker of therapeutic futility in adenoid cystic carcinoma.Oral oncology · 2025Trial
- Olaparib as a rescue treatment in platinum-refractory germ-cell tumors: the IGG-02 phase II trial.ESMO open · 2025Trial
- Prognostic utility of copy number variations in circulating tumor DNA in head and neck cancer.The journal of liquid biopsy · 2026Article
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Early experience with cerebrospinal fluid cell-free DNA molecular profiling in a neuro-oncology practice.Journal of neuro-oncology · 2026Article
- Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring.Blood advances · 2026Review
- Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Article
- Epigenetic Liquid Biopsy Enables Universal Mutation-Agnostic Molecular Surveillance for High-Risk Neuroblastoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Cell-free DNA genomic and fragmentomic features for early outcome prediction in large B cell lymphoma.Cell reports. Medicine · 2026Article
- Role of ctDNA Tumor Fraction in Selecting Immunotherapy-Based Regimens in Advanced Non-Small Cell Lung Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- A cfDNA fragmentomics classifier for noninvasive differentiation of benign and malignant renal masses.Molecular biomedicine · 2026Article
- CDK4/6 Inhibitors in Breast Cancer Therapy: Mechanisms, Resistance, and Emerging Opportunities.Targeted oncology · 2026Review
- Current Evidence for Circulating Tumor DNA in Sarcoma: Challenges and Opportunities for Clinical Application.Journal of surgical oncology · 2026Review
619 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
57 authors at 5 institutions in 1 country.
Viktor A AdalsteinssonEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA. viktor@broadinstitute.org.
Gavin HaEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Samuel S FreemanEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Atish D ChoudhuryDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Daniel G StoverDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.ORCID http://orcid.org/0000-0001-9003-8165
Heather A ParsonsDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Gregory GydushEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Sarah C ReedEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Denisse RotemEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Justin RhoadesEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Denis LoginovEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Dimitri LivitzEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0003-2528-1446
Daniel RosebrockEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Ignaty LeshchinerEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0001-8942-9265
Jaegil KimEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Chip StewartEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Mara RosenbergEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Joshua M FrancisEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Cheng-Zhong ZhangEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Ofir CohenEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Coyin OhEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0002-5732-3471
Huiming DingKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, 02142, MA, USA.
Paz PolakEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0002-2153-4488
Max LloydDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Sairah MahmudDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Karla HelvieDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Margaret S MerrillDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Rebecca A SantiagoDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Edward P O'ConnorDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Seong H JeongDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Rachel LeesonKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, 02142, MA, USA.
Rachel M BarryKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, 02142, MA, USA.
Joseph F KramkowskiDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Zhenwei ZhangDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Laura PolacekDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Jens G LohrEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Molly SchleicherEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Emily LipscombEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Andrea SaltzmanEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Nelly M OliverDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Lori MariniDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Adrienne G WaksDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Lauren C HarshmanDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Sara M TolaneyDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Eliezer M Van AllenEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Eric P WinerDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Nancy U LinDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Mari NakabayashiDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Mary-Ellen TaplinDana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, MA, USA.
Cory M JohannessenEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Levi A GarrawayEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Todd R GolubEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0003-0113-2403
Jesse S BoehmEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.ORCID http://orcid.org/0000-0002-6795-6336
Nikhil WagleEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.
Gad GetzEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA. gadgetz@broadinstitute.org.ORCID http://orcid.org/0000-0002-0936-0753
J Christopher LoveEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA. clove@mit.edu.
Matthew MeyersonEli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA. matthew_meyerson@dfci.harvard.edu.ORCID http://orcid.org/0000-0002-9133-8108
Broad Institute · USDana-Farber Cancer Institute · USHarvard University · USMassachusetts Institute of Technology · USBrigham and Women's Hospital · US
Funding
VIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Jacqueline A. Lees · 1985 to 2026
$93.9MDetermining the mutational landscape of circulating multiple myeloma cellsK08CA191026 · NCI · DANA-FARBER CANCER INST · PI LOHR, JENS G · 2015 to 2019
$886kCIHR MFE-140389NCI NIH HHS K08 CA191026NCI NIH HHS P30 CA014051
Abstract
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.
Indexed as
Antigens, NeoplasmBreast NeoplasmsCell-Free Nucleic AcidsDNA Mutational AnalysisDNA, NeoplasmExome SequencingFemaleGene DosageHumansMaleNeoplasm MetastasisProspective StudiesProstatic NeoplasmsSoftwareAntigens, NeoplasmCell-Free Nucleic AcidsDNA, Neoplasm
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
NCT01191697ClinicalTrials.gov
NCT04771871ClinicalTrials.gov
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.