Evidence map›Paper›PMID 29163793›Full record

ArticleOncotarget2017

Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy.

Daniel H Hovelson, Chia-Jen Liu, Yugang Wang, Qing Kang, James Henderson, Amy Gursky, Scott Brockman, Nithya Ramnath, John C Krauss, Moshe Talpaz and 22 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.

0numbers the graph read from it
0cells of the map it votes in
33citing papers in PubMed
–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

33 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors.

Daniel H HovelsonMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Chia-Jen LiuMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Yugang WangDepartment of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
Qing KangDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
James HendersonDepartment of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
Amy GurskyDepartment of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
Scott BrockmanMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Nithya RamnathDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
John C KraussDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Moshe TalpazDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Malathi KandarpaDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Rashmi ChughDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Missy TuckDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Kirk HermanDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Catherine S GrassoDivision of Hematology-Oncology, University of California, Los Angeles and the Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
Michael J QuistDivision of Hematology-Oncology, University of California, Los Angeles and the Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
Felix Y FengDepartments of Radiation Oncology, Urology, and Medicine, University of California at San Francisco, San Francisco, CA, USA.
Christine HaakensonTakara Bio USA, Ann Arbor, MI, USA.
John LangmoreTakara Bio USA, Ann Arbor, MI, USA.
Emmanuel KamberovTakara Bio USA, Ann Arbor, MI, USA.
Tim TesmerTakara Bio USA, Ann Arbor, MI, USA.
Hatim HusainMedical Oncology, University of California, San Diego Moore's Cancer Center, San Diego, CA, USA.
Robert J LonigroMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Dan RobinsonMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
David C SmithDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Ajjai S AlvaDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Maha H HussainDepartment of Internal Medicine (Hematology/Oncology), University of Michigan Medical School, Ann Arbor, MI, USA.
Arul M ChinnaiyanMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Muneesh TewariDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
Ryan E MillsDepartment of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
Todd M MorganMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Scott A TomlinsMichigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.

Funding

XenograftP30CA046592 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI THEODORE S LAWRENCE · 1988 to 2026
$178.2M
Michigan Institute for Clinical and Health Research (MCHR)UL1TR000433 · NCATS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MASHOUR, GEORGE ALEXANDER · 2012 to 2016
$49.9M
RNA as a Hormone: Systemic Signaling in Mammals via Circulating, Cell-Free SmallR01DK085714 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI TEWARI, MUNEESH · 2009 to 2015
$4.0M
Exploiting drivers of androgen receptor signaling negative prostate cancer for prR01CA183857 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI TOMLINS, SCOTT A · 2014 to 2018
$1.6M
Discovery and analysis of structural variation in whole genome sequencesR01HG007068 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MILLS, RYAN E · 2013 to 2016
$1.5M
NCATS NIH HHS UL1 TR000433NCI NIH HHS P30 CA046592NCI NIH HHS R01 CA183857NHGRI NIH HHS R01 HG007068NIDDK NIH HHS R01 DK085714
6 · The paper itself

Abstract

Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation = 0.87), and PRINCe detectable

Indexed as

cell-free DNAcopy-number analysisprecision oncologyprostate cancerwhole genome sequencing

Identifiers

PMID29163793
PMCPMC5685714

What OpenQuestion holds

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Read underepoch 390

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.