M
Mark Kennedy
Researcher at Foundation Medicine
Publications - 17
Citations - 2972
Mark Kennedy is an academic researcher from Foundation Medicine. The author has contributed to research in topics: Cancer & Breast cancer. The author has an hindex of 9, co-authored 15 publications receiving 1887 citations.
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Journal ArticleDOI
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden
Zachary R. Chalmers,Caitlin F. Connelly,David Fabrizio,Siraj M. Ali,Riley Ennis,Alexa B. Schrock,Brittany Campbell,Adam Shlien,Juliann Chmielecki,Franklin W. Huang,Yuting He,James Sun,Uri Tabori,Mark Kennedy,Daniel S. Lieber,Steven Roels,Jared White,G. Otto,Jeffrey S. Ross,Levi A. Garraway,Levi A. Garraway,Vincent A. Miller,Phillip J. Stephens,Garrett M. Frampton +23 more
TL;DR: Measurements of TMB from comprehensive genomic profiling are strongly reflective of measurements from whole exome sequencing and model that below 0.5 Mb the variance in measurement increases significantly, demonstrating that many disease types have a substantial portion of patients with high TMB who might benefit from immunotherapy.
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Beyond microsatellite testing: assessment of tumor mutational burden identifies subsets of colorectal cancer who may respond to immune checkpoint inhibition.
David Fabrizio,Thomas J. George,Richard F. Dunne,Garrett M. Frampton,James Sun,Kyle Gowen,Mark Kennedy,Joel R. Greenbowe,Alexa B. Schrock,Aram F. Hezel,Jeffrey S. Ross,Jeffrey S. Ross,Phillip J. Stephens,Siraj M. Ali,Vincent A. Miller,Marwan Fakih,Samuel J. Klempner +16 more
TL;DR: Conurrent TMB assessment accurately classifies MSI tumors as TMB-high and simultaneously identifies nearly 3% or CRC as MSS/TMB- high, which may expand the population of CRC who may benefit from immune checkpoint inhibitor based therapeutic approaches.
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Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin.
Ryan Woodhouse,Meijuan Li,Jason D. Hughes,David Delfosse,Joel Skoletsky,Pei Ma,Wei Meng,Ninad Dewal,Coren Milbury,Travis A. Clark,Amy Donahue,Dan Stover,Mark Kennedy,Jennifer Dacpano-Komansky,Christine Burns,Christine Vietz,Brian M. Alexander,Priti Hegde,Lucas Dennis +18 more
TL;DR: These study results demonstrate that FoundationOne Liquid CDx accurately and reproducibly detects the major types of genomic alterations in addition to complex biomarkers such as microsatellite instability, blood tumor mutational burden, and tumor fraction.
Journal ArticleDOI
Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA
Travis A. Clark,Jon Chung,Mark Kennedy,Jason D. Hughes,Niru Chennagiri,Daniel S. Lieber,Bernard Fendler,Lauren Young,Mandy Zhao,Michael Coyne,Virginia Breese,Geneva Young,Amy Donahue,Dean Pavlick,Alyssa Tsiros,Tim Brennan,Shan Zhong,Tariq I Mughal,Mark Bailey,Jie He,Steven Roels,Garrett M. Frampton,Jill M. Spoerke,Steven Gendreau,Mark R. Lackner,Erica B. Schleifman,Eric Peters,Jeffrey S. Ross,Siraj M. Ali,Vincent A. Miller,Jeffrey P. Gregg,Philip J. Stephens,Allison Welsh,Geoff Otto,Doron Lipson +34 more
TL;DR: High-sequencing coverage and molecular barcode–based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications in FoundationACT.
Journal ArticleDOI
Individualized Molecular Analyses Guide Efforts (IMAGE): A prospective study of molecular profiling of tissue and blood in metastatic triple-negative breast cancer
Heather A. Parsons,Julia A. Beaver,Ashley Cimino-Mathews,Siraj M. Ali,Jennifer E. Axilbund,David Chu,Roisin M. Connolly,Rory L. Cochran,Sarah Croessmann,Travis A. Clark,Christopher D. Gocke,Stacie Jeter,Mark Kennedy,Josh Lauring,Justin Lee,Doron Lipson,Vincent A. Miller,Geoff Otto,Gary L. Rosner,Jeffrey S. Ross,Shannon Slater,Philip J. Stephens,Dustin A. VanDenBerg,Antonio C. Wolff,Lauren Young,Daniel J. Zabransky,Zhe Zhang,Jane Zorzi,Vered Stearns,Ben Ho Park +29 more
TL;DR: This study demonstrates challenges of performing NGS on prospective tissue biopsies in patients with metastatic TNBC within 28 days, while also highlighting the potential use of blood as a more time-efficient and less invasive method of mutational assessment.