Memorial Hospital Research Laboratories

The Michael Berger Lab

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Research

Michael Berger, PhD
Michael F. Berger, PhD
Co-Director, Marie-Josée & Henry R. Kravis Center for Molecular Oncology; Chief Attending, Clinical Computational Diagnostics Service, Department of Pathology and Laboratory Medicine

The focus of the Berger laboratory is to use novel computational and experimental techniques to characterize the spectrum of genetic mutations in human tumors in order to identify biomarkers of cancer progression and drug response.

The identification of molecular drivers of cancer and the development of targeted therapies for these drivers offer hope for better outcomes for patients with cancer. Global efforts to comprehensively characterize the genomes of all major cancer types continue to reveal new genetic alterations with implications for tumor biology, prognosis, and treatment. Using massively parallel next-generation DNA sequencing, we are developing and applying methods of profiling individual tumor specimenspatient biospecimens for somatic base mutations and other genomicand inherited alterations that may influence response to therapy. Our research falls into two main categories: technology development and biomarker discovery.

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Researchers in the Berger laboratory

Featured News

In the Lab
Geneticist Michael Berger
How Do Inherited Gene Mutations Cause Cancer? A New Database Will Help Researchers Find Out
In a new paper, a collaborative team of MSK experts reports how a novel tool will help researchers learn more about the role of inherited hereditary mutations.
Feature
Group photo of researchers Michael Berger, Marc Ladanyi, Dana Tsui, Rose Brannon, Ryma Benayed, Ahmet Zehir, and David Klimstra.
How MSK-ACCESS Blood Test for Cancer was Created
MSK-ACCESS, a blood test that can detect mutations in 129 genes related to cancer, has already helped guide the treatment of more than 2,800 patients at MSK.
Finding
Illustration of a magnifying glass and DNA sequences
Machine Learning May Help Classify Cancers of Unknown Primary
MSK investigators report a new tool that may help them determine the origin of some metastatic tumors, potentially leading to better targeted treatments.

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Publications Highlights

Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort. Arora K, Tran TN, Kemel Y, Mehine M, Liu YL, Nandakumar S, Smith SA, Brannon AR, Ostrovnaya I, Stopsack KH, Razavi P, Safonov A, Rizvi HA, Hellmann MD, Vijai J, Reynolds TC, Fagin JA, Carrot-Zhang J, Offit K, Solit DB, Ladanyi M, Schultz N, Zehir A, Brown CL, Stadler ZK, Chakravarty D, Bandlamudi C, Berger MF. Cancer Discov. 2022 Nov 2;12(11):2552-2565. doi: 10.1158/2159-8290.CD-22-0312. PMID: 36048199; PMCID: PMC9633436.

The context-specific role of germline pathogenicity in tumorigenesis. Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS. Nat Genet. 2021 Nov;53(11):1577-1585. doi: 10.1038/s41588-021-00949-1. Epub 2021 Nov 5. PMID: 34741162; PMCID: PMC8957388.

Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care. Penson A, Camacho N, Zheng Y, Varghese AM, Al-Ahmadie H, Razavi P, Chandarlapaty S, Vallejo CE, Vakiani E, Gilewski T, Rosenberg JE, Shady M, Tsui DWY, Reales DN, Abeshouse A, Syed A, Zehir A, Schultz N, Ladanyi M, Solit DB, Klimstra DS, Hyman DM, Taylor BS, Berger MF. JAMA Oncol. 2020 Jan 1;6(1):84-91. doi: 10.1001/jamaoncol.2019.3985. PMID: 31725847; PMCID: PMC6865333.

Tracking tumour evolution in glioma through liquid biopsies of cerebrospinal fluid. Miller AM, Shah RH, Pentsova EI, Pourmaleki M, Briggs S, Distefano N, Zheng Y, Skakodub A, Mehta SA, Campos C, Hsieh WY, Selcuklu SD, Ling L, Meng F, Jing X, Samoila A, Bale TA, Tsui DWY, Grommes C, Viale A, Souweidane MM, Tabar V, Brennan CW, Reiner AS, Rosenblum M, Panageas KS, DeAngelis LM, Young RJ, Berger MF, Mellinghoff IK. Nature. 2019 Jan;565(7741):654-658. doi: 10.1038/s41586-019-0882-3. Epub 2019 Jan 23. PMID: 30675060; PMCID: PMC6457907.

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Nat Med. 2017 Jun;23(6):703-713. doi: 10.1038/nm.4333. Epub 2017 May 8. Erratum in: Nat Med. 2017 Aug 4;23 (8):1004. PMID: 28481359; PMCID: PMC5461196.

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People

Michael Berger, PhD

Michael F. Berger, PhD

Co-Director, Marie-Josée & Henry R. Kravis Center for Molecular Oncology; Chief Attending, Clinical Computational Diagnostics Service, Department of Pathology and Laboratory Medicine

  • Researcher Michael Berger focuses on massively parallel sequencing of tumor DNA for biomarker discovery and clinical diagnostics.
  • PhD, Harvard University
[email protected]
Email Address
646-888-3386
Office Phone
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Physician profile

Members

Chaitanya Bandlamudi, PhD
Chaitanya Bandlamudi

Assistant Lab Member

Kanika Arora photo
Kanika Arora

Principal Computational Biologist

Juan Blanco Heredia

Senior Computational Biologist I

Eric Buehler

Bioinformatics Software Engineer, CMO Cell-Free DNA Informatics

Karmelina Charalambous

Computational Biologist, CMO Cell-Free DNA Informatics

Caryn Hale
Caryn Hale

Senior Computational Biologist, CMO Technology Innovation

Brian Houck- Loomis, Manager, CMO Technology Innovation
Brian Loomis

Head of CMO Technology Innovation

Julia Louw
Julia Louw

WGS Graduate Student

Miika Mehine

Research Fellow

Fanli Meng
Fanli Meng

Research Lab Manager, CMO Technology Innovation

Daniel Muldoon

Computational Biologist

Maria Perry

Senior Computational Biologist I

Sandeep Raj

Instructor

Ezra Rosen
Ezra Rosen

Assistant Attending

Ronak Shah
Ronak Shah

Lead Scientist, CMO Cell-Free DNA Informatics

Picture of Berger lab member Karthigayini Sivaprakasm
Karthigayini Sivaprakasam

Senior Computational Biologist, CMO Cell-Free DNA Informatics

Shalabh Suman
Shalabh Suman

Principal Computational Biologist

Grittney Tam
Grittney Tam

Senior Research Assistant, CMO Technology Innovation

Alyssa Vann

Bioinformatics Software Engineer, CMO Cell-Free DNA Informatics

Lab Alumni
Angela Rose Brannon, PhD
Angela Rose Brannon

Research Fellow

Gregory McDermott
Gregory McDermott

Medical Student

Sasinya Scott
Sasinya Scott

Research Technician

Mukta Asnani

Senior Research Assistant, CMO Technology Innovation

Nancy Bouvier
Nancy Bouvier

Senior Project Manager

Niedzica Camacho-Ordonez
Niedzica Camacho-Ordonez

Research Fellow

Madison Darmofal

WGS Graduate Student

Sebastià Franch Exposito
Sebastià Franch Exposito

Research Scholar

Adrian Fraiha
Adrian Fraiha

Bioinformatics Software Engineer, cfDNA Informatics

Alexander Ham

WGS Graduate Student

Maysun Hasan, Computational Biologist, CMO Technology Innovation
Maysun Hasan

Computational Biologist, CMO Technology Innovation

Xiaohong Jing
Xiaohong Jing

Lab Manager, CMO Technology Innovation

Ian Johnson, Bioinformatics Engineer
Ian Johnson

Bioinformatics Engineer, CMO Technology Innovation

Charles Murphy

Senior Computational Biologist, cfDNA Informatics

Juber Ahamad Patel
Juber Ahamad Patel

Computational Biologist, CMO Technology Innovation

Dilmi Perera, Research Fellow
Dilmi Perera

Research Fellow

Johnathan Rafailov

Bioinformatics Tech

Jonathan Reichel
Jonathan Reichel

Computational Biologist, CMO Technology Innovation

Maha Shady
Maha Shady

Bioinformatics Tech

Preethi Srinivasan
Preethi Srinivasan

Graduate Student

Jiabin Tang
Jiabin Tang

Group Leader, Innovation Laboratory

Giang Vo

Research Assistant, CMO Technology Innovation

Helen Won, MS
Helen Won

Computational Biologist

Wendy Yang
Wendy Yang

Clinical Research Fellow

Peter Zheng
Peter Zheng

Bioinformatics Technician

Lab Affiliations

Open Positions

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Disclosures

Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Michael F. Berger discloses the following relationships and financial interests:

  • AstraZeneca
    Professional Services and Activities
  • JCO Precision Oncology
    Professional Services and Activities (Uncompensated)
  • Journal of Molecular Diagnostics
    Professional Services and Activities (Uncompensated)
  • Paige.AI, Inc.
    Professional Services and Activities
  • SOPHiA GENETICS S.A.
    Intellectual Property Rights; Professional Services and Activities (Uncompensated)

The information published here is a complement to other publicly reported data and is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.

This page and data include information for a specific MSK annual disclosure period (January 1, 2023 through disclosure submission in spring 2024). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].


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