Pathology & Laboratory Medicine

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Laboratory of Cancer Genomics

Marcin Imielinski, MD, PhD, Principal Investigator

The Imielinski lab applies cutting-edge sequencing and data science approaches to understand the evolution and impact of complex and noncoding variants in cancer genomes. We use long-range sequencing and chromatin profiling to assess how complex somatic rearrangements perturb cancer epigenomes. We are also interested in links between the chromatin state of healthy and precancerous cells and the patterns of somatic variation observed in cancer. Finally, we are interested in neutral somatic mutation patterns as readouts of mutagenic exposure, DNA repair defects, and endogenous mutation processes in human cells.

Active Projects

  • Cancer genome assembly from 10X Chromium linked reads
  • Profiling epigenomes in highly rearranged cancer samples
  • Identifying footprints of mutational processes in whole genomes sequences of human cancer samples and engineered model systems
  • Identifying signals of positive somatic selection in cancer whole genome data

Active Grants

  • Epigenetic landscapes of rearranged driver-negative cancers 
    PI: Marcin Imielinski, MD, PhD
    Doris Duke Charitable Foundation Clinical Scientist Development Award (CSDA) 
  • Burroughs Wellcome Career Award for Medical Scientists
    PI: Marcin Imielinski, MD, PhD
    Burroughs Wellcome Fund
  • U24 Center for Functional and Clinical Interpretation of Tumor Profiles
    PI: Olivier Elemento, PhD, Mark Rubin, MD
    National Institutes of Health/National Cancer Institute (NIH/NCI)
  • NIH U24 Center for the analysis of copy number changes across cancer
    PI: Rameen Beroukhim, MD, PhD
    National Institutes of Health/National Cancer Institute (NIH/NCI)
  • Doris Duke Clinical Scientist Development Award
    Doris Duke Charitable Foundation

Selected Publications

Modeling complex cancer rearrangement landscapes

Marcin Imielinski, MD, PhD

Modeling complex cancer rearrangement landscapes

Current Opinion in Systems Biology. 2016 Dec 26 [Epub ahead of print]

Maciejowski  J, Imielinski M. 

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Insertions and Deletions Target Lineage-Defining Genes in Human Cancers

Marcin Imielinski, MD, PhD

Insertions and Deletions Target Lineage-Defining Genes in Human Cancers

Cell. 2017 Jan 26;168(3):460-472.

Imielinski M, Guo G, Meyerson M.

PMID: 28089356

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The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

Marcin Imielinski, MD, PhD

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

J Am Med Inform Assoc. 2016 Oct 27. [Epub ahead of print]

Huang L, Fernandes H, Zia H, Tavassoli P, Rennert H, Pisapia D, Imielinski M, Sboner A, Rubin MA, Kluk M, Elemento O.

PMID: 27789569

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High-throughput Phenotyping of Lung Cancer Somatic Mutations

Marcin Imielinski, MD, PhD

High-throughput Phenotyping of Lung Cancer Somatic Mutations

Cancer Cell2016 Aug 8;30(2):214-28.

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

PMID: 27478040; PMCID: PMC5003022

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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Marcin Imielinski, MD, PhD

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Nat Genet. 2016 Jun;48(6):607-16. 

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network., Artyomov MN, Schreiber R, Govindan R, Meyerson M.

PMID: 27158780; PMCID: PMC4884143

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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

Marcin Imielinski, MD, PhD

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

Nat Genet. 2016 Feb;48(2):176-82. 

Zhang X, Choi PS, Francis JM, Imielinski M, Watanabe H, Cherniack AD, Meyerson M.

PMID: 26656844; PMCID: PMC4857881

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Genetic modifiers of EGFR dependence in non-small cell lung cancer

Marcin Imielinski, MD, PhD

Genetic modifiers of EGFR dependence in non-small cell lung cancer

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18661-6.

Sharifnia T, Rusu V, Piccioni F, Bagul M, Imielinski M, Cherniack AD, Pedamallu CS, Wong B, Wilson FH, Garraway LA, Altshuler D, Golub TR, Root DE, Subramanian A, Meyerson M.

PMID: 25512530; PMCID: PMC4284598

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Oncogenic RIT1 mutations in lung adenocarcinoma

Marcin Imielinski, MD, PhD

Oncogenic RIT1 mutations in lung adenocarcinoma

Oncogene. 2014 Aug 28;33(35):4418-23. 

Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M. 

PMID: 24469055; PMCID: PMC4150988

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Comprehensive molecular profiling of lung adenocarcinoma

Marcin Imielinski, MD, PhD

Comprehensive molecular profiling of lung adenocarcinoma

Nature. 2014 Jul 31;511(7511):543-50. Erratum in: Nature. 2014 Oct 9;514(7521):262. Rogers, K [corrected to Rodgers, K].

Cancer Genome Atlas Research Network.. 

PubMed PMID: 25079552; PubMed Central PMCID: PMC4231481.

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Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma

Marcin Imielinski, MD, PhD

Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma

J Clin Invest. 2014 Apr;124(4):1582-6.

Imielinski M, Greulich H, Kaplan B, Araujo L, Amann J, Horn L, Schiller J, Villalona-Calero MA, Meyerson M, Carbone DP.

PMID: 24569458; PMCID: PMC3973082

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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

Marcin Imielinski, MD, PhD

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

PLoS One. 2014 Jan 31;9(1):e87361. 

Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.

PMID:24498085; PMCID: PMC3909098

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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

Marcin Imielinski, MD, PhD

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

PLoS One. 2014 Jan 31;9(1):e87361.

Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.

PMID: 24498085; PMCID: PMC3909098

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Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Marcin Imielinski, MD, PhD

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Cell. 2012 Sep 14;150(6):1107-20. 

Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M.

PMID: 22980975; PMCID: PMC3557932

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A landscape of driver mutations in melanoma

Marcin Imielinski, MD, PhD

A landscape of driver mutations in melanoma

Cell. 2012 Jul 20;150(2):251-63. 

Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander  ES, Gabriel SB, Getz G, Garraway LA, Chin L.

PMID: 22817889; PMCID: PMC3600117

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Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse

Marcin Imielinski, MD, PhD

Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse

Mol Cell Proteomics. 2012 Jun;11(6):M111.014910. 

Imielinski M, Cha S, Rejtar T, Richardson EA, Karger BL, Sgroi DC.

PMID: 22240506; PMCID: PMC3433899

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Weill Cornell Medicine Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464 Fax: (212) 746-8192