Elli Papaemmanuil, PhD

Assistant Attending

Elli Papaemmanuil

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Dr. Papaemmanuil got her BSc and MSci in Human Molecular Genetics with Honors at the University of Glasgow and her PhD in Human population genetics at the Institute of Cancer Research in London. She performed her postdoctoral studies at the Wellcome Trust Sanger Center and joined the University of Cambridge as faculty, prior to moving to the Memorial Sloan Kettering Cancer Center. 

Dr. Papaemmanuil has employed genome profiling methodologies to study role of acquired mutations in cancer development and how these determine clinical phenotype and response to therapy. During her PhD using a combination of linkage and GWAS approaches, Dr. Papaemmanuil mapped novel genetic predisposition loci in colorectal cancer and childhood leukemia. During her postdoctoral research studies Dr. Papaemmanuil employed next generation sequencing approaches to characterize new gene mutations in myeloid neoplasms, and her work led to the first characterization of splicing factor mutations, CALR, CUX1 amongst other genes mutated I cancer. She used wholegenome sequencing and single cell sequencing approaches to characterize mechanisms that cause genomic rearrangements in childhood leukemia and identified aberrant RAG targeting as the dominant driver of childhood B-ALL. More recently she has established high-throughput laboratory profiling approaches and developed statistical modelling methodologies that integrate clinical and molecular parameters to inform patient tailored disease classification and clinical decision support (prognosis and treatment decisions). 

Her main research motivation is to develop research that helps translate recent cancer genome discoveries into clinical practice. Her current research spans, bioinformatic and algorithmic platform development, biomarker discovery and validation and experimental models of disease biology. 

For biomarker development Dr. Papaemmanuil employs large cohort analyses to study the genetic and clinical inter-relationships of well annotated clinical cohorts and develop patient tailored prognostic models. This includes: 
• International Working Group for Prognostication in MDS (IWG-PM)
• European, and US based analyses to define disease classification and prognostication in AML
• UK MRC trials in Adult Lymphoblastic Leukemia 
• Pan-myeloid consortium 
• International working group in Ovarian Clear Cell Carcinoma 

Additionally, Dr. Papaemmanuil has a strong interest to understand the effects of treatment in disease progression and genetic drivers of treatment response. This includes three major initiatives to include: 
• Population genomic approaches to study the impact of oncologic therapy in clonal hematopoiesis and risk of tMN. 
• Wholegenome sequencing studies of temporally and spatially separated samples at diagnosis, disease progression and metastasis
• Single-cell sequencing studies in myeloid neoplasms using paired pre and post treatment samples from patients receiving targeted therapies 

Experimentally, Dr. Papaemmanuil is using integrative single cell approaches (DNA and RNA) and iPSC modelling of mutations in myeloid disease to study disease progression and treatment response. 

Last, Dr. Papaemmanuil leads the Expanded Genomics Program for MSK Kids, which sets out to evaluate, validate and deliver a clinical prototype for integrative wholegenome and whole transcriptome sequencing analyses to understand mechanisms of disease biology and guide treatment strategies in pediatric cancers.


Selected peer-reviewed publications:

  1. Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P, Ganser A, McDermott U, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Precision oncology for acute myeloid leukemia using a knowledge bank approach. Nat Genet. 2017 Mar;49(3):332-340. doi: 10.1038/ng.3756.Epub 2017 Jan 16. PubMed PMID: 28092685; PubMed Central PMCID: PMC5764082.
  2. Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly  P, Mudie L, McLaren S, O’Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Genomic Classification and Prognosis in Acute Myeloid Leukemia. N Engl J Med. 2016 Jun 9;374(23):2209-2221. doi: 10.1056/NEJMoa1516192. PubMed PMID: 27276561; PubMed Central PMCID: PMC4979995.
  3. Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O’Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet. 2014 Feb;46(2):116-25. doi: 10.1038/ng.2874. Epub 2014 Jan 12. PubMed PMID: 24413735; PubMed Central PMCID: PMC3960636.
  4. Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011 Oct 13;365(15):1384-95. doi: 10.1056/NEJMoa1103283. Epub 2011 Sep 26. PubMed PMID: 21995386; PubMed Central PMCID: PMC3322589.
  5. Gerstung M, Papaemmanuil E, Campbell PJ. Subclonal variant calling with multiple samples and prior knowledge. Bioinformatics. 2014 May 1;30(9):1198-204.  doi: 10.1093/bioinformatics/btt750. Epub 2014 Jan 16. PubMed PMID: 24443148; PubMed Central PMCID: PMC3998123.

View a full listing of Elli Papaemmanuil’s journal articles.


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.

Elli Papaemmanuil discloses the following relationships and financial interests:

  • Isabl Technologies
    Fiduciary Role/Position; Intellectual Property Rights; Ownership / Equity Interests
  • Kyowa Hakko Kirin Pharma
    Provision of Services

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This page and data include information for a specific MSK annual disclosure period (January 1, 2019 through disclosure submission in spring 2020). This data reflects interests that may or may not still exist. This data is updated annually.

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