Research

We are driving the Pediatrics Precision Medicine Initiative for the Department of Pediatrics, and support clinical translational research for the Center for Heme Malignancies at MSK.

We benefit from a fully resourced computational and research environment. We have access to state-of-the-art computing and laboratory facilities to support truly ambitious and innovative research.

Highlighted

Clonal evolution during metastatic spread in high-risk neuroblastoma

Gunes Gundem, Max F. Levine, Stephen S. Roberts, Irene Y. Cheung, Juan S. Medina-Martínez, ..., Neerav Shukla, Christine A. Iacobuzio-Donahue, Andrew L. Kung, Nai-Kong V. Cheung, Elli Papaemmanuil

Nature Genetics · 11 May 2023 · doi:10.1038/s41588-023-01395-x

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Molecular International Prognostic Scoring System for Myelodysplastic Syndromes

Elsa Bernard, Heinz Tuechler, Peter L. Greenberg, Robert P. Hasserjian, Juan E. Arango Ossa, ..., Luca Malcovati, Mario Cazzola, Seishi Ogawa, Eva Hellström-Lindberg, Elli Papaemmanuil

NEJM Evidence · 28 Jun 2022 · doi:10.1056/EVIDoa2200008

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MDS Cancer Hematology

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

N. Shukla, M. F. Levine, G. Gundem, D. Domenico, B. Spitzer, ..., A. Zehir, A. Viale, M. F. Walsh, A. L. Kung, E. Papaemmanuil

Nature Communications · 18 May 2022 · doi:10.1038/s41467-022-30233-7

Pediatrics Whole Genome Sequencing Isabl

Isabl Platform, a digital biobank for processing multimodal patient data

Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung, Elli Papaemmanuil

BMC Bioinformatics · 30 Nov 2020 · doi:10.1186/s12859-020-03879-7

Documentation

Platform Bioinformatics Biobank

Genomic Classification and Prognosis in Acute Myeloid Leukemia

Elli Papaemmanuil, Moritz Gerstung, Lars Bullinger, Verena I. Gaidzik, Peter Paschka, ..., Arnold Ganser, Konstanze Döhner, Richard F. Schlenk, Hartmut Döhner, Peter J. Campbell

New England Journal of Medicine · 09 Jun 2016 · doi:10.1056/NEJMoa1516192

Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms

Luca Malcovati, Elli Papaemmanuil, David T. Bowen, Jacqueline Boultwood, Matteo G. Della Porta, ..., P. Andrew Futreal, Michael R. Stratton, Peter J. Campbell, Eva Hellström-Lindberg, Mario Cazzola

Blood · 08 Dec 2011 · doi:10.1182/blood-2011-09-377275

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2023

Clonal evolution during metastatic spread in high-risk neuroblastoma

Gunes Gundem, Max F. Levine, Stephen S. Roberts, Irene Y. Cheung, Juan S. Medina-Martínez, ..., Neerav Shukla, Christine A. Iacobuzio-Donahue, Andrew L. Kung, Nai-Kong V. Cheung, Elli Papaemmanuil

Nature Genetics · 11 May 2023 · doi:10.1038/s41588-023-01395-x

2022

Unified classification and risk-stratification in Acute Myeloid Leukemia

Yanis Tazi, Juan E. Arango-Ossa, Yangyu Zhou, Elsa Bernard, Ian Thomas, ..., Michael Dennis, Nigel H. Russell, Sean M. Devlin, Brian J. P. Huntly, Elli Papaemmanuil

Nature Communications · 08 Aug 2022 · doi:10.1038/s41467-022-32103-8

Molecular International Prognostic Scoring System for Myelodysplastic Syndromes

Elsa Bernard, Heinz Tuechler, Peter L. Greenberg, Robert P. Hasserjian, Juan E. Arango Ossa, ..., Luca Malcovati, Mario Cazzola, Seishi Ogawa, Eva Hellström-Lindberg, Elli Papaemmanuil

NEJM Evidence · 28 Jun 2022 · doi:10.1056/EVIDoa2200008

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

N. Shukla, M. F. Levine, G. Gundem, D. Domenico, B. Spitzer, ..., A. Zehir, A. Viale, M. F. Walsh, A. L. Kung, E. Papaemmanuil

Nature Communications · 18 May 2022 · doi:10.1038/s41467-022-30233-7

Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs

Georgios Asimomitis, André G. Deslauriers, Andriana G. Kotini, Elsa Bernard, Davide Esposito, ..., Mario Cazzola, Stuart A. Aaronson, Eva Hellström-Lindberg, Elli Papaemmanuil, Eirini P. Papapetrou

Blood Advances · 16 May 2022 · doi:10.1182/bloodadvances.2021006325

“Randomized phase II study of azacitidine ± lenalidomide in higher-risk myelodysplastic syndromes and acute myeloid leukemia with a karyotype including Del(5q)”

Bengt Rasmussen, Gudrun Göhring, Elsa Bernard, Lars Nilsson, Magnus Tobiasson, ..., Astrid Olsnes Kittang, Jan Maxwell Nørgaard, Leonie Saft, Lars Möllgård, Eva Hellström-Lindberg

Leukemia · 11 Mar 2022 · doi:10.1038/s41375-022-01537-w

2021

Genetic and genomic analysis of acute lymphoblastic leukemia in older adults reveals a distinct profile of abnormalities: analysis of 210 patients from the UKALL14 and UKALL60+ clinical trials

Thomas Creasey, Emilio Barretta, Sarra L. Ryan, Ellie Butler, Amy A. Kirkwood, ..., Clare J. Rowntree, Nick Morley, David I. Marks, Adele K. Fielding, Anthony V. Moorman

Haematologica · 18 Nov 2021 · doi:10.3324/haematol.2021.279177

Prognostic impact of chromosomal abnormalities and copy number alterations in adult B-cell precursor acute lymphoblastic leukaemia: a UKALL14 study

Anthony V. Moorman, Emilio Barretta, Ellie R. Butler, Eleanor J. Ward, Katie Twentyman, ..., Andrew K. McMillan, Christine J. Harrison, Clare J. Rowntree, David I. Marks, Adele K. Fielding

Leukemia · 16 Oct 2021 · doi:10.1038/s41375-021-01448-2

2020

Isabl Platform, a digital biobank for processing multimodal patient data

Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung, Elli Papaemmanuil

BMC Bioinformatics · 30 Nov 2020 · doi:10.1186/s12859-020-03879-7

Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes

Elsa Bernard, Yasuhito Nannya, Robert P. Hasserjian, Sean M. Devlin, Heinz Tuechler, ..., Peter L. Greenberg, Mario Cazzola, Eva Hellström-Lindberg, Seishi Ogawa, Elli Papaemmanuil

Nature Medicine · 03 Aug 2020 · doi:10.1038/s41591-020-1008-z

2016

Genomic Classification and Prognosis in Acute Myeloid Leukemia

Elli Papaemmanuil, Moritz Gerstung, Lars Bullinger, Verena I. Gaidzik, Peter Paschka, ..., Arnold Ganser, Konstanze Döhner, Richard F. Schlenk, Hartmut Döhner, Peter J. Campbell

New England Journal of Medicine · 09 Jun 2016 · doi:10.1056/NEJMoa1516192

2015

Effect of Mutation Order on Myeloproliferative Neoplasms

Christina A. Ortmann, David G. Kent, Jyoti Nangalia, Yvonne Silber, David C. Wedge, ..., Claire N. Harrison, George S. Vassiliou, Alessandro Vannucchi, Peter J. Campbell, Anthony R. Green

New England Journal of Medicine · 12 Feb 2015 · doi:10.1056/NEJMoa1412098

Recurrent ETNK1 mutations in atypical chronic myeloid leukemia

Carlo B. Gambacorti-Passerini, Carla Donadoni, Andrea Parmiani, Alessandra Pirola, Sara Redaelli, ..., Graham R. Bignell, Elli Papaemmanuil, Peter J. Campbell, Mario Cazzola, Rocco Piazza

Blood · 15 Jan 2015 · doi:10.1182/blood-2014-06-579466

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

Moritz Gerstung, Andrea Pellagatti, Luca Malcovati, Aristoteles Giagounidis, Matteo G Della Porta, ..., Eva Hellström-Lindberg, Mario Cazzola, Elli Papaemmanuil, Peter J. Campbell, Jacqueline Boultwood

Nature Communications · 09 Jan 2015 · doi:10.1038/ncomms6901

2014

Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells

H Dolatshad, A Pellagatti, M Fernandez-Mercado, B H Yip, L Malcovati, ..., S Ogawa, J P Maciejewski, M Cazzola, K I Savage, J Boultwood

Leukemia · 27 Nov 2014 · doi:10.1038/leu.2014.331

Nongenetic stochastic expansion of JAK2V617F-homozygous subclones in polycythemia vera?

Anna L. Godfrey, Jyoti Nangalia, E. Joanna Baxter, Charles E. Massie, David G. Kent, Elli Papaemmanuil, Peter J. Campbell, Anthony R. Green

Blood · 20 Nov 2014 · doi:10.1182/blood-2014-09-603043

Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol

N. Bolli, N. Manes, T. McKerrell, J. Chi, N. Park, ..., E. Papaemmanuil, P. J. Campbell, I. Varela, P. Costeas, G. S. Vassiliou

Haematologica · 07 Nov 2014 · doi:10.3324/haematol.2014.113381

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, ..., Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, Peter J Campbell

eLife · 01 Oct 2014 · doi:10.7554/eLife.02935

Driver somatic mutations identify distinct disease entities within myeloid neoplasms with myelodysplasia

Luca Malcovati, Elli Papaemmanuil, Ilaria Ambaglio, Chiara Elena, Anna Gallì, ..., Maurizio Ferrari, Emanuela Boveri, Rosangela Invernizzi, Peter J. Campbell, Mario Cazzola

Blood · 28 Aug 2014 · doi:10.1182/blood-2014-03-560227

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Jose M. C. Tubio, Yilong Li, Young Seok Ju, Inigo Martincorena, Susanna L. Cooke, ..., Sam M. Janes, G. Steven Bova, Michael R. Stratton, Ultan McDermott, Peter J. Campbell

Science · 01 Aug 2014 · doi:10.1126/science.1251343

Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo

Petter S. Woll, Una Kjällquist, Onima Chowdhury, Helen Doolittle, David C. Wedge, ..., Rickard Sandberg, Elli Papaemmanuil, Eva Hellström-Lindberg, Sten Linnarsson, Sten Eirik W. Jacobsen

Cancer Cell · 01 Jun 2014 · doi:10.1016/j.ccr.2014.03.036

Minimal morphological criteria for defining bone marrow dysplasia: a basis for clinical implementation of WHO classification of myelodysplastic syndromes

M G Della Porta, E Travaglino, E Boveri, M Ponzoni, L Malcovati, ..., E Morra, P J Campbell, A Orazi, R Invernizzi, M Cazzola

Leukemia · 20 May 2014 · doi:10.1038/leu.2014.161

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

Serena Nik-Zainal, David C Wedge, Ludmil B Alexandrov, Mia Petljak, Adam P Butler, ..., Ingrid Simonic, Yali Xue, Chris Tyler-Smith, Peter J Campbell, Michael R Stratton

Nature Genetics · 13 Apr 2014 · doi:10.1038/ng.2955

Processed pseudogenes acquired somatically during cancer development

Susanna L. Cooke, Adam Shlien, John Marshall, Christodoulos P. Pipinikas, Inigo Martincorena, ..., Anne-Lise Børresen-Dale, Ming Ta Michael Lee, Bernice Huimin Wong, Benita Kiat Tee Tan, Gerrit K.J. Hooijer

Nature Communications · 09 Apr 2014 · doi:10.1038/ncomms4644

Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia

Yilong Li, Claire Schwab, Sarra L. Ryan, Elli Papaemmanuil, Hazel M. Robinson, ..., Jiqiu Cheng, Peter Van Loo, Michael R. Stratton, Peter J. Campbell, Christine J. Harrison

Nature · 23 Mar 2014 · doi:10.1038/nature13115

Recurrent PTPRB and PLCG1 mutations in angiosarcoma

Sam Behjati, Patrick S Tarpey, Helen Sheldon, Inigo Martincorena, Peter Van Loo, ..., Michael R Stratton, P Andrew Futreal, Adrienne M Flanagan, Adrian Harris, Peter J Campbell

Nature Genetics · 16 Mar 2014 · doi:10.1038/ng.2921

Subclonal variant calling with multiple samples and prior knowledge

Moritz Gerstung, Elli Papaemmanuil, Peter J. Campbell

Bioinformatics · 16 Jan 2014 · doi:10.1093/bioinformatics/btt750

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

Elli Papaemmanuil, Inmaculada Rapado, Yilong Li, Nicola E Potter, David C Wedge, ..., Markus Muschen, Anthony M Ford, Michael R Stratton, Mel Greaves, Peter J Campbell

Nature Genetics · 12 Jan 2014 · doi:10.1038/ng.2874

2013

SomaticCALRMutations in Myeloproliferative Neoplasms with NonmutatedJAK2

J. Nangalia, C.E. Massie, E.J. Baxter, F.L. Nice, G. Gundem, ..., D. Ron, A.M. Vannucchi, E. Papaemmanuil, P.J. Campbell, A.R. Green

New England Journal of Medicine · 19 Dec 2013 · doi:10.1056/NEJMoa1312542

Inactivating CUX1 mutations promote tumorigenesis

Chi C Wong, Inigo Martincorena, Alistair G Rust, Mamunur Rashid, Constantine Alifrangis, ..., Sarah J Bray, Ultan McDermott, Elli Papaemmanuil, Peter J Campbell, David J Adams

Nature Genetics · 08 Dec 2013 · doi:10.1038/ng.2846

Clinical and biological implications of driver mutations in myelodysplastic syndromes

Elli Papaemmanuil, Moritz Gerstung, Luca Malcovati, Sudhir Tauro, Gunes Gundem, ..., Eva Hellstrom-Lindberg, David Bowen, Mario Cazzola, Michael R. Stratton, Peter J. Campbell

Blood · 21 Nov 2013 · doi:10.1182/blood-2013-08-518886

Single-cell mutational profiling and clonal phylogeny in cancer

Nicola E. Potter, Luca Ermini, Elli Papaemmanuil, Giovanni Cazzaniga, Gowri Vijayaraghavan, Ian Titley, Anthony Ford, Peter Campbell, Lyndal Kearney, Mel Greaves

Genome Research · 20 Sep 2013 · doi:10.1101/gr.159913.113

Signatures of mutational processes in human cancer

Ludmil B. Alexandrov, Serena Nik-Zainal, David C. Wedge, Samuel A. J. R. Aparicio, Sam Behjati, ..., Elías Campo, Tatsuhiro Shibata, Stefan M. Pfister, Peter J. Campbell, Michael R. Stratton

Nature · 14 Aug 2013 · doi:10.1038/nature12477

Whole exome sequencing of adenoid cystic carcinoma

Philip J. Stephens, Helen R. Davies, Yoshitsugu Mitani, Peter Van Loo, Adam Shlien, ..., Ultan McDermott, Michael R. Stratton, Peter J. Campbell, Adel K. El-Naggar, P. Andrew Futreal

Journal of Clinical Investigation · 17 Jun 2013 · doi:10.1172/JCI67201

Inappropriately low hepcidin levels in patients with myelodysplastic syndrome carrying a somatic mutation of SF3B1

I. Ambaglio, L. Malcovati, E. Papaemmanuil, C. M. Laarakkers, M. G. Della Porta, ..., E. Travaglino, R. Albertini, P. J. Campbell, D. W. Swinkels, M. Cazzola

Haematologica · 08 Jan 2013 · doi:10.3324/haematol.2012.077446

2012

Recurrent SETBP1 mutations in atypical chronic myeloid leukemia

Rocco Piazza, Simona Valletta, Nils Winkelmann, Sara Redaelli, Roberta Spinelli, ..., Peter J Campbell, Andrew J Chase, William J Tapper, Nicholas C P Cross, Carlo Gambacorti-Passerini

Nature Genetics · 09 Dec 2012 · doi:10.1038/ng.2495

The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts

M Nikpour, C Scharenberg, A Liu, S Conte, M Karimi, ..., P Campbell, M Cazzola, J Boultwood, A Grandien, E Hellström-Lindberg

Leukemia · 16 Oct 2012 · doi:10.1038/leu.2012.298

The landscape of cancer genes and mutational processes in breast cancer

Philip J. Stephens, Patrick S. Tarpey, Helen Davies, Peter Van Loo, Chris Greenman, ..., Anne-Lise Børresen-Dale, Andrea L. Richardson, Peter J. Campbell, P. Andrew Futreal, Michael R. Stratton

Nature · 16 May 2012 · doi:10.1038/nature11017

The Life History of 21 Breast Cancers

Serena Nik-Zainal, Peter Van Loo, David C. Wedge, Ludmil B. Alexandrov, Christopher D. Greenman, ..., Andrea L. Richardson, Anne-Lise Børresen-Dale, P. Andrew Futreal, Michael R. Stratton, Peter J. Campbell

Cell · 01 May 2012 · doi:10.1016/j.cell.2012.04.023

Mutational Processes Molding the Genomes of 21 Breast Cancers

Serena Nik-Zainal, Ludmil B. Alexandrov, David C. Wedge, Peter Van Loo, Christopher D. Greenman, ..., Andrea L. Richardson, Michael S. Neuberger, P. Andrew Futreal, Peter J. Campbell, Michael R. Stratton

Cell · 01 May 2012 · doi:10.1016/j.cell.2012.04.024

2011

Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms

Luca Malcovati, Elli Papaemmanuil, David T. Bowen, Jacqueline Boultwood, Matteo G. Della Porta, ..., P. Andrew Futreal, Michael R. Stratton, Peter J. Campbell, Eva Hellström-Lindberg, Mario Cazzola

Blood · 08 Dec 2011 · doi:10.1182/blood-2011-09-377275

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

E. Papaemmanuil, M. Cazzola, J. Boultwood, L. Malcovati, P. Vyas, ..., N.C.P. Cross, A.R. Green, P.A. Futreal, M.R. Stratton, P.J. Campbell

New England Journal of Medicine · 13 Oct 2011 · doi:10.1056/NEJMoa1103283

MHC variation and risk of childhood B-cell precursor acute lymphoblastic leukemia

Fay J. Hosking, Stephen Leslie, Alexander Dilthey, Loukas Moutsianas, Yufei Wang, ..., James M. Allan, Malcolm Taylor, Mel Greaves, Gilean McVean, Richard S. Houlston

Blood · 03 Feb 2011 · doi:10.1182/blood-2010-08-301598

2010

Genome-wide homozygosity signatures and childhood acute lymphoblastic leukemia risk

Fay J. Hosking, Elli Papaemmanuil, Eammon Sheridan, Sally E. Kinsey, Tracy Lightfoot, ..., James M. Allan, Malcolm Taylor, Ian P. Tomlinson, Mel Greaves, Richard S. Houlston

Blood · 03 Jun 2010 · doi:10.1182/blood-2009-09-244483

Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk

Amy L Sherborne, Fay J Hosking, Rashmi B Prasad, Rajiv Kumar, Rolf Koehler, ..., Seishi Ogawa, H Phillip Koeffler, Kari Hemminki, Mel Greaves, Richard S Houlston

Nature Genetics · 09 May 2010 · doi:10.1038/ng.585

Verification of the susceptibility loci on 7p12.2, 10q21.2, and 14q11.2 in precursor B-cell acute lymphoblastic leukemia of childhood

Rashmi B. Prasad, Fay J. Hosking, Jayaram Vijayakrishnan, Elli Papaemmanuil, Rolf Koehler, ..., Martin Schrappe, Claus R. Bartram, Richard S. Houlston, Rajiv Kumar, Kari Hemminki

Blood · 04 Mar 2010 · doi:10.1182/blood-2009-09-241513

2009

Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia

Elli Papaemmanuil, Fay J Hosking, Jayaram Vijayakrishnan, Amy Price, Bianca Olver, ..., James M Allan, Ian P Tomlinson, Malcolm Taylor, Mel Greaves, Richard S Houlston

Nature Genetics · 16 Aug 2009 · doi:10.1038/ng.430

2008

Deciphering the genetics of hereditary non-syndromic colorectal cancer

Eli Papaemmanuil, Luis Carvajal-Carmona, Gabrielle S Sellick, Zoe Kemp, Emily Webb, ..., Juul Wijnen, Jean-Baptiste Cazier, Huw Thomas, Richard S Houlston, Ian Tomlinson

European Journal of Human Genetics · 16 Jul 2008 · doi:10.1038/ejhg.2008.129

Analysis of a large multi-generational family provides insight into the genetics of chronic lymphocytic leukemia

Stephen J. Fuller, Elli Papaemmanuil, Leah McKinnon, Emily Webb, Gabrielle S. Sellick, Lan-Phuong Dao-Ung, Kristen K. Skarratt, Dalemari Crowther, Richard S. Houlston, James S. Wiley

British Journal of Haematology · 01 Jul 2008 · doi:10.1111/j.1365-2141.2008.07188.x