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Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing

Author

Listed:
  • Ryan N. Ptashkin

    (Memorial Sloan Kettering Cancer Center
    C2i Genomics)

  • Mark D. Ewalt

    (Memorial Sloan Kettering Cancer Center)

  • Gowtham Jayakumaran

    (Memorial Sloan Kettering Cancer Center
    Guardant Health)

  • Iwona Kiecka

    (Memorial Sloan Kettering Cancer Center)

  • Anita S. Bowman

    (Memorial Sloan Kettering Cancer Center)

  • JinJuan Yao

    (Memorial Sloan Kettering Cancer Center)

  • Jacklyn Casanova

    (Memorial Sloan Kettering Cancer Center)

  • Yun-Te David Lin

    (Memorial Sloan Kettering Cancer Center)

  • Kseniya Petrova-Drus

    (Memorial Sloan Kettering Cancer Center)

  • Abhinita S. Mohanty

    (Memorial Sloan Kettering Cancer Center)

  • Ruben Bacares

    (Memorial Sloan Kettering Cancer Center)

  • Jamal Benhamida

    (Memorial Sloan Kettering Cancer Center)

  • Satshil Rana

    (Memorial Sloan Kettering Cancer Center)

  • Anna Razumova

    (Memorial Sloan Kettering Cancer Center)

  • Chad Vanderbilt

    (Memorial Sloan Kettering Cancer Center)

  • Anoop Balakrishnan Rema

    (Memorial Sloan Kettering Cancer Center)

  • Ivelise Rijo

    (Memorial Sloan Kettering Cancer Center)

  • Julie Son-Garcia

    (Memorial Sloan Kettering Cancer Center)

  • Ino Bruijn

    (Memorial Sloan Kettering Cancer Center)

  • Menglei Zhu

    (Memorial Sloan Kettering Cancer Center)

  • Sean Lachhander

    (Memorial Sloan Kettering Cancer Center)

  • Wei Wang

    (Memorial Sloan Kettering Cancer Center)

  • Mohammad S. Haque

    (Memorial Sloan Kettering Cancer Center)

  • Venkatraman E. Seshan

    (Memorial Sloan Kettering Cancer Center)

  • Jiajing Wang

    (Memorial Sloan Kettering Cancer Center)

  • Ying Liu

    (Memorial Sloan Kettering Cancer Center)

  • Khedoudja Nafa

    (Memorial Sloan Kettering Cancer Center)

  • Laetitia Borsu

    (Memorial Sloan Kettering Cancer Center)

  • Yanming Zhang

    (Memorial Sloan Kettering Cancer Center)

  • Umut Aypar

    (Memorial Sloan Kettering Cancer Center)

  • Sarah P. Suehnholz

    (Memorial Sloan Kettering Cancer Center)

  • Debyani Chakravarty

    (Memorial Sloan Kettering Cancer Center)

  • Jae H. Park

    (Memorial Sloan Kettering Cancer Center)

  • Omar Abdel-Wahab

    (Memorial Sloan Kettering Cancer Center
    Memorial Sloan Kettering Cancer Center)

  • Anthony R. Mato

    (Memorial Sloan Kettering Cancer Center)

  • Wenbin Xiao

    (Memorial Sloan Kettering Cancer Center)

  • Mikhail Roshal

    (Memorial Sloan Kettering Cancer Center)

  • Mariko Yabe

    (Memorial Sloan Kettering Cancer Center)

  • Connie Lee Batlevi

    (Memorial Sloan Kettering Cancer Center)

  • Sergio Giralt

    (Memorial Sloan Kettering Cancer Center)

  • Gilles Salles

    (Memorial Sloan Kettering Cancer Center)

  • Raajit Rampal

    (Memorial Sloan Kettering Cancer Center)

  • Martin Tallman

    (Memorial Sloan Kettering Cancer Center
    Northwestern University)

  • Eytan M. Stein

    (Memorial Sloan Kettering Cancer Center)

  • Anas Younes

    (Memorial Sloan Kettering Cancer Center
    Oncology R&D, AstraZeneca)

  • Ross L. Levine

    (Memorial Sloan Kettering Cancer Center
    Memorial Sloan Kettering Cancer Center)

  • Miguel-Angel Perales

    (Memorial Sloan Kettering Cancer Center
    Weill Cornell Medical College)

  • Marcel R. M. Brink

    (Memorial Sloan Kettering Cancer Center
    Memorial Sloan Kettering Cancer Center)

  • Ahmet Dogan

    (Memorial Sloan Kettering Cancer Center)

  • Marc Ladanyi

    (Memorial Sloan Kettering Cancer Center)

  • Michael F. Berger

    (Memorial Sloan Kettering Cancer Center
    Memorial Sloan Kettering Cancer Center)

  • A. Rose Brannon

    (Memorial Sloan Kettering Cancer Center)

  • Ryma Benayed

    (Memorial Sloan Kettering Cancer Center
    Oncology R&D, AstraZeneca)

  • Ahmet Zehir

    (Memorial Sloan Kettering Cancer Center
    Oncology R&D, AstraZeneca)

  • Maria E. Arcila

    (Memorial Sloan Kettering Cancer Center)

Abstract

Genomic profiling of hematologic malignancies has augmented our understanding of variants that contribute to disease pathogenesis and supported development of prognostic models that inform disease management in the clinic. Tumor only sequencing assays are limited in their ability to identify definitive somatic variants, which can lead to ambiguity in clinical reporting and patient management. Here, we describe the MSK-IMPACT Heme cohort, a comprehensive data set of somatic alterations from paired tumor and normal DNA using a hybridization capture-based next generation sequencing platform. We highlight patterns of mutations, copy number alterations, and mutation signatures in a broad set of myeloid and lymphoid neoplasms. We also demonstrate the power of appropriate matching to make definitive somatic calls, including in patients who have undergone allogeneic stem cell transplant. We expect that this resource will further spur research into the pathobiology and clinical utility of clinical sequencing for patients with hematologic neoplasms.

Suggested Citation

  • Ryan N. Ptashkin & Mark D. Ewalt & Gowtham Jayakumaran & Iwona Kiecka & Anita S. Bowman & JinJuan Yao & Jacklyn Casanova & Yun-Te David Lin & Kseniya Petrova-Drus & Abhinita S. Mohanty & Ruben Bacares, 2023. "Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42585-9
    DOI: 10.1038/s41467-023-42585-9
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    References listed on IDEAS

    as
    1. Monkol Lek & Konrad J. Karczewski & Eric V. Minikel & Kaitlin E. Samocha & Eric Banks & Timothy Fennell & Anne H. O’Donnell-Luria & James S. Ware & Andrew J. Hill & Beryl B. Cummings & Taru Tukiainen , 2016. "Analysis of protein-coding genetic variation in 60,706 humans," Nature, Nature, vol. 536(7616), pages 285-291, August.
    2. Rameen Beroukhim & Ming Lin & Yuhyun Park & Ke Hao & Xiaojun Zhao & Levi A Garraway & Edward A Fox & Ephraim P Hochberg & Ingo K Mellinghoff & Matthias D Hofer & Aurelien Descazeaud & Mark A Rubin & M, 2006. "Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-10, May.
    3. Francesco Maura & Andrea Degasperi & Ferran Nadeu & Daniel Leongamornlert & Helen Davies & Luiza Moore & Romina Royo & Bachisio Ziccheddu & Xose S. Puente & Herve Avet-Loiseau & Peter J. Campbell & Se, 2019. "Author Correction: A practical guide for mutational signature analysis in hematological malignancies," Nature Communications, Nature, vol. 10(1), pages 1-1, December.
    4. S. Kasar & J. Kim & R. Improgo & G. Tiao & P. Polak & N. Haradhvala & M. S. Lawrence & A. Kiezun & S. M. Fernandes & S. Bahl & C. Sougnez & S. Gabriel & E. S. Lander & H. T. Kim & G. Getz & J. R. Brow, 2015. "Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution," Nature Communications, Nature, vol. 6(1), pages 1-12, December.
    5. Francesco Maura & Andrea Degasperi & Ferran Nadeu & Daniel Leongamornlert & Helen Davies & Luiza Moore & Romina Royo & Bachisio Ziccheddu & Xose S. Puente & Herve Avet-Loiseau & Peter J. Campbell & Se, 2019. "A practical guide for mutational signature analysis in hematological malignancies," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    6. Ludmil B. Alexandrov & Jaegil Kim & Nicholas J. Haradhvala & Mi Ni Huang & Alvin Wei Tian Ng & Yang Wu & Arnoud Boot & Kyle R. Covington & Dmitry A. Gordenin & Erik N. Bergstrom & S. M. Ashiqul Islam , 2020. "The repertoire of mutational signatures in human cancer," Nature, Nature, vol. 578(7793), pages 94-101, February.
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