Cell-free DNA from nail clippings as source of normal control for genomic studies in hematologic malignancies.

Abstract

Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patient management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs. In contrast to solid tumors, conventional sources of normal control (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we find nail cfDNA is a robust source of germline control for paired genomic studies. In a subset of patients, nail DNA may have tumor DNA contamination, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1482) compared to lymphoid diseases (5.4%; 61/1128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. For nails collected after allogeneic stem-cell transplantation, donor DNA was identified in 22% (11/50). In this cohort, an association with recent history of graft-vs-host disease was identified. These findings should be considered as a potential limitation for the use of nail as normal control but could also provide important diagnostic information regarding the disease process.

• Authors: Melissa Krystel-Whittemore, Kseniya Petrova-Drus, Ryan N Ptashkin, Mark D Ewalt, JinJuan Yao, Ying Liu, Menglei Zhu, Jamal Benhamida, Benjamin Durham, Jyoti Kumar, Khedoudja Nafa, Iwona Kiecka, Anita S Bowman, Erika Gedvilaite, Jacklyn Casanova, Yun-Te Lin, Abhinita S Mohanty, Satshil Rana, Anoop Balakrishnan Rema, Ivelise Rijo, Nelio Chaves, Paulo Salazar, Anita Yun, Sean Lachhander, Wei Wang, Mohammad S Haque, Wenbin Xiao, Mikhail Roshal, Sergio Giralt, Gilles Salles, Raajit Rampal, Eytan M Stein, Miguel-Angel Perales, Steven Horwitz, Ann Jakubowski, Doris Ponce, Alina Markova, Ozge Birsoy, Diana Mandelker, Simon Mantha, Ahmet Dogan, Ryma Benayed, Marc Ladanyi, Michael F Berger, A Rose Brannon, Ahmet Zehir, Chad Vanderbilt, Maria E Arcila
• Journal: Haematologica (Haematologica) (Mar 07 2024) ISSN: 1592-8721 [Electronic] Italy
• PMID: 38450530 (Publication Type: Journal Article)