Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study - 01/12/15

Doi : 10.1016/S1470-2045(15)00369-1

Takaya Moriyama, MD ^a,^g,^{^{†
Contributed equally}}, Monika L Metzger, MD ^b,^{^{†
Contributed equally}}, Gang Wu, PhD ^c,^{^{†
Contributed equally}}, Rina Nishii, MS ^a,^h, Maoxiang Qian, PhD ^a, Meenakshi Devidas, PhD ⁱ, Wenjian Yang, PhD ^a, Cheng Cheng, ProfPhD ^d, Xueyuan Cao, PhD ^d, Emily Quinn, MS ^b, Susana Raimondi, ProfPhD ^e, Julie M Gastier-Foster, ProfPhD ^j, Elizabeth Raetz, ProfMD ^l, Eric Larsen, MD ^m, Paul L Martin, MD ⁿ, W Paul Bowman, MD ^o, Naomi Winick, ProfMD ^p, Yoshihiro Komada, ProfMD ^g, Shuoguo Wang, PhD ^c, Michael Edmonson, BA ^c, Heng Xu, PhD ^q, Elaine Mardis, ProfPhD ^r, Robert Fulton, MS ^r, Ching-Hon Pui, ProfMD ^b,^e,^f, Charles Mullighan, ProfMBBS ^e,^f, William E Evans, ProfPharmD ^a,^f, Jinghui Zhang, ProfPhD ^c, Stephen P Hunger, ProfMD ^s, Mary V Relling, ProfPharmD ^a,^f, Kim E Nichols, ProfMD ^b, Mignon L Loh, ProfMD ^t, Jun J Yang, DrPhD ^a,^f,^⁎
^a Department of Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
^b Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
^c Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, TN, USA
^d Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, TN, USA
^e Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
^f Hematological Malignancies Program, Comprehensive Cancer Center, St Jude Children’s Research Hospital, Memphis, TN, USA
^g Department of Pediatrics, Mie University Graduate School of Medicine, Mie, Japan
^h Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
ⁱ Department of Biostatistics, College of Medicine, Public Health and Health Professions, University of Florida, Gainesville, FL, USA
^j Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, and Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH, USA
^l Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
^m Maine Children’s Cancer Program, Scarborough, ME, USA
ⁿ Department of Pediatrics, Duke University, Durham, NC, USA
^o Cook Children’s Medical Center, Fort Worth, TX, USA
^p Pediatric Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
^q Department of Laboratory Medicine, National Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
^r McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
^s Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
^t Department of Pediatrics, Benioff Children’s Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA

^*Correspondence to: Dr Jun J Yang, Hematologic Malignancies Program, Pharmaceutical Sciences, St Jude Children’s Research Hospital, MS313, 262 Danny Thomas Place Memphis, TN 38105-3678, USACorrespondence to: Dr Jun J YangHematologic Malignancies ProgramPharmaceutical SciencesSt Jude Children’s Research HospitalMS313262 Danny Thomas Place MemphisTN38105-3678USA

Summary

Background

Hereditary predisposition is rarely suspected for childhood acute lymphoblastic leukaemia (ALL). Recent reports of germline ETV6 variations associated with substantial familial clustering of haematological malignancies indicated that this gene is a potentially important genetic determinant for ALL susceptibility. Our aims in this study were to comprehensively identify ALL predisposition variants in ETV6 and to determine the extent to which they contributed to the overall risk of childhood ALL.

Methods

Whole-exome sequencing of an index family with several cases of ALL was done to identify causal variants for ALL predisposition. Targeted sequencing of ETV6 was done in children from the Children’s Oncology Group and St Jude Children’s Research Hospital front-line ALL trials. Patients were included in this study on the basis of their enrolment in these clinical trials and the availability of germline DNA. ETV6 variant genotypes were compared with non-ALL controls to define ALL-related germline risk variants. ETV6 variant function was characterised bioinformatically and correlated with clinical and demographic features in children with ALL.

Findings

We identified a novel non-sense ETV6 variant (p.Arg359X) with a high penetrance in an index family. Subsequent targeted sequencing of ETV6 in 4405 childhood ALL cases identified 31 exonic variants (four non-sense, 21 missense, one splice site, and five frameshift variants) that were potentially related to ALL risk in 35 cases (1%). 15 (48%) of 31 ALL-related ETV6 variants clustered in the erythroblast transformation specific domain and were predicted to be highly deleterious. Children with ALL-related ETV6 variants were significantly older at leukaemia diagnosis than those without (10·2 years [IQR 5·3–13·8] vs 4·7 years [3·0–8·7]; p=0·017). The hyperdiploid leukaemia karyotype was highly over-represented in ALL cases harbouring germline ETV6 risk variants compared with the wild-type group (nine [64%] of 14 cases vs 538 [27%] of 2007 cases; p=0·0050).

Interpretation

Our findings indicated germline ETV6 variations as the basis of a novel genetic syndrome associated with predisposition to childhood ALL. The development of recommendations for clinical interventions and surveillance for individuals harbouring ALL-related ETV6 variants are needed.

Funding

US National Institutes of Health and American Lebanese Syrian Associated Charities.

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Vol 16 - N° 16

P. 1659-1666 - décembre 2015 Retour au numéro

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Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study - 01/12/15

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