These authors contributed equally: Shinju Iyoda, Kenichi Yoshida, Kota Shoji.

Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan

Shinju Iyoda, Kota Shoji, Nana Ito, Miu Tanaka, Momoko Nishikori, Souichi Adachi & Hidemasa Matsuo

Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan

Kenichi Yoshida, Yasuhito Nannya & Seishi Ogawa

Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan

Kenichi Yoshida

Division of Hematopoietic Disease Control, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

Yasuhito Nannya

Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan

Genki Yamato

Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan

Shinichi Tsujimoto & Norio Shiba

Institute of Physiology and Medicine, Jobu University, Takasaki, Japan

Yasuhide Hayashi

Laboratory of Molecular Analysis, Nippon Medical School, Tokyo, Japan

Yusuke Shiozawa

Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan

Yuichi Shiraishi, Kenichi Chiba & Ai Okada

Department of Integrated Analytics, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan

Hiroko Tanaka & Satoru Miyano

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan

Yuhki Koga

Division of Hematology/Oncology, Kanagawa Children’s Medical Center, Yokohama, Japan

Hiroaki Goto

Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan

Hiroshi Moritake

Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan

Kiminori Terui & Etsuro Ito

Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan

Nobutaka Kiyokawa

Division of Leukemia and Lymphoma, Children’s Cancer Center, National Center for Child Health and Development, Tokyo, Japan

Daisuke Tomizawa

Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan

Takashi Taga

Department of Pediatrics, Higashiosaka Aramoto Heiwa Clinic, Higashiosaka, Japan

Akio Tawa

Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan

Junko Takita

Shiga General Hospital, Moriyama, Japan

Souichi Adachi

Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan

Hidemasa Matsuo

SI, KY, KS, and H Matsuo analyzed the clinical and sequencing data; NI and MT helped with the analysis; YN, GY, ST, NS, and YH performed sequencing; Y Shiozawa, Y Shiraishi, KC, AO, HT, and SM developed sequence data processing pipelines; YK, HG, H Moritake, KT, EI, NK, DT, TT, AT, JT, and SA collected clinical samples; KY, MN, SA, SO, and H Matsuo supervised the project. SI, KY, KS, and H Matsuo wrote the manuscript.