A dedicated caller for DUX4 rearrangements from whole-genome sequencing data

被引：0

作者：

Grobecker, Pascal ^{[1
]}

Berri, Stefano ^{[1
]}

Peden, John F. ^{[2
]}

Chow, Kai-Jie ^{[1
]}

Fielding, Claire ^{[1
]}

Armogida, Ivana ^{[1
]}

Northen, Helen ^{[1
]}

Mcbride, David J. ^{[1
]}

Campbell, Peter J. ^{[1
]}

Becq, Jennifer ^{[1
]}

Ryan, Sarra L. ^{[3
]}

Bentley, David R. ^{[1
]}

Harrison, Christine J. ^{[3
]}

Moorman, Anthony V. ^{[3
]}

Ross, Mark T. ^{[1
]}

Mijuskovic, Martina ^{[1
]}

机构：

[1] Illumina Cambridge Ltd, Granta Pk, Cambridge, England

[2] Genpax Ltd, Off 4 05,53,64 Chancery Ln, London, England

[3] Newcastle Univ, Translat & Clin Res Inst, Fac Med Sci, Leukaemia Res Cytogenet Grp,Ctr Canc, Newcastle Upon Tyne, England

来源：

BMC MEDICAL GENOMICS | 2025年 / 18卷 / 01期

关键词：

<italic>DUX4</italic>; Acute lymphoblastic leukaemia; ALL; Whole-genome sequencing; <italic>IGH</italic>:<italic>DUX4</italic>; <italic>IGH</italic> enhancer hijacking; ACUTE LYMPHOBLASTIC-LEUKEMIA; CLASSIFICATION; RECOMBINATION; SARCOMAS; GENES;

D O I：

10.1186/s12920-024-02069-1

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Rearrangements involving the DUX4 gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no 'standard of care' diagnostic method for their confident identification. Here, we present an open-source software tool designed to detect DUX4-r from short-read, whole-genome sequencing (WGS) data. Evaluation on a cohort of 210 paediatric ALL cases showed that our method detects all known, as well as previously unidentified, cases of IGH::DUX4 and rearrangements with other partner genes. These findings demonstrate the possibility of robustly detecting DUX4-r using WGS in the routine clinical setting.

引用

页数：11

共 34 条

[1] Sarcomas With CIC-rearrangements Are a Distinct Pathologic Entity With Aggressive Outcome: A Clinicopathologic and Molecular Study of 115 Cases [J].

Antonescu, Cristina R. ;

Owosho, Adepitan A. ;

Zhang, Lei ;

Chen, Sonja ;

Deniz, Kemal ;

Huryn, Joseph M. ;

Kao, Yu-Chien ;

Huang, Shih-Chiang ;

Singer, Samuel ;

Tap, William ;

Schaefer, Inga-Marie ;

Fletcher, Christopher D. .

AMERICAN JOURNAL OF SURGICAL PATHOLOGY, 2017, 41 (07) :941-949

[2] HTSlib: C library for reading/writing high-throughput sequencing data [J].

Bonfield, James K. ;

Marshall, John ;

Danecek, Petr ;

Li, Heng ;

Ohan, Valeriu ;

Whitwham, Andrew ;

Keane, Thomas ;

Davies, Robert M. .

GIGASCIENCE, 2021, 10 (02)

[3] DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes [J].

Choi, Si Ho ;

Gearhart, Micah D. ;

Cui, Ziyou ;

Bosnakovski, Darko ;

Kim, Minjee ;

Schennum, Natalie ;

Kyba, Michael .

NUCLEIC ACIDS RESEARCH, 2016, 44 (11) :5161-5173

[4] PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia [J].

Gu, Zhaohui ;

Churchman, Michelle L. ;

Roberts, Kathryn G. ;

Moore, Ian ;

Zhou, Xin ;

Nakitandwe, Joy ;

Hagiwara, Kohei ;

Pelletier, Stephane ;

Gingras, Sebastien ;

Berns, Hartmut ;

Payne-Turner, Debbie ;

Hill, Ashley ;

Iacobucci, Ilaria ;

Shi, Lei ;

Pounds, Stanley ;

Cheng, Cheng ;

Pei, Deqing ;

Qu, Chunxu ;

Newman, Scott ;

Devidas, Meenakshi ;

Dai, Yunfeng ;

Reshmi, Shalini C. ;

Gastier-Foster, Julie ;

Raetz, Elizabeth A. ;

Borowitz, Michael J. ;

Wood, Brent L. ;

Carroll, William L. ;

Zweidler-McKay, Patrick A. ;

Rabin, Karen R. ;

Mattano, Leonard A. ;

Maloney, Kelly W. ;

Rambaldi, Alessandro ;

Spinelli, Orietta ;

Radich, Jerald P. ;

Minden, Mark D. ;

Rowe, Jacob M. ;

Luger, Selina ;

Litzow, Mark R. ;

Tallman, Martin S. ;

Racevskis, Janis ;

Zhang, Yanming ;

Bhatia, Ravi ;

Kohlschmidt, Jessica ;

Mrozek, Krzysztof ;

Bloomfield, Clara D. ;

Stock, Wendy ;

Kornblau, Steven ;

Kantarjian, Hagop M. ;

Konopleva, Marina ;

Evans, Williams E. .

NATURE GENETICS, 2019, 51 (02) :296-+

[5] Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome [J].

Harvey, Richard C. ;

Mullighan, Charles G. ;

Wang, Xuefei ;

Dobbin, Kevin K. ;

Davidson, George S. ;

Bedrick, Edward J. ;

Chen, I-Ming ;

Atlas, Susan R. ;

Kang, Huining ;

Ar, Kerem ;

Wilson, Carla S. ;

Wharton, Walker ;

Murphy, Maurice ;

Devidas, Meenakshi ;

Carroll, Andrew J. ;

Borowitz, Michael J. ;

Bowman, W. Paul ;

Downing, James R. ;

Relling, Mary ;

Yang, Jun ;

Bhojwani, Deepa ;

Carroll, William L. ;

Camitta, Bruce ;

Reaman, Gregory H. ;

Smith, Malcolm ;

Hunger, Stephen P. ;

Willman, Cheryl L. .

BLOOD, 2010, 116 (23) :4874-4884

[6] Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons [J].

Hendrickson, Peter G. ;

Dorais, Jessie A. ;

Grow, Edward J. ;

Whiddon, Jennifer L. ;

Lim, Jong-Won ;

Wike, Candice L. ;

Weaver, Bradley D. ;

Pflueger, Christian ;

Emery, Benjamin R. ;

Wilcox, Aaron L. ;

Nix, David A. ;

Peterson, C. Matthew ;

Tapscott, Stephen J. ;

Carrell, Douglas T. ;

Cairns, Bradley R. .

NATURE GENETICS, 2017, 49 (06) :925-+

[7] Fusion between CIC and DUX4 up-regulates PEA3 family genes in Ewing-like sarcomas with t(4;19)(q35;q13) translocation [J].

Kawamura-Saito, Miho ;

Yamazaki, Yukari ;

Kaneko, Keiko ;

Kawaguchi, Noriyoshi ;

Kanda, Hiroaki ;

Mukai, Hiroyuki ;

Gotoh, Takahiro ;

Motoi, Tohru ;

Fukayama, Masashi ;

Aburatani, Hiroyuki ;

Takizawa, Toichiro ;

Nakamura, Takuro .

HUMAN MOLECULAR GENETICS, 2006, 15 (13) :2125-2137

[8] BLAT - The BLAST-like alignment tool [J].

Kent, WJ .

GENOME RESEARCH, 2002, 12 (04) :656-664

[9] Enhancements and modifications of primer design program Primer3 [J].

Koressaar, Triinu ;

Remm, Maido .

BIOINFORMATICS, 2007, 23 (10) :1289-1291

[10] Primer3_masker: integrating masking of template sequence with primer design software [J].

Koressaar, Triinu ;

Lepamets, Maarja ;

Kaplinski, Lauris ;

Raime, Kairi ;

Andreson, Reidar ;

Remm, Maido .

BIOINFORMATICS, 2018, 34 (11) :1937-1938

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