Number of patients:

Non-random distribution:
Subgroups:

Group 'other' involves fusions via:
ABL1 inversion
BCR or ABL1 duplication or
third partner

Difference in breakpoint sites distribution (ks test):
blunt-end vs. short homology
Choose the area to be shown in detail (using mouse) on left plot

BCR::ABL1

ABL1::BCR

From following plots are excluded data about features founded in individual cases
From following plots are excluded data about features founded in individual cases

BCR::ABL1

ABL1::BCR

Negative values represents deletions, positive values represents duplications
Zero represents balanced translocation

select and doubleclick to zoom the plot

Negative values represents deletions, positive values represents duplications
Zero represents balanced translocation
Due to different scaling, the plots are divided into 2 and 3 parts, respectively
Distance in between forw and rev breakpoint position on chromosome 22
Distance in between forw and rev breakpoint position on chromosome 9
select motif(s)
Number of patients:

Non-random distribution:
Subgroups:

Group 'other' invloves fusion partners as follows:
AF1Q (17 cases)
EPS15 (15 cases)
PTD (65 cases)
and 58 more fusion partners in 114 cases

Difference in breakpoint sites distribution (ks test):
AF4 vs. ENL
select motif(s)
The alignment was done against GRCh38 reference primary assembly human genome.

BCR::ABL1 rearrangements

The BCR::ABL1 rearrangements data were obtained from laboratories in:

Czech Republic

CLIP, Second Faculty of Medicine, Charles University Prague - Jan Zuna, Lenka Hovorkova, Marketa Zaliova, Lucie Winkowska, Justina Krotka - childhood ALL and CML;

IHBT, Prague - Cyril Salek, Katerina Machova - adult ALL and CML

Germany

University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Kiel - Gunnar Cario - childhood ALL;

Department of Pediatrics, University Hospital Erlangen, Erlangen - Markus Metzler, Manuela Krumbholz - childhood CML

Australia

Molecular Diagnostics, Children's Cancer Institute, Sydney - Rosemary Sutton, Nicola C Venn

Italy

Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza - Giovanni Cazzaniga, Michela Bardini - childhood ALL

France

Hematology Laboratory, Saint-Louis Hospital and Saint-Louis Research Institute, Université de Paris, Paris - Emmanuelle Clappier, Rathana Kim - adult ALL

KMT2A rearrangements

The KMT2A rearrangements data were obtained by courtesy of Claus Meyer and Rolf Marschalek , Diagnostic Center of Acute Leucemia (DCAL), Institute of Pharmaceutical Biology, Goethe University Frankfurt, Germany.

DNA motifs search

MEME

Bailey TL, Boden M, Buske FA, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202-W208. PMID:19458158;

https://meme-suite.org

Repeatmasker

Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0. 2013-2015

http://www.repeatmasker.org


Tandem Repeats Finder

Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27(2):573-80 PMID:9862982;

https://tandem.bu.edu/trf/trf.html

RSS database

Merelli I, Guffanti A, Fabbri M, et al. RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. Nucleic Acids Res. 2010;38(Web Server issue):W262-W267. PMID:20478831

https://www.itb.cnr.it/rss/index.html

Motif sequences adopted from:

Ross DM, O'Hely M, Bartley PA, et al. Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients. Leukemia. 2013;27(10):2105-2107

PMID:23588714

Epigenetic data

Luo Y, Hitz BC, Gabdank I, Hilton JA et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res 2020 Jan 8;48(D1):D882-D889 PMID: 31713622

ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74 PMID:22955616

Bujold et al. The International Human Epigenome Consortium Data Portal. Cell Systems 3.5 (2016): 496-499.

Corces MR, Buenrostro JD, Wu B, Greenside PG et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet 2016 Oct;48(10):1193-203. PMID:27526324


Satpathy AT, Granja JM, Yost KE, Qi Y et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 2019 Aug;37(8):925-936. PMID:31375813


Takayama N, Murison A, Takayanagi SI, et al. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell. 2021;28(3):488-501.e10. PMID:33242413.