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Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

posted on 2023-06-16, 14:17 authored by Fatemah RezayeeFatemah Rezayee, Jesper Eisfeldt, Aron skafteson, Ingegerd Öfverholm, Shumaila SayyabShumaila Sayyab, Ann-Christine Syvänen, khurram Maqbool, Henrik LilljebjörnHenrik Lilljebjörn, Bertil Johansson, Linda Olsson-Arvidsson, Christina Orsmark-Pietras, Anna Staffas, Lars Palmqvist, Thoas Fioretos, Lucia Cavelier, Linda Fogelstrand, Jessica Nordlund, Valtteri Wirta, Richard Rosenquist BrandellRichard Rosenquist Brandell, Gisela Barbany


Data from a study of 88 cases with B cell precursor acute lymphoblastic leukemia. Whole genome sequencing was performed in all cases with the aim of identifying genomic aberrations. The study was approved by the Ethical Review Board at Stockholm County and written informed consent was obtained from the patients’ guardians.

The data consists of BAM/cram files from whole genome sequencing (WGS) of diagnostic bone marrow and remission samples (Normal). Leukemia and remission samples were sequenced with a coverage of 90x and 30x respectively on Illumina HiSeq X or NovaSeq 6000 instruments. The annotation was performed by applying FindSV which merges variant caller CNVnator and TIDDIT or Manta, Delly and TIDDIT (in BALSAMIC version 10.0.5). Subsequently variant effect predictor was applied. For filtering of recurrent normal variants, Swegene and locusDB (in BALSAMIC). Furthermore, to narrow down the variants list, a list of diagnostic relevant gene/coordinate list were applied. The variants were then manually analyzed by using IGV, vcf2cytosure and ASCAT tools.


Data Access Statement

The WGS datasets are only to be used for research aimed at advancing the understanding of genetic factors in the development of pediatric acute lymphoblastic leukemia. Applications, including those aimed at method development and bioinformatics, would only be considered as acceptable if proof of approved ethical consent is provided. Access requests should be sent to the email address below. 


Science for Life Laboratory Swedish Genomes Program

Knut and Alice Wallenberg Foundation

Swedish Childhood Cancer Fund

Swedish Research Council



Karolinska Institutet

Access request email