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

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.

本数据集来源于对88例B细胞前体急性淋巴细胞白血病的研究，旨在通过全基因组测序（WGS）识别基因组变异。研究已获得斯德哥尔摩郡伦理审查委员会的批准，并从患者监护人处获得书面知情同意。数据包括诊断性骨髓和缓解样本（正常）的全基因组测序（WGS）的BAM/cram文件。白血病和缓解样本分别采用Illumina HiSeq X或NovaSeq 6000仪器进行90x和30x的测序覆盖率。注释是通过应用FindSV实现的，该工具整合了CNVnator和TIDDIT或Manta、Delly和TIDDIT（在BALSAMIC版本10.0.5中）。随后，应用了变异效应预测器。为了过滤重复的正常变异，使用了Swegene和locusDB（在BALSAMIC中）。此外，为了缩小变异列表，还应用了一组诊断相关基因/坐标列表。随后，通过使用IGV、vcf2cytosure和ASCAT工具对变异进行了手动分析。

数据访问声明：全基因组测序数据集仅限于用于旨在推进对儿童急性淋巴细胞白血病发展中的遗传因素理解的研究。包括旨在开发方法和生物信息学在内的应用，只有在提供已批准的伦理同意证明的情况下才被视为可接受。访问请求应发送至以下电子邮件地址。