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WGS for patient specific MRD in pediatric ALL

posted on 2022-05-02, 13:02 authored by Cecilia ArthurCecilia Arthur, Fatemah Rezayee, Nina Mogensen, Leonie Saft, Richard Rosenquist BrandellRichard Rosenquist Brandell, Magnus Nordenskjöld, Arja Harila-Saari, Emma Tham, Gisela Barbany

Data from a study of six children with acute lymphoblastic leukemia (four patients with precursor B-cell ALL (Acute lymphoblastic leukemia) and two patients with T-cell ALL). None had stratifying genetics or central nervous system involvement. The study was approved by the Ethical Review Board at Stockholm County and written informed consent was obtained from the patients’ guardians.

The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic bone marrow samples (30X coverage on an Illumina HiSeqX Ten platform). The Human GRCh37 (hg19) RefSeq was used for annotation and SV detection was performed using CNVnator V0.3.2 with 1kb bins, Delly, TIDDIT V2.0.0 and Manta. Filtering was performed using a list of recurrent aberrations in ALL. Assays for measurable residual disease (MRD) monitoring were designed from SV sequences and used for ddPCR analysis of gDNA and cfDNA from bone marrow, plasma and cerebrospinal fluid samples from diagnosis and follow-up.

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 adress below. 



Karolinska Institutet

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