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Whole-genome sequencing in B-cell lymphomas for circulating tumor DNA analysis by multiplex digital PCR for disease monitoring

posted on 2023-05-12, 13:55 authored by Zahra HaiderZahra Haider, Tove Wästerlid, Linn Deleskog Spångberg, Leily RabbaniLeily Rabbani, Cecilia Jyhlä, Birna Thorvaldsdottir, Aron Skaftason, Hero Nikdin Awier, Aleksandra Krstic, Anna Gellerbring, Anna Lyander, Moa Hägglund, Ashwini Jeggari, Georgios Rassidakis, Kristina Sonnevi, Birgitta Sander, Richard Rosenquist BrandellRichard Rosenquist Brandell, Emma ThamEmma Tham, Karin Ekström Smedby

WGS data of paired tumor and normal samples in 9 patients (6 diffuse large B-cell lymphomas, 1 transformed follicular lymphoma and 2 follicular lymphoma) with a median depth of 37X (range: 27-50X). 

The study was approved by the Stockholm Regional Ethical committee (2017/2538-31) and conducted in accordance with the Declaration of Helsinki. Written informed consent  was obtained from the patients. 

The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic fresh frozen lymph node biopsies and matching whole blood for germline analysis. Sequencing was performed on a NovaSeq 6000 system (Illumina) using paired-end 150 bp readout, aiming at 300 M paired reads.  Pre-processing of raw FASTQ files and variant calling was performed by Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (BALSAMIC) version 10.0.2.

Data Access Statement

The WGS dataset are only to be used for academic research purposes at advancing the understanding of genetic factors in the pathogenesis of B-cell lymphomas. 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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