Targeted capture, whole genome sequencing, and RNAseq to identify rearrangements in B-cell lymphomas

This study contains whole genome and custom targeted capture sequencing of mature B-cell lymphomas (DLBCL, FL, BL, HGBCL-DH-BCL2, HGBCL-DH-BCL6) to identify translocation breakpoints of common oncogene rearrangements (MYC, BCL2, BCL6). It is complemented by RNAseq data where available. Complete details are available in the publication Hilton et al, 2024, Blood. Capture sequencing: 357 samples; 364 unique libraries; cram file format aligned to hg38 Whole genome sequencing: 12 samples; 12 unique libraries; cram file format aligned to grch37 RNAseq: 257 samples; 257 unique libraries; fastq file format

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets 2 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000474	Whole genome sequencing (WGS) data of 12 tumours was generated on an Illumina NovaSeq or HiSeqX instrument. For frozen samples, libraries were constructed using a PCR-free library construction method. For tumours preserved by formalin fixation and paraffin embedding (FFPE), libraries were constructed with a method that included S1 nuclease treatment. Reads were aligned to the grch37 reference with bwa-mem 0.7.17.	Illumina NovaSeq X	12
EGAD50000000489	Targeted capture sequencing of 364 samples representing a mix of Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and high-grade B-cell lymphomas with MYC and BCL2 or BCL6 rearrangements. Capture space covers 3.5 Mb of the human genome including regions around MYC, BCL2, BCL6, PAX5, and IGH/K/L.	Illumina HiSeq X	364
EGAD50000000496	Paired-end ribodepletion RNAseq performed on 257 samples of Burkitt lymphoma, diffuse large B cell lymphoma, follicular lymphoma, and high-grade B cell lymphoma with MYC and BCL2 or BCL6 rearrangements. RNA was derived from either fresh frozen or formalin fixed/paraffin embedded (FFPE) tissues. Sequencing was performed on Illumina HiSeqX or NovaSeqX instruments.	Illumina NovaSeq X	257

Publications	Citations
High-resolution architecture and partner genes of <i>MYC</i> rearrangements in lymphoma with DLBCL morphology. Chong LC, Ben-Neriah S, Slack GW, Freeman C, Ennishi D, Mottok A, Collinge B, Abrisqueta P, Farinha P, Boyle M, Meissner B, Kridel R, Gerrie AS, Villa D, Savage KJ, Sehn LH, Siebert R, Morin RD, Gascoyne RD, Marra MA, Connors JM, Mungall AJ, Steidl C, Scott DW. Blood Adv 2: 2018 2755-2765	45
Motive and Opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC and BCL2 rearrangements-an LLMPP study. Hilton LK, Collinge B, Ben-Neriah S, Alduaij W, Shaalan H, Weng AP, Cruz M, Slack GW, Farinha P, Miyata-Takata T, Boyle M, Meissner B, Cook JR, Ondrejka SL, Ott G, Rosenwald A, Campo E, Amador C, Greiner TC, Raess PW, Song JY, Inghirami G, Jaffe ES, Weisenburger DD, Chan WC, Beiske K, Fu K, Delabie J, Pittaluga S, Iqbal J, Wright G, Sehn LH, Savage KJ, Mungall AJ, Feldman AL, Staudt LM, Steidl C, Rimsza LM, Morin RD, Scott DW. Blood 144: 2024 525-540	2

Publications

Citations

High-resolution architecture and partner genes of <i>MYC</i> rearrangements in lymphoma with DLBCL morphology.
Chong LC, Ben-Neriah S, Slack GW, Freeman C, Ennishi D, Mottok A, Collinge B, Abrisqueta P, Farinha P, Boyle M, Meissner B, Kridel R, Gerrie AS, Villa D, Savage KJ, Sehn LH, Siebert R, Morin RD, Gascoyne RD, Marra MA, Connors JM, Mungall AJ, Steidl C, Scott DW. Blood Adv 2: 2018 2755-2765

Motive and Opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC and BCL2 rearrangements-an LLMPP study.
Hilton LK, Collinge B, Ben-Neriah S, Alduaij W, Shaalan H, Weng AP, Cruz M, Slack GW, Farinha P, Miyata-Takata T, Boyle M, Meissner B, Cook JR, Ondrejka SL, Ott G, Rosenwald A, Campo E, Amador C, Greiner TC, Raess PW, Song JY, Inghirami G, Jaffe ES, Weisenburger DD, Chan WC, Beiske K, Fu K, Delabie J, Pittaluga S, Iqbal J, Wright G, Sehn LH, Savage KJ, Mungall AJ, Feldman AL, Staudt LM, Steidl C, Rimsza LM, Morin RD, Scott DW. Blood 144: 2024 525-540