Sequencing Lymphoma

This repository contains sequencing data to describe the genomic profiles of several B-cell lymphomas including follicular lymphoma and Hodgkin lymphoma. We have used several different high throughput sequencing technologies to interrogate genomic DNA and RNA from tumor cells obtained from lymph node biopsies and normal cells obtained from skin biopsies and peripheral blood mononuclear cells.

A number of sequencing platforms for DNA, RNA, and protein were used to generate the data. These platforms include exome sequencing and a custom capture panel (NimbleGen) that targets 7.05 MB corresponding to the exons and splice sites of 1716 genes related to lymphoma biology (WUSM-LP). Other platforms include single-cell RNA-seq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), which was used to describe transcriptional and proteomic changes in immune cell subsets within lymphoma patients pre- and post-therapy. ]]>
For exome sequenced samples, all patients provided written informed consent for the use of their samples in sequencing as part of the Washington University School of Medicine (WUSM) Lymphoma Banking Program. This includes the follicular and Hodgkin lymphoma patients. For scRNA-seq/CITE-seq data, all patients provided written informed consent for the use of their samples in sequencing as part of WUSM Lymphoma Banking Program and were enrolled on NCT02384954.

For the exome sequencing, all patients with adequate excisional biopsy tissue available from 2008-2013 (follicular lymphoma patients) and 2008-2016 (Hodgkin lymphoma patients) were included. Non-malignant samples were also collected (skin punch biopsies). Pathology review was performed on frozen lymph node samples to confirm the diagnosis and estimate tumor cell content. Frozen sections (tumor and skin) were cut and used for genomic DNA isolation.
For follicular lymphoma cases that were flow sorted, CD19+ and light chain restricted B cells were purified (>98% pure) using a Reflection instrument. For additional capture sequencing, a cohort of follicular lymphoma patients was identified from those evaluated at WUSM/Siteman Cancer Center from 2001-2013. Patients were included if Formalin-Fixed Paraffin-Embedded (FFPE) blocks from an excisional biopsy and clinical information regarding initial treatment and follow-up were available. All FFPE tissues were reviewed to confirm the pathology diagnosis and marked for block punches in confirmed tumor-containing areas. ]]>