Whole Exome Sequencing of Chronic Lymphocytic Leukemia

Description: Summary from the dbGaP: "The somatic genetic basis of chronic lymphocytic leukemia (CLL), a common and clinically heterogenous adult leukemia, remains poorly understood. Massively parallel sequencing technology now provides a method for systematic discovery of genetic alterations that underlie disease, and for uncovering new therapeutic targets and biomarkers. We present a dataset consisting of DNA sequencing from 169 CLL samples (with matched germline controls). Samples were collected from patients displaying a wide range of characteristics representing the broad clinical spectrum of CLL.

Understanding the mutational landscape of CLL provides a starting point for systematic analyses to address fundamental questions in CLL, including how mutated genes alter cellular networks and phenotypes, and thereby contribute to disease heterogeneity."

Note: This version of the study has been superseded.

Subject of Study

Homo sapiens

Subject(s)

Leukemia, Lymphocytic, Chronic, B-Cell

OncoTree Cancer Type(s)

Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma
Lymphoid Neoplasm

Access via dbGaP
BAM and SRA files of whole exome sequencing
Accession #: phs000435.v2.p1
Access Restrictions: Application Required
Access Instructions: Full access to this dataset in dbGaP requires authorization through an Authorized Access Portal which can be requested for either 'data download' or 'view only'. Individual level data download requires a project request. With dbGaP DataBrowser approval, users may view the compilation of individual-level data of general research use. Upon approval, data can be downloaded.

A full list of and information about the SRA runs, BioSamples, and experiments is publicly viewable by going to the 'Molecular Datasets' tab and clicking on 'RunSelector' at the bottom of the page. This will take you to the NCBI SRA Run Selector platform. View and download of the datasets themselves, however, still requires authorization through dbGaP.

Publicly available data such as data dictionaries, variable summaries, documents and truncated analysis are available the public download site FTP link
Associated Publications: Pastore A, Gaiti F, Lu S, et al. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nature Communications. 2019; 10:1874.

Wang L, Lawrence MS, Wan Y, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 2011;365(26):2497-2506.

Landau DA, Carter SL, Stojanov P, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell. 2013;152(4):714-726.
Data Type: Genomic
Equipment Used: Illumina Genome Analyzer

Illumina HiSeq 2000
High throughput gene sequencing system

Illumina HiSeq 2500
High throughput sequencing system

Illumina MiSeq
The MiSeq is an integrated instrument that performs clonal amplification, genomic DNA sequencing, and data analysis with base calling, alignment, variant calling, and reporting in a single run.
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): SRA, BAM, CONTIGS
Data Tool(s): RNA Seq

WXS

WGS

Bisulfite-Seq
Dataset Size: 3.73 TB

Data Catalog Record Updated: 2021-06-24