Towards a Genomic Understanding of Myeloma

UID: 10663

Publisher(s): Multiple Myeloma Research Foundation

Description: Study Description from dbGaP: "This project was designed to describe genetic abnormalities in primary samples from patients with multiple myeloma by next generation sequencing.

We generated sequence data from multiple myeloma (MM) patients analyzing DNA both from tumor cells (purified from bone marrow using CD138 selection as a marker of plasma cells) and from normal peripheral blood cells (either whole blood or Ficoll-purified mononuclear cells). Using massively parallel sequencing technology (Illumina GA-2 or HiSeq)), we performed whole-genome sequencing (WGS) and/or whole-exome sequencing (WES). The initial set currently deposited contains data from 38 MM patients (23 patients surveyed by WGS and 16 patients by WES, with one patient analyzed by both approaches).

Genomes were sampled to high depth, obtaining an average of 33X coverage and 104X coverage for WGS and WES tumors, respectively. The normal samples had similar coverage. Our goal is to help researchers understand the complex genetic landscape of multiple myeloma and provide a resource for the generation of biological hypotheses."

The dataset includes WGS and WXS sequencing data of 408 samples.

Subject of Study

Homo sapiens

Subject(s)

Multiple Myeloma

OncoTree Cancer Type(s)

Plasma Cell Myeloma

Access via dbGaP
BAM and SRA files of whole genome and exome sequencing
Accession #: phs000348.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: Oben B, Froyen G, Maclachlan K, et al. Whole-genome sequencing reveals progressive versus stable myeloma precursor conditions as two distinct entities. Nature Communications. 2021; 12:1861.
Data Type: Genomic
Equipment Used: Illumina Genome Analyzer II (Homo sapiens)

Illumina HiSeq 2000
High throughput gene sequencing system
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
Data Tool(s): WES

WXS

WGS
Dataset Size: 5.5 TB

Data Catalog Record Updated: 2021-07-06

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