Data · dataset · 2021
WGS in familial chronic lymphocytic leukemia
Listed in Researchdata.se
Data Set Description This repository contains data from a study of three families in which two or more siblings developed chronic lymphocytic leukemia (CLL).
Description
Informed consent was provided in accordance with the declaration of Helsinki and the study was approved by the hospital medical ethics committee (METC2015-741). The data consists of BAM-files from whole-genome sequencing (WGS) of nine individuals with data from tumor and matched normal tissue.
WGS libraries where prepared using the TruSeq Nano Kit (Illumina Inc.) and sequenced in paired-end mode (2x150bp) on the Illumina HiSeqX Ten system (Illumina Inc.) with 30x target coverage. Reads from each library were aligned to the Grch37 reference genome using BWA mem and merged and de-duplicated using Picard. Re-alignment around known and novel indel-sites was performed with GATK.
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All SAM/BAM-conversion steps were completed using SAMtools. The repository also contains results from Sanger sequencing of the immunoglobulin rearrangements from the tumor samples. The data is under restricted access and can be accessed upon request through the email-adress below.
Terms for accessThe WGS datasets are only to be used for research aimed at advancing the understanding of genetic factors in the development of familial chronic lymphocytic leukemia. Applications aimed at method development including bioinformatics would not be considered as acceptable for use of this dataset.
Links
Where it is published
- DOI doi.org/10.17044/scilifelab.14932062 ↗
DOI / persistent id · from researchdata se
Catalogue records · 1
- OAI-PMH record api.researchdata.se/oai-pmh?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3A… ↗
metadata API · from researchdata se
Topics
- From keywords
- Earth & Environmental Science · Medicine & Health
- Inferred from text
- Cancer 65% · Genome sequencing 65% · Oncology and carcinogenesis 73% · Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Researchdata.se | oai:researchdata.se:doi-10-17044-scilifelab-14932062/0 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · researchdata se | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[field].anzsrc:group:3211 | enrichment · researchdata se | taxonomy-embedding@1.1.0 | title+keywords+description (73%) |
| concepts[field].local:field:earth-environmental | mapping · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[modality].local:modality:genome-sequencing | enrichment · researchdata se | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · researchdata se | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · researchdata se | connector:researchdata_se@1.0.0 | /metadata/dc/description |
| license_text | source · researchdata se | connector:researchdata_se@1.0.0 | |
| publication_date | source · researchdata se | connector:researchdata_se@1.0.0 | |
| title | source · researchdata se | connector:researchdata_se@1.0.0 | /metadata/dc/title |