Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15110%2F21%3A73610461" target="_blank" >RIV/61989592:15110/21:73610461 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41587-021-00993-6" target="_blank" >https://www.nature.com/articles/s41587-021-00993-6</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41587-021-00993-6" target="_blank" >10.1038/s41587-021-00993-6</a>
Alternative languages
Result language
angličtina
Original language name
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Original language description
Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
NATURE BIOTECHNOLOGY
ISSN
1087-0156
e-ISSN
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Volume of the periodical
39
Issue of the periodical within the volume
9
Country of publishing house
US - UNITED STATES
Number of pages
27
Pages from-to
1151-1177
UT code for WoS article
000694844000026
EID of the result in the Scopus database
2-s2.0-85115970978