Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Identifikátory výsledku
Kód výsledku v 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>
Výsledek na webu
<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>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Popis výsledku v původním jazyce
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.
Název v anglickém jazyce
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Popis výsledku anglicky
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.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10606 - Microbiology
Návaznosti výsledku
Projekt
—
Návaznosti
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Ostatní
Rok uplatnění
2021
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
NATURE BIOTECHNOLOGY
ISSN
1087-0156
e-ISSN
—
Svazek periodika
39
Číslo periodika v rámci svazku
9
Stát vydavatele periodika
US - Spojené státy americké
Počet stran výsledku
27
Strana od-do
1151-1177
Kód UT WoS článku
000694844000026
EID výsledku v databázi Scopus
2-s2.0-85115970978