Validated WGS and WES protocols proved saliva-derived gDNA as
an equivalent to blood-derived gDNA for clinical and population
genomic analyses

J 2024

Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses

KVAPILOVA, Katerina; Pavol MISENKO; Jan RADVANSZKY; Ondrej BRZON; Jaroslav BUDIS et al.

Základní údaje

Originální název

Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses

Autoři

KVAPILOVA, Katerina; Pavol MISENKO; Jan RADVANSZKY; Ondrej BRZON; Jaroslav BUDIS; Juraj GAZDARICA; Ondrej POS; Marie KORABECNA; Martin KAŠNÝ; Tomas SZEMES; Petr KVAPIL; Jan PACES a Zbynek KOZMIK

Vydání

BMC Genomics, London, BioMed Central Ltd, 2024, 1471-2164

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10603 Genetics and heredity

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.700

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00138541

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Genomics variant analysis; Saliva-derived gDNA; Whole genome sequencing; Whole exome sequencing; Validation guideline

Štítky

14314020, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 1. 2025 10:49, Mgr. Lucie Jarošová, DiS.

Anotace

V originále

BackgroundWhole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols.MethodsThe genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results.ResultsThe quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol.ConclusionSaliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.

Citovat

KVAPILOVA, Katerina; Pavol MISENKO; Jan RADVANSZKY; Ondrej BRZON; Jaroslav BUDIS; Juraj GAZDARICA; Ondrej POS; Marie KORABECNA; Martin KAŠNÝ; Tomas SZEMES; Petr KVAPIL; Jan PACES a Zbynek KOZMIK. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. BMC Genomics. London: BioMed Central Ltd, 2024, roč. 25, č. 1, s. "187", 17 s. ISSN 1471-2164. Dostupné z: https://doi.org/10.1186/s12864-024-10080-0.

@article{2468898,
   author = {Kvapilova, Katerina and Misenko, Pavol and Radvanszky, Jan and Brzon, Ondrej and Budis, Jaroslav and Gazdarica, Juraj and Pos, Ondrej and Korabecna, Marie and Kašný, Martin and Szemes, Tomas and Kvapil, Petr and Paces, Jan and Kozmik, Zbynek},
   article_location = {London},
   article_number = {1},
   doi = {https://doi.org/10.1186/s12864-024-10080-0},
   keywords = {Genomics variant analysis; Saliva-derived gDNA; Whole genome sequencing; Whole exome sequencing; Validation guideline},
   language = {eng},
   issn = {1471-2164},
   journal = {BMC Genomics},
   title = {Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses},
   url = {https://doi.org/10.1186/s12864-024-10080-0},
   volume = {25},
   year = {2024}
}

TY  - JOUR
ID  - 2468898
AU  - Kvapilova, Katerina - Misenko, Pavol - Radvanszky, Jan - Brzon, Ondrej - Budis, Jaroslav - Gazdarica, Juraj - Pos, Ondrej - Korabecna, Marie - Kašný, Martin - Szemes, Tomas - Kvapil, Petr - Paces, Jan - Kozmik, Zbynek
PY  - 2024
TI  - Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses
JF  - BMC Genomics
VL  - 25
IS  - 1
SP  - "187"
EP  - "187"
PB  - BioMed Central Ltd
SN  - 14712164
KW  - Genomics variant analysis
KW  - Saliva-derived gDNA
KW  - Whole genome sequencing
KW  - Whole exome sequencing
KW  - Validation guideline
UR  - https://doi.org/10.1186/s12864-024-10080-0
N2  - BackgroundWhole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols.MethodsThe genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results.ResultsThe quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol.ConclusionSaliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
ER  -

KVAPILOVA, Katerina; Pavol MISENKO; Jan RADVANSZKY; Ondrej BRZON; Jaroslav BUDIS; Juraj GAZDARICA; Ondrej POS; Marie KORABECNA; Martin KAŠNÝ; Tomas SZEMES; Petr KVAPIL; Jan PACES a Zbynek KOZMIK. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. \textit{BMC Genomics}. London: BioMed Central Ltd, 2024, roč.~25, č.~1, s.~''187'', 17 s. ISSN~1471-2164. Dostupné z: https://doi.org/10.1186/s12864-024-10080-0.

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