Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses
Abstract Background Whole 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 an...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10080-0 |
| _version_ | 1797275769877037056 |
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| author | Katerina Kvapilova Pavol Misenko Jan Radvanszky Ondrej Brzon Jaroslav Budis Juraj Gazdarica Ondrej Pos Marie Korabecna Martin Kasny Tomas Szemes Petr Kvapil Jan Paces Zbynek Kozmik |
| author_facet | Katerina Kvapilova Pavol Misenko Jan Radvanszky Ondrej Brzon Jaroslav Budis Juraj Gazdarica Ondrej Pos Marie Korabecna Martin Kasny Tomas Szemes Petr Kvapil Jan Paces Zbynek Kozmik |
| author_sort | Katerina Kvapilova |
| collection | DOAJ |
| description | Abstract Background Whole 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. Methods The 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. Results The 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. Conclusion Saliva 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. |
| first_indexed | 2024-03-07T15:19:12Z |
| format | Article |
| id | doaj.art-a0a7b7e5449b4f6383ccc83c0d0fa3f4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:19:12Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-a0a7b7e5449b4f6383ccc83c0d0fa3f42024-03-05T17:46:23ZengBMCBMC Genomics1471-21642024-02-0125111710.1186/s12864-024-10080-0Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analysesKaterina Kvapilova0Pavol Misenko1Jan Radvanszky2Ondrej Brzon3Jaroslav Budis4Juraj Gazdarica5Ondrej Pos6Marie Korabecna7Martin Kasny8Tomas Szemes9Petr Kvapil10Jan Paces11Zbynek Kozmik12Faculty of Science, Charles UniversityGeneton s.r.oGeneton s.r.oInstitute of Applied Biotechnologies a.sGeneton s.r.oGeneton s.r.oGeneton s.r.oInstitute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in PragueInstitute of Applied Biotechnologies a.sGeneton s.r.oInstitute of Applied Biotechnologies a.sLaboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of SciencesLaboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of SciencesAbstract Background Whole 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. Methods The 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. Results The 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. Conclusion Saliva 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.https://doi.org/10.1186/s12864-024-10080-0Genomics variant analysisSaliva-derived gDNAWhole genome sequencingWhole exome sequencingValidation guideline |
| spellingShingle | Katerina Kvapilova Pavol Misenko Jan Radvanszky Ondrej Brzon Jaroslav Budis Juraj Gazdarica Ondrej Pos Marie Korabecna Martin Kasny Tomas Szemes Petr Kvapil Jan Paces 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 Genomics variant analysis Saliva-derived gDNA Whole genome sequencing Whole exome sequencing Validation guideline |
| title | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses |
| title_full | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses |
| title_fullStr | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses |
| title_full_unstemmed | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses |
| title_short | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses |
| title_sort | validated wgs and wes protocols proved saliva derived gdna as an equivalent to blood derived gdna for clinical and population genomic analyses |
| topic | Genomics variant analysis Saliva-derived gDNA Whole genome sequencing Whole exome sequencing Validation guideline |
| url | https://doi.org/10.1186/s12864-024-10080-0 |
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