Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data
Rattachement africain : fr. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
Abstract This study sets out to establish the suitability of saliva-based whole-genome sequencing (WGS) through a comparison against blood-based WGS. To fully appraise the observed differences, we developed a novel technique of pseudo-replicates. We also investigated the potential of characterising individual salivary microbiomes from non-human DNA fragments found in saliva. We observed the majority of discordant genotype calls between blood and saliva calls fell into known regions of the human genome that are typically sequenced with low confidence; and could be identified by quality control measures. Pseudo-replication demonstrated that the levels of discordance between blood- and saliva-derived WGS data were entirely similar to what one would expect between technical replicates if an individual’s blood or saliva had been sequenced twice. Finally, we successfully sequenced salivary microbiomes in parallel to human genomes as demonstrated by a comparison against the Human Microbiome Project. Author Summary DNA is usually collected from blood for the analysis of human genomes. In France, a new and very large genetic dataset will be created where selected participants will be sent saliva-collection kits in the post as this data collection method presents numerous logistical benefits. It has been previously shown that good quality genetic data can be created from saliva, though existing studies have often not considered the latest technologies or have only analysed a very small number of individuals. In this study, we have analysed genetic data derived from saliva for 39 individuals to give a firm conclusion that the proposed genome sequencing approach of the new French dataset will be capable of provided high quality data by making a comparison to pre-existing genetic data derived from blood for these 39 individuals. In order to do so, we developed a novel method (presented here) to establish the similarity between two sets of genetic data for the same individual that are generated from separate DNA samples. Finally, we have also demonstrated an added bonus of colleting saliva samples: that it is possible to gather both human genetic data and potentially interesting salivary microbiome data at the same time by separating and analysing in parallel human and non-human DNA fragments.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data
- Date Crossref
- 16/11/2020
- Éditeur
- openRxiv
- Type
- posted-content
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Inserm pays non établi dans la noticeOrganisme public
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Université de Bretagne Occidentale pays non établi dans la noticeUniversité ou école supérieure
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École nationale d'ingénieurs de Brest Tunisie (ville ou établissement reconnu, pays non nommé)Université ou école supérieure
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Centre Hospitalier Régional Universitaire de Brest pays non établi dans la noticeÉtablissement de santé
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Commissariat à l'Énergie Atomique et aux Énergies Alternatives pays non établi dans la noticeOrganisme public
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Université Paris-Saclay Institut de Biologie François Jacob pays non établi dans la noticeUniversité ou école supérieure
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Centre National de Recherche en Génomique Humaine pays non établi dans la noticeStructure de recherche
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CEA Paris-Saclay pays non établi dans la noticeOrganisme public
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Génétique Médicale & Génomique Fonctionelle pays non établi dans la noticeStructure de recherche
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Institut de biologie François Jacob pays non établi dans la noticeStructure de recherche
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Fondation Jean Dausset-CEPH pays non établi dans la noticeOrganisation à but non lucratif
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Centre d’Investigation Clinique 1436 pays non établi dans la noticeStructure de recherche
Inserm, Université de Bretagne Occidentale et École nationale d'ingénieurs de Brest (Tunisie), avec 9 autres affiliations. Pays d’affiliation : Tunisie.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.