Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data

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 SummaryDNA 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.

RAVAQ: An integrative pipeline from quality control to region‐based rare variant association analysis

“…The first data set, referred to as MMD‐FREX, consists of whole‐exome sequencing (WES) of cases diagnosed with Moyamoya disease (MMD) and controls from the French general population (French Exome Project—FREX) (Bocher et al, 2021; Guey et al, 2017). The second data set consists of whole‐genome sequencing (WGS) data from blood and saliva samples from the same individuals, this is part of the GAZEL‐ADN project (Herzig et al, 2021). Both datasets are prone to technical bias as the samples are from different projects and sequenced in different laboratories in the case of the MMD‐FREX data, and the samples are from two different tissues and sequenced with two different technologies in the case of the GAZEL‐ADN data.…”