Dental Caries study with SNP/CNV Genotypes (NGS) data on dbGaP (538 participants)

phs004182 — Characterization of Taste Genetics and Oral Microbiome in Early Childhood    Caries

This study included 538 participants under the age of 72 months, recruited between December 2017 and July 2022 from various community clinics across Winnipeg, Manitoba. Samples were collected from buccal swabs to sequence the taste-related genes. For the sequencing, 55 candidate genes were selected based on their roles in taste signal transduction, including receptors for bitter, sweet, umami, salt, sour, carbonation, and fatty acids, and some of their associated signaling proteins. DNA was isolated using the QIAamp Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. The candidate genes were amplified using primers designed for the Fluidigm platform to facilitate Illumina sequencing, ensuring that each amplified region covered approximately 250–300 base pairs for compatibility with 150 × 2 paired-end sequencing. The raw sequences of the candidate genes were mapped to the GRCh38 human reference genome using the BWA mapping tool. To identify the genetic variants in the candidate genes, the workflow adhered to the GATK best practice guidelines, with the exception of PCR duplicate removal, as this step is not recommended for targeted region amplification. A combined variant calling format (VCF) file containing genotyping information for the genes included in the study was generated for all 538 samples. This file was cleaned and filtered using VCFtools. Quality control steps included filtering for a Phred quality score greater than 25, missing data less than 50%, and a sequencing depth greater than 5. SNPs were annotated using BCFtools with the human dbSNP138 database, and variant annotation was performed using SnpEff based on the human genome version, GRCh38. This VCF file will be available from dbGaP. In this study, we found significant associations of variants in the bitter taste receptor gene <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/338398/">TAS2R60</a> (rs35195910), sodium ion transport gene <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/6339/">SCNN1D</a> (rs111819661), and phospholipase gene <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/5330/">PLCB2</a> (rs2305645) with early childhood caries.