Computational protocol: A Putative Association of a Single Nucleotide Polymorphism in GPR126 with Aggressive Periodontitis in a Japanese Population

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Protocol publication

[…] Exome capture and sequencing was completed by a commercial company (BGI Tech., Shenzhen, China). Genomic DNA was extracted from peripheral whole blood (Fujifilm, Tokyo, Japan), and exome capture was performed with Agilent SureSelect Human All Exon V4 or V5 kits (Agilent Technologies, Santa Clara, CA). Exome sequencing was undertaken with paired-end 100 or 101 base pair reads using Illumina HiSeq 2000 or 4000 platform (Illumina, Inc., San Diego, CA). The sequencing reads were aligned to the human reference genome (UCSC build HG19/HG18) using BWA software. Variants were called using GATK and SAMtools program pileup and annotated with the dbSNP database and 1000 Genomes Project database. The exome database is deposited in the DNA Data Bank of Japan (JGAS00000000024 and JGAS00000000040). […]

Pipeline specifications

Software tools BWA, GATK, SAMtools
Application WES analysis
Organisms Homo sapiens
Diseases Periodontitis