From among them we selected 40 controls who were seropositive for HBsAb, but had no hepatitis B vaccination history and were healthy, as confirmed

by annual medical examination for the last 5 consecutive years (Supporting Table 2). Written informed consent was obtained from all participants. The project was approved by the Ethics Committee of the University for Human Study and was conducted according to the principles of the 1975 Declaration of Helsinki. Exome sequences were captured by NimbleGen2.1 M array targeting 34 Mb of the human genome, containing 180,000 coding exons and 551 miRNA genes (http://www.nimblegen.com). The enriched library was sequenced on Illumina HighSeq2000. Sequencing reads were aligned to NCBI build 36.3. After removing reads duplicates, the average sequencing depth per sample was 43×. Of the targeted bases 93.54% had coverage of ≥8× SAHA HDAC purchase and genotype quality score ≥30. Single nucleotide variations (SNVs) were identified (“called”) by SOAPsnp (http://soap.genomics.org.cn/index.html)

and SAMTools (http://samtools.sourceforge.net). Small insertions and deletions (indels) were called by programs Dindel, Mpileup group, and Mpileup individual (http://www.sanger. ac.uk/resources/software/dindel/). Variants were annotated Selleck H 89 with information from the Consensus Coding Sequences Database at the NCBI. In selecting candidate genetic variants, we modified various existing protocols for Mendelian gene discovery.7 Rare variants were identified by comparing their frequencies in the Chinese Han data in HapMap (August 2010 release) (http://hapmap.ncbi.nlm.nih.gov/)

and our in-house data. Variations novel to HapMap Chinese Han data and our in-house data were treated as rare variants, as the HapMap already included data from 248 Chinese Han subjects and our in-house data from another 100 subjects. We reasoned that the following criteria might provide the most effective approach: (1) generally rare variants that were not shared by sequenced cases and controls and appeared more frequently (i.e., gave higher oxyclozanide “call counts”); (2) those that were predictively deleterious on the genes’ functions (e.g., truncating or missense mutations to highly conserved amino acids and/or were expected to be damaging according to PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) or SIFT (http://sift.jcvi.org/www/SIFT_chr_coords_submit.html)); (3) variants of genes with known antiviral/immune functions. Using these criteria, we performed two rounds of selections. In the first round we focused on rare variants that appeared more frequently and were predictively more deleterious, regardless of their known functions. In the second round we focused on known functions of the genes in combination with call counts. We first selected genes involved in immunity by comparing the genes of the variants with two databases, Gene Ontology (http://wiki.geneontology.org/index.php/Immunologically_Important_Genes) and Ensembl (http://www.