Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians

Abstract

Whole genome sequencing studies are essential to obtain a comprehensive understanding of the vast pattern of human genomic variations. Here we report the results of a high-coverage whole genome sequencing study for 44 unrelated healthy Caucasian adults, each sequenced to over 50-fold coverage (averaging 65.8×). We identified approximately 11 million single nucleotide polymorphisms (SNPs), 2.8 million short insertions and deletions, and over 500,000 block substitutions. We showed that, although previous studies, including the 1000 Genomes Project Phase 1 study, have catalogued the vast majority of common SNPs, many of the low-frequency and rare variants remain undiscovered. For instance, approximately 1.4 million SNPs and 1.3 million short indels that we found were novel to both the dbSNP and the 1000 Genomes Project Phase 1 data sets, and the majority of which (∼96%) have a minor allele frequency less than 5%. On average, each individual genome carried ∼3.3 million SNPs and ∼492,000 indels/block substitutions, including approximately 179 variants that were predicted to cause loss of function of the gene products. Moreover, each individual genome carried an average of 44 such loss-of-function variants in a homozygous state, which would completely "knock out" the corresponding genes. Across all the 44 genomes, a total of 182 genes were "knocked-out" in at least one individual genome, among which 46 genes were "knocked out" in over 30% of our samples, suggesting that a number of genes are commonly "knocked-out" in general populations. Gene ontology analysis suggested that these commonly "knocked-out" genes are enriched in biological process related to antigen processing and immune response. Our results contribute towards a comprehensive characterization of human genomic variation, especially for less-common and rare variants, and provide an invaluable resource for future genetic studies of human variation and diseases.

Figure 1. Summary characterizations of the identified variants.

A–B, Venn diagram showing SNPs and indels identified in the present study overlapping with those archived in the dbSNP (v131) and the 1000 Genomes Project Phase 1 data sets (released on 5/21/2011). To account for differences in placement of many indels between different data sets, indels were considered to match if they were within 25 bp distance and of the same size. Only SNPs and indels mapped to autosomes and X chromosome were analyzed. C, Genome-wide distribution of novel SNPs. Total number of novel SNPs (compared to dbSNP v131 and the 1000 Genomes Project pilot phase) were calculated in non-overlap 1-megabases (Mb) windows across the human genome and plotted in ideograms using Idiographica . The diversities were illustrated by colors, with red indicating higher numbers or proportions and blue indicating lower numbers or proportions. Genomic regions in which no SNPs were identified or no reference sequences could be determined are shown in grey. D, Allele frequency spectrum of novel SNPs.

Figure 2. Identification of “knocked-out” genes.

A, Frequency spectrum of observed “knocked-out” genes. Genes containing homozygous LoF variants were expected to be silent or knocked-out. Numbers of “knocked-out” genes were counted with respect to the frequency of “knock-out” occurrence in the 44 genomes.

Figure 3. The number of novel SNPs and indels discovered as the number of sequenced genomes increased.

We evaluated how many additional “new” A) SNPs and B) indels, respectively, were identified per genome as the number of sequenced genomes increased, considering both variants archived in databases (dbSNP v131 and the 1000 Genome Project Phase 1 data) and variants “discovered” in previously considered genomes. The 44 genomes were added into the analyses in a random order. With 1000 permutations, the average numbers of novel variants added per genome are shown, along with the best fitting trendline for each plot.