Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

Abstract

Here, we demonstrate how comparative sequence analysis facilitates genome-wide base-pair-level interpretation of individual genetic variation and address two questions of importance for human personal genomics: first, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; and, second, whether populationspecific or globally-present polymorphisms contribute more to functional variation in any given individual. Neither has been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair-level resolution for identifying functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary constraint and also analyzed variation within three published human genomes. We find that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments are strongly predictive of reductions in modern-day genetic diversity across a range of annotation categories and across the allele frequency spectrum from rare (<1%) to high frequency (>10% minor allele frequency). Furthermore, we show that putatively functional variation in an individual genome is dominated by polymorphisms that do not change protein sequence and that originate from our shared ancestral population and commonly segregate in human populations. These observations show that common, noncoding alleles contribute substantially to human phenotypes and that constraint-based analyses will be of value to identify phenotypically relevant variants in individual genomes.[Supplemental material is available online at http://www.genome.org. All sequences can be retrieved from the NCBI Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi) using the search string CENTER_NAME = ''SHGC'' and SPE-CIES_CODE = ''HOMO SAPIENS' '.] As the sequencing of human genomes becomes routine, a growing challenge is how to assess the functional consequences of the genetic variation carried by a given individual. Of the >3 million variants present in any given human genome (Levy et al. 2007;Bentley et al. 2008;Wang et al. 2008;Kim et al. 2009;Mardis et al. 2009;McKernan et al. 2009), only a small fraction are expected to be phenotypically relevant (Kimura 1983;Ng et al. 2008;Mardis et al. 2009); among those that are, there is a great range in the degree to which they contribute to phenotype . Therefore, to fully leverage the benefits of genome-wide variation data, methods for detecting and evaluating functional variants across the entire genome are required, as is an improved understanding of the nature of functional human genetic variation.One strategy for identifying potentially important genetic variants is to focus on polymorphisms that fall into regions that have well-defined molecular functions, such as protein-coding exons. Several methods exist to estimate the impact of nonsynonymous changes on protein function, using data on the physicochem...

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

“…If we also consider the deep intronic polymorphic variants that have the potential to confer susceptibility to disease Emison et al, 2005;Fraser and Xie, 2009;Grant et al, 1996;Mann et al, 2001;Susa et al, 2008], it is very likely that splicing-relevant intronic variation will have been seriously underascertained thus far. Consistent with this statement, Goode et al [2010] have recently reported that the vast majority of putatively functional variants in the human genome actually reside in either intronic or intergenic locations. …”

“…Finally, it should be understood that whereas the deleteriousness of the average synonymous mutation is always likely to be less than that of that of a nonsynonymous (missense) mutation , the higher prevalence of synonymous mutations means that they may actually make a significantly greater contribution to the phenotype than nonsynonymous mutations [Goode et al, 2010].…”

Human genomic disease variants: A neutral evolutionary explanation

“…Functionally important regions of the genome show much lower degrees of genetic variation than others with no known function (e.g., coding versus noncoding; Fig. 1A; Goode et al 2010;Mu et al 2011). Exonic variants that have become common in the population (frequency $5%) are overabundantly synonymous (do not change the amino acid encoded).…”

The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit

“…Specifically, GERP scores represent the deficiency in the number of substitutions at putatively functional sites compared to the number of substitutions seen in neutral DNA. Thus, the lower the number of substitutions at a site across the phylogeny, the higher the level of purifying selection at that site (Goode et al 2010;Henn et al 2016). We used the same approach as Henn et al (2015) for the GERP score annotation.…”