Estimating the number of unseen variants in the human genome

Abstract

The different genetic variation discovery projects (The SNP Consortium, the International HapMap Project, the 1000 Genomes Project, etc.) aim to identify as much as possible of the underlying genetic variation in various human populations. The question we address in this article is how many new variants are yet to be found. This is an instance of the species problem in ecology, where the goal is to estimate the number of species in a closed population. We use a parametric beta-binomial model that allows us to calculate the expected number of new variants with a desired minimum frequency to be discovered in a new dataset of individuals of a specified size. The method can also be used to predict the number of individuals necessary to sequence in order to capture all (or a fraction of) the variation with a specified minimum frequency. We apply the method to three datasets: the ENCODE dataset, the SeattleSNPs dataset, and the National Institute of Environmental Health Sciences SNPs dataset. Consistent with previous descriptions, our results show that the African population is the most diverse in terms of the number of variants expected to exist, the Asian populations the least diverse, with the European population in-between. In addition, our results show a clear distinction between the Chinese and the Japanese populations, with the Japanese population being the less diverse. To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small ( approximately 350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals ( approximately 150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants. Finally, our results also show a much higher diversity in environmental response genes compared with the average genome, especially in African populations.

Fig. 1.

YRI, CEPH, CHB, and JPT: Estimates of Δ_f(t) for values of t ∈ [0.1,16] and values of f ∈ [0 − 0.1] for the four populations.

Fig. 2.

YRI, CEPH, CHB, and JPT: The number of individuals necessary to sequence in order to detect a percentage of all the variation with frequency at least 0.001. The horizontal lines are drawn at 150 and 1,000 individuals, respectively.