Defining Individual-Level Genetic Diversity and Similarity Profiles

Abstract

Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei (1973: PNAS) and Nei & Li (1979: PNAS) nucleotide diversity were defined within the context of populations. Although variations are often measured in population context, the basic carriers of variation are individuals. Hence, measuring variations such as SNP of individual against a reference genome, which has been ignored currently, is certainly of its own right. Indeed, similar practice has been a tradition in ecology, where the basic framework of diversity measure is individual community sample. We propose to use Renyi's-entropy-derived Hill numbers to define SNP (single nucleotide polymorphism) diversity (including alpha-, beta-, and gammadiversities) and similarity profiles. Hill numbers are derived from Renyi's entropy, of which Shannon's entropy is a special case and which have found widely applications including measuring the quantum information entanglement, wealth distribution in economics and ecological diversity. The newly proposed SNP diversity not only complements the existing genetic diversity concepts by offering individual-level metrics, but also offers building blocks for comparative genetic analysis at higher levels. The profile concept also helps to resolve a dilemma in measuring diversity-the choice from various diversity indexes, because diversity profile unifies some of the most commonly used indexes (as special cases) with different diversity orders (along the rareness-commonness spectrum of gene mutations). Finally, the profiles can be estimated with rarefaction approach, which may help to relieve some effect of insufficient sequencing coverage.

Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

“…A fundamental challenge in assessing the genetic diversity of dromedary populations concerns accessibility to camel samples representing the different populations, and defining informative statistics with which to evaluate their diversity. Several diversity indices exist that measure species diversity at ecological levels, which can also be used to evaluate the genetic diversity of livestock species 11 , 12 . Shannon’s entropy, Simpson’s index and Renyi’s entropy are examples of such indices, which translated mathematically into number of equivalents called Hill numbers, behave in a way that can be used to express diversity 11 .…”

“…Recently, Ma et al 12 applied these ecological diversity measures to quantify SNP diversity at the level of the individual. These proposed alpha and beta diversity measures are able to account for the uneven, non-random, distribution of SNPs along chromosomes.…”

“…These proposed alpha and beta diversity measures are able to account for the uneven, non-random, distribution of SNPs along chromosomes. Ma et al 12 proposed four Hill-number-based similarity measures to compare SNP similarity between populations. These measures investigate SNPs similarities at different levels: local SNP overlap (Cq N ) that quantifies the proportion of shared SNPs among individuals; regional SNP overlap (UqN) that looks at the proportion of shared SNPs in the pooled population; SNP homogeneity (Sq N ) that measures SNP evenness between populations; and SNP turnover complement (Vq N ) that represents the relative rate of SNP turnover per individual.…”

Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires

“…There are other variables to consider before TCR therapy, including “personal genetics” and “infectious history” which likely influence our personal T-cell repertoire makeup. Any two individuals can differ by up to 800 million single nucleotide polymorphisms (SNPs) between genomes [ 60 ]. This is termed personal genetics, and we currently do not understand how our personal genomes fully impact immune function.…”

On the Intergenerational Transmission of Health Inequality

“…Genetic polymorphisms are the simultaneous occurrence of two or more discontinuous genotypes or alleles in a population (33). It determines the diversity of individuals (34). In general, a susceptible gene is strongly associated with an individual's susceptibility to a particular disease (35).…”