Summary: A team led by CAS Fellow Ya-Ping Zhang and Prof. Zhanshan (Sam) Ma (Chinese Academy of Sciences) recently proposes a new concept, termed “individual-level genetic diversity.” The new concept is contrastingly different from existing concepts of genetic diversity, since existing genetic diversities (heterogeneities) have been traditionally defined and measured for population(s), rather than for an individual. A practical application of the new individual-level genetic diversity can be in personalized precision medicine, such as measuring and monitoring one’s genetic mutation changes in routine medical exams or in disease risk predictions.
Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei & Li’s nucleotide diversity were defined within a population context. Although variations are often measured in population context, the basic carriers of variation are individuals. Hence, measuring variations such as SNP of an individual against a reference genome, which has been ignored previously, is certainly in its own right. Indeed, similar practice has been a tradition in community ecology, where the basic unit of diversity measure is individual community sample. In the newly published paper, Ma, Li & Zhang propose to define and measure the individual-level genetic diversity by using Renyi’s-entropy-based Hill numbers. They further defined similarity metrics for comparing individual-level diversities.They demonstrated their concepts (definitions) and metrics with the SNP (single nucleotide polymorphism) datasets from the 1000-Genomes Project. Hill numbers, derived from Renyi’s entropy (of which Shannon’s entropy is a special case), have found widely applications including measuring the quantum information entanglement and ecological diversity. The demonstrated individual-level SNP diversity not only complements the existing population-level genetic diversity concepts, but also offers building blocks for comparative genetic analysis at higher levels.
The entity of “individual” in the “individual-level diversity/similarity”covers, but is not limited to, individual chromosome, region of chromosome, gene cluster(s), or whole genome. Similarly, although SNP was used to demonstrate the individual-level diversity, the SNP can be replaced by other structural variants or mutation types such as indels. A practical application of the new individual-level genetic diversity can be in personalized precision medicine, such as measuring and monitoring one’s genetic mutation changes in routine medical exams, or disease risk predictions.