Despite the critical importance of germline mutation in human genetics, we still lack the answer to basic questions, notably about how and why rates differ among individuals. We also lack a comparative context for interpreting findings, as, other than for one chimpanzee family, there are no direct estimates of germline mutation rates for non-human primates. These gaps in our understanding have important implications for evolutionary biology as well, leading in particular to considerable uncertainty about the steadiness of the ?molecular clock? in primates. We therefore propose to obtain direct estimates of germline mutation rates within humans, in chimpanzees, and in three Old World monkey (OWM) species.
In Aim 1, we will elucidate variation in human mutation rates with age, sex, and across families, separately for different mutation types. We will generate and analyze high-quality genome sequences for eight nuclear families of Hutterites (86 individuals) who belong to a single, 13-generation pedigree. Their relatively high consanguinity allows us to estimate mutation rates both in transmissions from parents to children and in autozygous segments descended from an older common ancestor. By relying on three-generation families with 3?6 children each, instead of the standard trio design, we can assign mutations to male or female germlines, verify transmission of putative mutations, and estimate rates of germline mosaicism. To these ends, we will also resequence a subset of mutations at deep coverage.
In Aim 2, we will obtain the first direct estimate of mutation rates in an OWM species. Specifically, we will generate and analyze high- quality genome sequences for seven three-generation families of vervet monkeys (43 individuals, for which ages are known). These individuals belong to a colony of 2,000+ in an 11-generation pedigree, so the data are very similar in structure to that of the Hutterites, and will be analyzed by the same approaches, providing a well-matched comparison to humans.
In Aim 3, we will examine the evolution of mutation rates across apes and OWMs. We will generate high-quality genome sequences for ten overlapping nuclear families of western chimpanzees (54 individuals), five families of rhesus macaques (22), and two families of olive baboons (13), for which parental ages are known. The genomic data will be generated using a uniform approach, and a subset of putative mutations will be resequenced to estimate error rates. This analysis will yield the first direct look at the evolution of mutation rates across a set of closely related species, and allow us to revisit the chronology of primate evolution with a more reliable molecular clock. Thus, this study will elucidate variation in the mutation process within human and among closely related species. As a byproduct, the data will enable primate evolutionary genomics and mapping efforts in primate model organisms.

Public Health Relevance

We propose to elucidate variation in germline mutation rates among humans and obtain direct estimates of germline mutation rates in chimpanzees and three non-human primate model organisms (baboons, rhesus macaques, and vervet monkeys). This work will lead to the first characterization of variation in mutation rates across a set of closely related species and generate important genomic resources for the study of non-human primates.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM122975-04
Application #
9903385
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Janes, Daniel E
Project Start
2017-05-15
Project End
2021-03-31
Budget Start
2020-04-01
Budget End
2021-03-31
Support Year
4
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Biology
Type
Graduate Schools
DUNS #
049179401
City
New York
State
NY
Country
United States
Zip Code
10027
Chen, Chen; Qi, Hongjian; Shen, Yufeng et al. (2017) Contrasting Determinants of Mutation Rates in Germline and Soma. Genetics 207:255-267