Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree

Abstract

Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11x or 20x, respectively. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in approximately 10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 x 10(-8) mutations/nucleotide/generation (95% CI: 8.9 x 10(-9)-7.0 x 10(-8)), consistent with estimates of 2.3 x 10(-8)-6.3 x 10(-8) mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed.

Figure 1

Capillary Sequence Traces of the Four Confirmed Mutations in Cell Line and Blood DNAs The red arrowhead indicates the mutant position.

Figure 2

Locations of the Four Confirmed Mutations on the DFNY1 Pedigree The sequenced chromosomes (66 and 101) are indicated by yellow arrows, and the additional family members typed for mutations are labeled with their numbers and haplotypes at the mutant positions. The possible locations of each mutation are shown by one or more colored circle. Filled squares represent DFNY1 affected individuals; open squares represent unaffected individuals.