title: Imputation approach for deducing a complete mitogenome sequence from low-depth-coverage next-generation sequencing data: application to ancient remains from the Moon Pyramid, Mexico.
abstract: It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation. The number of missing nucleotides was drastically reduced in all the panels, but the contents obtained by imputation were quite different among the panels. The efficiency of the imputation method differed according to the panels used. The missing nucleotides were most credibly imputed using sequences of the estimated haplogroup from the population most closely related to the individual under investigation as a panel.
authors.affiliation: Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.|Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
authors.forename: Fuzuki
authors.initials: F
authors.lastname: Mizuno
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
authors.forename: Masahiko
authors.initials: M
authors.lastname: Kumagai
authors.affiliation: Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Kurosaki
authors.affiliation: Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.
authors.forename: Michiko
authors.initials: M
authors.lastname: Hayashi
authors.affiliation: Graduate school of International Cultural Studies, Cultural Symbiosis Research Institute, Aichi Prefectural University, Aichi, Japan.
authors.forename: Saburo
authors.initials: S
authors.lastname: Sugiyama
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.|School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China.
authors.forename: Shintaroh
authors.initials: S
authors.lastname: Ueda
authors.affiliation: School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
mesh_terms: D000072441:DNA, Ancient / Q000032:analysis*; D005787:Gene Frequency; D054629:Genome, Mitochondrial / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008800:Mexico; D020641:Polymorphism, Single Nucleotide
chemical_list: D000072441:DNA, Ancient