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

Fuzuki Mizuno, Masahiko Kumagai, Kunihiko Kurosaki, Michiko Hayashi, Saburo Sugiyama, Shintaroh Ueda, Li Wang

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)631-635
Number of pages5
JournalJournal of Human Genetics
Volume62
Issue number6
DOIs
StatePublished - Jun 1 2017
Externally publishedYes

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Mexico
Nucleotides
Population
Information Storage and Retrieval

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

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. / Mizuno, Fuzuki; Kumagai, Masahiko; Kurosaki, Kunihiko; Hayashi, Michiko; Sugiyama, Saburo; Ueda, Shintaroh; Wang, Li.

In: Journal of Human Genetics, Vol. 62, No. 6, 01.06.2017, p. 631-635.

Research output: Contribution to journalArticle

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