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Research ID

hum0364-v1Release info

Latest

Research title

Comprehensive analysis of microsatellite polymorphisms in human populations

Research overview

Aims
Next generation sequencing technologies (NGS) enable whole genome sequencing (WGS) analysis. In the past decade, applications of NGS and the development of algorithms for the analysis have successfully identified various types of genetic variations. However, due to the short read length and the high sequencing error rate in repeat regions, the identification of mutations and polymorphisms in microsatellite (MS) regions has been difficult. In this study, we analyzed approximately nine million MS regions using a previously developed MS caller (MIVcall) for three large publicly available human genome sequencing data sets: Simons Genome Diversity Project (SGDP), and Human Genome Diversity Project (HGDP).
Methods
MS regions were detected by MIVcall method
Participants/materials
Publicly available whole genome sequencing data of healthy individuals were downloaded and used for MS analysis. After evaluating the quality of the data, we analyzed 276 samples from SGDP, 693 from HGDP, and one Jomon Individual (F23).
URL
N/A

Datasets

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
NHA000176NGS (WGS)
  • WGS
Unrestricted-access2022-08-29

Data provider

Principal investigator
Akihiro Fujimoto
Affiliation
School of Integrated Health Sciences, Faculty of Medicine, The University of Tokyo

Research projects

No research projects.

Grants

NameTitleProject number
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data
  • 18H05511
Grant-in-Aid for Scientific Research on Innovative Areas from Japan Society for the Promotion of Science (JSPS)
Comprehensive analysis of microsatellite polymorphism in the human population
  • 18H02680
Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED)
Development of advanced data analysis methods for genome sequencing
  • JP20km0405207

Related publications

No related publications.