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PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform.

Yimin Wang1, Yunchao Ling1, Jiao Gong2,3

  • 1Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Nucleic Acids Research
|October 16, 2022
PubMed
Summary

The PGG.SV database offers a comprehensive resource for structural variants (SVs), crucial for understanding human evolution and disease. It provides high-quality data from diverse global populations, enhancing genomic research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Human Genetics

Background:

  • Structural variations (SVs) are vital in human evolution and disease, yet data resources for representative populations, particularly East Asians, are limited.
  • Existing databases often lack comprehensive coverage of underrepresented SVs.

Purpose of the Study:

  • To develop PGG.SV, a practical database for regionally and globally representative structural variants.
  • To provide a platform for analyzing and understanding SVs in diverse human populations.

Main Methods:

  • Integrated next-generation sequencing (NGS) and third-generation sequencing (TGS) whole-genome data.
  • Collected data from 6048 samples, including 1030 long-read genomes from 177 global populations.
  • Developed precise genomic location mapping and annotation tools.

Main Results:

  • Archived 584,277 high-quality SVs with precise locations in GRCh37 and GRCh38.
  • Included hierarchical estimation of SV prevalence across geographical populations.
  • Provided annotations for SV-related genes, functions, and clinical effects.
  • Integrated an analysis platform for SV-based association studies and visualization tools.

Conclusions:

  • PGG.SV offers a user-friendly online interface with easy-to-use analysis tools and detailed results presentation.
  • The database enhances the study of structural variants, particularly for underrepresented populations.
  • PGG.SV is freely accessible, promoting broader genomic research.