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Updated: Aug 25, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
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.
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.
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.
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