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HUPAN: a pan-genome analysis pipeline for human genomes
Zhongqu Duan1,2, Yuyang Qiao1, Jinyuan Lu1
1School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Genome Biology
|August 2, 2019
Summary
Researchers built a human pan-genome system (HUPAN) to identify novel genomic sequences and protein-coding genes missing from the current human reference genome (GRCh38). This resource aids biomedical studies, including cancer genome analysis.
Area of Science:
- Genomics
- Bioinformatics
- Human Genetics
Background:
- The human reference genome (GRCh38) is incomplete, lacking population-specific and individual-specific genomic regions.
- These missing regions may harbor crucial functional elements impacting human health and disease.
Purpose of the Study:
- To develop a system for constructing a comprehensive human pan-genome.
- To identify novel genomic sequences and protein-coding genes absent in the current reference genome.
Main Methods:
- Development of the HUman Pan-genome ANalysis (HUPAN) system.
- Application of HUPAN to analyze 185 deep sequencing and 90 assembled Han Chinese genomes.
Main Results:
- Detection of 29.5 Mb of novel genomic sequences.
- Identification of at least 188 novel protein-coding genes not present in GRCh38.
- Construction of a more complete human pan-genome.
Conclusions:
- The HUPAN system effectively expands the human genome sequence.
- The identified novel sequences and genes represent a valuable resource for human genome-related biomedical research.
- This work enhances the foundation for studies in areas like cancer genomics.
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