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          Featured Discovery

          Home > Featured Discovery > Progress made in construction of the pan-genome of Han Chinese

          Progress made in construction of the pan-genome of Han Chinese

          August 05, 2019      Author:

          Recently, two cross-disciplinary teams from Shanghai Jiao Tong University released a novel analysis system for large scale human genome deep sequencing data, Human Pan-genome Analysis system (HUPAN). The construction of this system is an important step to reveal those “dark materials” in the human genome.

          It is well known that the initial human reference genome was based on a few individuals, and the reference genome is the gold standard for almost all biomedical researches. However, with the progress of the sequencing technology, many more individual genomes from different populations were sequenced and the current human reference genome was found incomplete, especially for some genomic regions that are specific to a certain populations or some individuals. In another words, the human genome is more complicate than the reference human genome and there are still unknown sequences (or “dark materials”) to be discovered.

          Pan-genome is the total genomic sequence of all individuals of a certain population. The accumulation of sequencing data for many individuals of some certain populations provided an unprecedented opportunity for human pan-genome analysis. However, the human genome size is big, and the sample size can be big, which make human pan-genome analysis a challenge. Especially, the genome assembly step of the human pan-genome analysis is error prone if we don’t improve the existing methods, which require huge memory and computing time. The scientists from School of Life Sciences and Biotechnology and School of Medicine of Shanghai Jiao Tong University created a novel pan-genome analysis pipeline, which can assemble the individual human genome with less misassembled regions and with reduced memory requirement. It also has improved pan-genome variation analysis with a faster speed and higher confidence.

          This method has been applied to 185 Han Chinese whole genome deep sequencing data and 90 Han Chinese whole genome assembled from deep sequencing data from public databases. It showed that Han Chinese pan-genome contains at least 29.5 Mb novel sequences missing in the human reference genome, of which about 40% are Han Chinese specific. Gene prediction analysis showed that 188 novel genes are missing in the human reference genome.

           

          This novel method can be an important tool for the study of the human genome, including the evolution and migration of human, genome variations between populations and the association between human diseases and genes. It can also be applied to pan-genome study for eukaryotes with big sized genomes.

           

          The results of this research was published online on July 31, 2019 at Genome Biology (impact fact 14.03). This research was done jointly by Professor Chaochun Wei group from the School of Life Science and Biotechnology and Professor Yingyan Yu group from Ruijin Hospital affiliated to School of Medicine, Shanghai Jiao Tong University. Doctoral student Zhongqu Duan is the first author.

           

          This work was supported by grants from the Cross-Institute Research Fund of Shanghai Jiao Tong University, the National Natural Science Foundation of China, National Key R&D Program of China, the National Basic Research Program of China, Shanghai Science and Technology Committee, Innovation Foundation of Translational Medicine of Shanghai Jiao Tong University School of Medicine, Technology Transfer Project of Science & Technology Dept. Shanghai Jiao Tong University School of Medicine, the Neil Shen’s SJTU Medical Research Fund and SJTU-Yale Collaborative Research Seed Fund. This work was also supported by High Performance Computing Center (HPCC) at Shanghai Jiao Tong University.  

          Chaochun Wei, Sc.D., Professor, Department of Bioinformatics and Biostatistics in the School of Life Sciences and Biotechnology at Shanghai Jiao Tong University. He obtained his B.S in Mathematics from Beijing University and Sc.D. in Computer Science from Washington University in St. Louis. His research interests are in genomics and evolutionary genomics, including the identification of functional elements in genomes and their evolution and functional analysis, pan-genome analysis for eukaryotes, pan-genome analysis for cancer genomes and metagenomics.

           

          Yingyan Yu, M.D., Ph.DProfessor of Ruijin hospital affiliated to School of Medicine, Shanghai Jiao Tong University, Associate Director of Shanghai Institute of Digestive Surgery, Committee member of Chinese Gastric Cancer Association, member of  Standing Committee of Biobank and Chronic Diseases Control of Chinese Association of Biopharmacology and Biotechnology. Shanghai Pujiang Talent Program award, Shanghai Municipal Science and Technology Committee outstanding academic leaders award. She is engaged in digestive pathology, molecular classification of cancers, biomarker and translational medicine studies. She has been awarded with grants for the precision medicine and chronic disease projects of the National Key R&D Program of China, the National Basic Research Program of China, Shanghai Science and Technology Committee, Innovation Foundation of Translational Medicine of Shanghai Jiao Tong University School of Medicine, Cross-Institute Research Fund of Shanghai Jiao Tong University and etc.

           

           
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