The diploid genome sequence of an Asian individual

By Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, G. Tian, L. Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang and 66 more. Nature, 2008

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Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual’s genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f50aa6fd3219148e91a614c1033fd5e6ac33b225

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Citations in the corpus

The sequence and de novo assembly of the giant panda genome (2009, neutral): “Step Paired-end insert size (bp)* Sequence coverage (3){ Physical coverage (3){ N50 (bp) { N90 (bp) { Total length (bp)”
Searching for SNPs with cloud computing (2009, methodology): “To demonstrate performance on real-world data, we used Crossbow to align and call SNPs from the set of 2.7 billion reads and paired-end reads sequenced from a Han Chinese male by Wang et al [5].”
The yak genome and adaptation to life at high altitude (2012, background): “Third, matching of ORFs to PFAM domain families at the protein level showed expansion in the numbers of specific domains ( Supplementary Table 12 ).”
IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler (2010, background): “Applications such as detection of structural variations [1] cannot be done easily based on resequencing techniques and there are evidences that show genome assembly based on resequencing may produce errors especially for species with high mutation rates [1].”
Genome assembly reborn: recent computational challenges (2009, methodology): “Since the introduction of the chain termination sequencing method by Frederick Sanger in 1977 [1], the genomes of more than 800 bacteria and 100 eukaryotes have been sequenced, including the genomes of several human individuals [2–4].”
A window into third-generation sequencing. (2010, methodology): “While this assembly approach is efficient for accurately identifying SNPs in the human genome (44,45), it does not enable a thorough characterization of structural variations, insertions and deletions.”
Toward better understanding of artifacts in variant calling from high-coverage samples (2014, methodology): “…of the ﬁrst personal genome (Levy et al., 2007) and in particular the ﬁrst genomes sequenced with the Illumina technologies (Bentley et al., 2008; Wang et al., 2008), resequencing has been widely used for personal and cancer genomics (Watson et al., 2013), for the discovery of de novo mutations…”
Using bioinformatics to predict the functional impact of SNVs (2011, background): “There is increasing interest in bioinformatics approaches to identify variants that are functionally important from millions of candidate variants.”
VarScan: variant detection in massively parallel sequencing of individual and pooled samples (2009, background): “The genomes of a Nobel laureate (Wheeler et al., 2008), anonymous African and Asian individuals (Bentley et al., 2008; Wang et al., 2008), and both tumor and normal cells of a cancer patient (Ley et al., 2008) have been fully sequenced; ambitious efforts like the 1,000 Genomes Project aim to extend…”