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Comparative Study

The diploid genome sequence of an Asian individual (VSports)

Jun Wang et al. Nature. .

Abstract

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 VSports手机版. 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. .

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Figures

Figure 1
Figure 1. The percentage of detected SNPs (a) and small indels (b) that overlap with SNPs and small indels in the dbSNP database (http://www.ncbi.nlm.nih.gov/SNP/, build 128)
The dbSNP alleles were separated into validated and non-validated SNPs, and the detected SNPs that were not present in dbSNP were classified as novel.
Figure 2
Figure 2. Genome coverage of the assembled consensus sequence and the accuracy of SNP detection as a function of sequencing depth
Analyses were carried out on human chromosome 12, and subsets of reads from all mapped 22.5× single-end and 13.5× paired-end reads were randomly extracted from areas of different average depth. The same method and filtering threshold (Q20) was used for SNP detection over different sequencing depths. The error rate for SNP calling—the sum of ‘over call’, ‘under call’ and ‘misses’ rate (see Supplementary Information)—was separated into heterozygotes (HET) and homozygotes (HOM), and was validated against the Illumina 1M genotyping alleles.
Figure 3
Figure 3. Summary of structural variations
a, Abundance of each class of structural variation. The overlap with known structural variations in the DGV (http://projects.tcag.ca/variation/) and with transposons (transposable elements, TEs) was calculated. About 34% of our identified structural variations are novel (having less than 10% of a portion of the YH structural variations overlapping with structural variations in the DGV). Transposable elements are a major component of the identified deletions, with Alus and LINEs involved in 49% and 34% of the deletions, respectively. b, An example of a deletion of a transposon complex on YH chromosome 1. The sequencing depth by both single-end and paired-end reads are shown. Normally aligned paired-end reads are shown in green, whereas abnormally aligned paired-end reads, which have unexpected long insert sizes or an incorrect orientation relationship, are shown in red. c, An example of an inversion on YH chromosome 19. Local assembly showed that a 102,405-bp fragment was inverted and reinserted in the genome. There are three genes in this sequence fragment, and the last exon of gene CYP4F12 was destroyed by this inversion event.
Figure 4
Figure 4. Size distribution of predicted haplotype blocks of autosomes
Haplotypes were constructed using PHASE software with the 700,300 autosomal heterozygous SNPs that overlapped with the CHB/JPT genotypes from the HapMap phase II data.
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