Haplotype-resolved genome sequencing of a Gujarati Indian individual

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Nature Biotechnology (Impact Factor: 41.51). 01/2011; 29(1):59-63. DOI: 10.1038/nbt.1740
Source: PubMed


Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. Although individual human genome sequencing is increasingly routine, nearly all such genomes are unresolved with respect to haplotype. Here we combine the throughput of massively parallel sequencing with the contiguity information provided by large-insert cloning to experimentally determine the haplotype-resolved genome of a South Asian individual. A single fosmid library was split into a modest number of pools, each providing ∼3% physical coverage of the diploid genome. Sequencing of each pool yielded reads overwhelmingly derived from only one homologous chromosome at any given location. These data were combined with whole-genome shotgun sequence to directly phase 94% of ascertained heterozygous single nucleotide polymorphisms (SNPs) into long haplotype blocks (N50 of 386 kilobases (kbp)). This method also facilitates the analysis of structural variation, for example, to anchor novel insertions to specific locations and haplotypes.

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    • "These results demonstrate that CPT-seq and fragScaff can improve the contiguity of assemblies generated from shotgun and short-range mate-pair libraries to a point suitable for chromosome-scale scaffolding (Supplemental Fig. S7). In Kitzman et al. (2011), we described a method that utilized the subhaploid content of each fosmid pool to anchor de novo assembled contigs from reads that did not align to the human reference genome, as well as a set of previously anchored sequences (hg18) described in Kidd et al. (2010) (Supplemental Fig. S8). This method worked on the premise that each window in the genome is hit by a discrete set of pools, as is each novel contig, and the window with maximum pool overlap with a novel contig is the most probable anchor location. "
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    ABSTRACT: We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9,216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to over 1 megabase. These pools are 'sub-haploid', in that the lengths of fragments contained in each pool sums to approximately 5 to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate 'joins' are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by 8 to 57 fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing mid-range contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.
    Genome Research 10/2014; 24(12). DOI:10.1101/gr.178319.114 · 14.63 Impact Factor
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    • "Its main drawback is a higher computational cost: its worst-case running time increases exponentially with the read coverage. Fortunately, modern long read technologies cover the genome at a relatively low depth (Duitama et al., 2012; Kitzman et al., 2010), making it possible to apply our algorithm to such data. In cases when the coverage is extremely high, ProbHap also uses a preprocessing heuristic to merge similar reads (see Section 4). "
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    ABSTRACT: Motivation: Accurate haplotyping—determining from which parent particular portions of the genome are inherited—is still mostly an unresolved problem in genomics. This problem has only recently started to become tractable, thanks to the development of new long read sequencing technologies. Here, we introduce ProbHap, a haplotyping algorithm targeted at such technologies. The main algorithmic idea of ProbHap is a new dynamic programming algorithm that exactly optimizes a likelihood function specified by a probabilistic graphical model and which generalizes a popular objective called the minimum error correction. In addition to being accurate, ProbHap also provides confidence scores at phased positions. Results: On a standard benchmark dataset, ProbHap makes 11% fewer errors than current state-of-the-art methods. This accuracy can be further increased by excluding low-confidence positions, at the cost of a small drop in haplotype completeness. Availability: Our source code is freely available at: Contact:
    Bioinformatics 09/2014; 30(17):i379-i385. DOI:10.1093/bioinformatics/btu484 · 4.98 Impact Factor
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    • "The 1000 Genomes Project has now systematically completed mapping the genomes of >1000 Africans, Americans, East Asians, and Europeans for genetic variation [1]. In contrast the genetic sequences of just two South Asians have been reported [2], [3]. South Asians are included in phases II and III of the 1000 Genome Project, but the present lack of knowledge of the South Asian genome remains an important obstacle to understanding the genetic mechanisms and biological pathways influencing the phenotypic differences and susceptibility to diseases among South Asians. "
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    ABSTRACT: The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.
    PLoS ONE 08/2014; 9(8):e102645. DOI:10.1371/journal.pone.0102645 · 3.23 Impact Factor
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