Whole-genome shotgun assembly and comparison of human genome assemblies

Istrail, Sorin; Sutton, Granger; Florea, Liliana; Halpern, Aaron L.; Mobarry, Clark; Lippert, Ross A.; Walenz, Brian P.; Shatkay, Hagit; Dew, Ian; Miller, Jason R.; Flanigan, Michael J.; Edwards, Nathan; Bolanos, Randall; Fasulo, Daniel; Halldórsson, Bjarni V.; Hannenhalli, Sridhar; Turner, Russell James; Yooseph, Shibu; Lu, Fu; Nusskern, Deborah; Shue, Bixiong Chris; Zheng, Xiangqun H.; Zhong, Fei; Delcher, Arthur L.; Huson, Daniel H.; Kravitz, Saul; Mouchard, Laurent; Reinert, Knut; Remington, Karin; Clark, Andrew G.; Waterman, Michael S.; Eichler, Evan E.; Adams, Mark D.; Hunkapiller, Michael W.; Myers, Eugene W.; Venter, J. Craig

doi:10.1073/pnas.0307971100

Cited by 162 publications

(117 citation statements)

References 32 publications

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“…Next, evidence for accurate long-range ordering and orienting of sequence contigs might naturally emerge from the broader whole-genome scaffolds, with any additional confirmation or refinement being performed, as needed. Of relevance, whole-genome shotgun sequencing projects typically include the generation of insert-end sequence reads from large-insert clones (e.g., BACs, fosmids, and large-insert plasmids) (Mouse Genome Sequencing Consortium 2002; Stein et al 2003;Istrail et al 2004); thus, following incorporation of such reads into a genome-wide sequence assembly, the corresponding clones could be used as substrates for PCR-based confirmation of contig order and orientation. Finally, the types of verification steps performed for BAC-derived sequences (e.g., comparisons to reference sequences and experimentally-derived restriction maps) could be scaled for use with whole-genome sequence assemblies, either globally or in a more targeted fashion.…”

Section: Discussionmentioning

confidence: 99%

An intermediate grade of finished genomic sequence suitable for comparative analyses

Blakesley

Hansen²,

Mullikin³

et al. 2004

Genome Res.

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Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires ∼40-fold less reagents and ∼10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses.

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Section: Discussionmentioning

confidence: 99%

An intermediate grade of finished genomic sequence suitable for comparative analyses

Blakesley

Hansen²,

Mullikin³

et al. 2004

Genome Res.

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“…To generate more SNPs and obtain validation information, shotgun sequencing of DNA from whole-genome libraries and flow-sorted chromosomes was performed 31 , augmented by analysis of sequence traces produced by Applied Biosystems 97,98 , and information on 1.6 million SNPs genotyped by Perlegen Sciences 77 , including 425,000 not in dbSNP when released (Supplementary Table 7). The HapMap Project contributed about 6 million new SNPs to dbSNP.…”

Section: Methodsmentioning

confidence: 99%

A haplotype map of the human genome

Belmont¹,

Boudreau²,

Leal³

et al. 2005

Nature

5,223

1,633

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A haplotype map of the human genomeThe International HapMap Consortium* Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

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“…The Celera sequences represent unconnected scaffolds grouped by chromosome. We also retrieved the Celera whole genome shotgun assembly (WGSA) sequences from GenBank (accessions AADD01000001-AADD01211493, Istrail et al, 2004). All sequences in fasta format were downloaded onto our local bioinformatics server for analyses.…”

Section: Sources For Genomic Sequencesmentioning

confidence: 99%

“…2 shows two examples of newly identified polymorphic Alu insertions. From the 236 polymorphic insertions identified in CHGS, we identified 190 from the Celera whole genome shotgun assembly (WGSA) sequences that were obtained exclusively using the Celera proprietary whole genome shotgun sequences (Istrail et al, 2004). The remaining 46 CHGS polymorphic elements were likely from the public human BAC sequences that may have not been used for the assembly of PHGS.…”

Section: Identification Of Alu Insertion Polymorphismsmentioning

confidence: 99%

“…In this study, we took advantage of the availability of two different assemblies of the human genome sequence, representing approximately two genomes plus partial genome sequences from additional ethnically diverse individuals (Istrail et al, 2004;Lander et al, 2001;Venter et al, 2001). The ascertainment of the polymorphic status of the each Alu element is based on in silico detection of presence and absence of an Alu sequence in the corresponding genomic regions of the two genome sequences.…”

Section: In Silico Comparative Genomics Approach To Identify Alu Insementioning

confidence: 99%

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Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Wang

Song

Gonder

et al. 2006

Gene

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Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

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Whole-genome shotgun assembly and comparison of human genome assemblies

Cited by 162 publications

References 32 publications

An intermediate grade of finished genomic sequence suitable for comparative analyses

An intermediate grade of finished genomic sequence suitable for comparative analyses

A haplotype map of the human genome

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

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