Ewen F Kirkness

Publications (37)483.09 Total impact

• Article: Sequencing of isolated sperm cells for direct haplotyping of a human genome.

  Ewen F Kirkness, Rashel V Grindberg, Joyclyn Yee-Greenbaum, Christian R Marshall, Stephen W Scherer, Roger S Lasken, J Craig Venter
  [show abstract] [hide abstract]
  ABSTRACT: There is increasing evidence that the phenotypic effects of genomic sequence variants are best understood in terms of variant haplotypes rather than as isolated polymorphisms. Haplotype analysis is also critically important for uncovering population histories, and for the study of evolutionary genetics. Although the sequencing of individual human genomes to reveal personal collections of sequence variants is now well established, there has been slower progress in the phasing of these variants into pairs of haplotypes along each pair of chromosomes. Here, we have developed a distinct approach to haplotyping that can yield chromosome-length haplotypes, including the vast majority of heterozygous SNPs in an individual human genome. This approach exploits the haploid nature of sperm cells, and employs a combination of genotyping and low-coverage sequencing on a short-read platform. In addition to generating chromosome-length haplotypes, the approach can directly identify recombination events (averaging 1.1 per chromosome) with a median resolution of less than 100 kb.
  Genome Research 01/2013; · 13.61 Impact Factor
• Source

  Available from: Carlos A Machado

  Dataset: nature06341-s1

  Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, Brian Oliver, Therese A Markow, Thomas C Kaufman, Manolis Kellis, William Gelbart, Venky N Iyer, [......], Chiao-Feng Lin, Michael F Lin, Kerstin Lindblad-Toh, Ana Llopart, Manyuan Long, Lloyd Low, Elena Lozovsky, Jian Lu, Meizhong Luo, Carlos A Machado
• Source

  Available from: Fabio Navarro

  Article: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.

  Pedro A F Galante, Raphael B Parmigiani, Qi Zhao, Otávia L Caballero, Jorge E de Souza, Fábio C P Navarro, Alexandra L Gerber, Marisa F Nicolás, Anna Christina M Salim, Ana Paula M Silva, [......], Ewen F Kirkness, Samuel Levy, Wilson A da Silva, Ana Tereza R Vasconcelos, Bing Ren, Marco Antonio Zago, Robert L Strausberg, Andrew J G Simpson, Sandro J de Souza, Anamaria A Camargo
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  ABSTRACT: Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.
  Nucleic Acids Research 04/2011; 39(14):6056-68. · 8.03 Impact Factor
• Source

  Available from: Raphael B Parmigiani

  Article: Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.

  Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew Jg Simpson, Robert L Strausberg
  [show abstract] [hide abstract]
  ABSTRACT: To identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity and allele-specific expression. The analysis was conducted on the breast cancer cell line HCC1954, and a lymphoblast cell line from the same individual, HCC1954BL. By comparing exome sequences from the two cell lines, we identified loss of heterozygosity events at 403 genes in HCC1954 and at one gene in HCC1954BL. The combination of exome and transcriptome sequence data also revealed 86 and 50 genes with allele specific expression events in HCC1954 and HCC1954BL, which comprise 5.4% and 2.6% of genes surveyed, respectively. Many of these genes identified by loss of heterozygosity and allele-specific expression are known or putative tumor suppressor genes, such as BRCA1, MSH3 and SETX, which participate in DNA repair pathways. Our results demonstrate that the combined application of high throughput sequencing to exome and allele-specific transcriptome analysis can reveal genes with known tumor suppressor characteristics, and a shortlist of novel candidates for the study of tumor suppressor activities.
  Genome biology 11/2010; 11(11):R114. · 6.63 Impact Factor
• Article: The dynamic genome of Hydra.

  Jarrod A Chapman, Ewen F Kirkness, Oleg Simakov, Steven E Hampson, Therese Mitros, Thomas Weinmaier, Thomas Rattei, Prakash G Balasubramanian, Jon Borman, Dana Busam, [......], J Craig Venter, Ulrich Technau, Bert Hobmayer, Thomas C G Bosch, Thomas W Holstein, Toshitaka Fujisawa, Hans R Bode, Charles N David, Daniel S Rokhsar, Robert E Steele
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  ABSTRACT: The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
  Nature 03/2010; 464(7288):592-6. · 36.28 Impact Factor
• Source

  Available from: Andy Wing Chun Pang

  Article: Towards a comprehensive structural variation map of an individual human genome.

  Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer
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  ABSTRACT: Several genomes have now been sequenced, with millions of genetic variants annotated. While significant progress has been made in mapping single nucleotide polymorphisms (SNPs) and small (<10 bp) insertion/deletions (indels), the annotation of larger structural variants has been less comprehensive. It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions. We have combined computational re-analysis of existing whole genome sequence data with novel microarray-based analysis, and detect 12,178 structural variants covering 40.6 Mb that were not reported in the initial sequencing of the first published personal genome. We estimate a total non-SNP variation content of 48.8 Mb in a single genome. Our results indicate that this genome differs from the consensus reference sequence by approximately 1.2% when considering indels/CNVs, 0.1% by SNPs and approximately 0.3% by inversions. The structural variants impact 4,867 genes, and >24% of structural variants would not be imputed by SNP-association. Our results indicate that a large number of structural variants have been unreported in the individual genomes published to date. This significant extent and complexity of structural variants, as well as the growing recognition of their medical relevance, necessitate they be actively studied in health-related analyses of personal genomes. The new catalogue of structural variants generated for this genome provides a crucial resource for future comparison studies.
  Genome biology 01/2010; 11(5):R52. · 6.63 Impact Factor
• Article: Whole genome sequencing.

  Pauline C Ng, Ewen F Kirkness
  [show abstract] [hide abstract]
  ABSTRACT: Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences. The reference-based assembly approach involves mapping each read to a reference genome sequence. We discuss methods for identifying genetic variation (single nucleotide polymorphisms, small indels, and copy number variants) and building haplotypes from genome assemblies, and discuss potential pitfalls. We expect methodologies to evolve rapidly as sequencing technologies improve and more human genomes are sequenced.
  Methods in molecular biology (Clifton, N.J.) 01/2010; 628:215-26.
• Source

  Available from: Venu M Margam

  Article: Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

  Ewen F Kirkness, Brian J Haas, Weilin Sun, Henk R Braig, M Alejandra Perotti, John M Clark, Si Hyeock Lee, Hugh M Robertson, Ryan C Kennedy, Eran Elhaik, [......], Terry R Utterback, Granger G Sutton, Daniel Lawson, Robert M Waterhouse, J Craig Venter, Robert L Strausberg, May R Berenbaum, Frank H Collins, Evgeny M Zdobnov, Barry R Pittendrigh
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  ABSTRACT: As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
  Proceedings of the National Academy of Sciences 01/2010; 107(27):12168-12173. · 9.68 Impact Factor
• Article: Mobile elements create structural variation: analysis of a complete human genome.

  Jinchuan Xing, Yuhua Zhang, Kyudong Han, Abdel Halim Salem, Shurjo K Sen, Chad D Huff, Qiong Zhou, Ewen F Kirkness, Samuel Levy, Mark A Batzer, Lynn B Jorde
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  ABSTRACT: Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed approximately 126 kb of sequence from the HuRef genome. Overall, approximately 10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation.
  Genome Research 06/2009; 19(9):1516-26. · 13.61 Impact Factor
• Article: The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus.

  Renfu Shao, Ewen F Kirkness, Stephen C Barker
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  ABSTRACT: The mitochondrial (mt) genomes of animals typically consist of a single circular chromosome that is approximately 16-kb long and has 37 genes. Our analyses of the sequence reads from the Human Body Louse Genome Project and the patterns of gel electrophoresis and Southern hybridization revealed a novel type of mt genome in the sucking louse, Pediculus humanus. Instead of having all mt genes on a single chromosome, the 37 mt genes of this louse are on 18 minicircular chromosomes. Each minicircular chromosome is 3-4 kb long and has one to three genes. Minicircular mt chromosomes are also present in the four other species of sucking lice that we investigated, but not in chewing lice nor in the Psocoptera, to which sucking lice are most closely related. We also report unequivocal evidence for recombination between minicircular mt chromosomes in P. humanus and for sequence variation in mt genes generated by recombination. The advantages of a fragmented mt genome, if any, are currently unknown. Fragmentation of mt genome, however, has coevolved with blood feeding in the sucking lice. It will be of interest to explore whether or not life history features are associated with the evolution of fragmented chromosomes.
  Genome Research 04/2009; 19(5):904-12. · 13.61 Impact Factor
• Chapter: Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps

  Christophe Hitte, Ewen F. Kirkness, Elaine A. Ostrander, Francis Galibert
  [show abstract] [hide abstract]
  ABSTRACT: Radiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value. A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than ×7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes. Key WordsRH Mapping–survey sequencing–comparative genomics–synteny–canine genome–high-coverage genome sequencing.
  07/2008: pages 65-77;
• Chapter: The TIGR Human cDNA Database

  Ewen F. Kirkness, Anthony R. Kerlavage
  [show abstract] [hide abstract]
  ABSTRACT: The Human cDNA Database (HCD) is a repository for human cDNA sequences and related data that is curated and maintained at The Institute for Genomic Research (TIGR). The foundation of the database is ∼160,000 partial cDNA sequences that have been generated by TIGR and Human Genome Sciences (HGS). These expressed sequence tags (ESTs) were derived from 250 cDNA libraries that represent the expressed genes of 37 distinct human organs and tissues (1). A combination of these ESTs and the human ESTs from dbEST has been assembled to yield ∼56,000 consensus sequences and ∼106,000 nonoverlapping ESTs. Of these ∼162,000 distinct sequences, approx 18% display statistically significant similarity to previously known genes, whereas the remainder identify previously unknown cDNAs. The HCD data include nucleotide sequences, putative identifications of the sequences, and tissue-based expression information. New EST sequences that are acquired by TIGR are assembled and curated in an ongoing process that aims to provide a comprehensive database of human genes and their expression patterns. The development of HCD required the construction of a sister database, the Expressed Gene Anatomy Database (EGAD). This database contains a nonredundant dataset of human transcript sequences, together with information on expression patterns and cellular roles. Extensive links between HCD and EGAD permit browsing of sequence information, functional classifications, and tissue expression patterns for particular genes of interest. Owing to the random nature of large-scale EST sampling and the wide range of tissues that have been sampled, the data that can be extracted from HCD are of particular value for several common types of cDNA sequence analyses.
  02/2008: pages 261-268;
• Article: Survey sequencing and radiation hybrid mapping to construct comparative maps.

  Christophe Hitte, Ewen F Kirkness, Elaine A Ostrander, Francis Galibert
  [show abstract] [hide abstract]
  ABSTRACT: Radiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value.A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than x7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes.
  Methods in molecular biology (Clifton, N.J.) 01/2008; 422:65-77.
• Article: Breed relationships facilitate fine-mapping studies: a 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds.

  Heidi G Parker, Anna V Kukekova, Dayna T Akey, Orly Goldstein, Ewen F Kirkness, Kathleen C Baysac, Dana S Mosher, Gustavo D Aguirre, Gregory M Acland, Elaine A Ostrander
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  ABSTRACT: The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage.
  Genome Research 12/2007; 17(11):1562-71. · 13.61 Impact Factor
• Source

  Available from: Carlos A Machado

  Article: Evolution of genes and genomes on the Drosophila phylogeny.

  Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, Brian Oliver, Therese A Markow, Thomas C Kaufman, Manolis Kellis, William Gelbart, Venky N Iyer, [......], Andrew Zimmer, Zac Zwirko, Pablo Alvarez, Will Brockman, Jonathan Butler, CheeWhye Chin, Manfred Grabherr, Michael Kleber, Evan Mauceli, Iain MacCallum
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  ABSTRACT: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
  Nature 12/2007; 450(7167):203-18. · 36.28 Impact Factor
• Article: Evolution of genes and genomes on the Drosophila phylogeny

  Andrew G. Clark, Michael B. Eisen, Douglas R. Smith, Casey M. Bergman, Brian Oliver, Therese A. Markow, Thomas C. Kaufman, Manolis Kellis, William Gelbart, Venky N. Iyer, [......], Andrew Zimmer, Zac Zwirko, Pablo Alvarez, Will Brockman, Jonathan Butler, CheeWhye Chin, Manfred Grabherr, Michael Kleber, Evan Mauceli, Iain MacCallum
  [show abstract] [hide abstract]
  ABSTRACT: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
  Nature 11/2007; 450(7167):203-218. · 36.28 Impact Factor
• Source

  Available from: Andy Wing Chun Pang

  Article: The diploid genome sequence of an individual human.

  Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, [......], Tina C McIntosh, Karin A Remington, Josep F Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E Frazier, Stephen W Scherer, Robert L Strausberg, J Craig Venter
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  ABSTRACT: Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2-206 bp), 292,102 heterozygous insertion/deletion events (indels)(1-571 bp), 559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.
  PLoS Biology 09/2007; 5(10):e254. · 11.45 Impact Factor
• Source

  Available from: Galt Prager Barber

  Article: Evolutionary and biomedical insights from the rhesus macaque genome.

  Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, Elaine R Mardis, Karin A Remington, Robert L Strausberg, J Craig Venter, Richard K Wilson, [......], Peng Wang, Andy Peng Xiang, Fan Yang, Galt P Barber, David Haussler, Donna Karolchik, Andy D Kern, Robert M Kuhn, Kayla E Smith, Ann S Zwieg
  [show abstract] [hide abstract]
  ABSTRACT: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
  Science 05/2007; 316(5822):222-34. · 31.20 Impact Factor
• Source

  Available from: PubMed Central

  Article: Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome.

  Byrappa Venkatesh, Ewen F Kirkness, Yong-Hwee Loh, Aaron L Halpern, Alison P Lee, Justin Johnson, Nidhi Dandona, Lakshmi D Viswanathan, Alice Tay, J Craig Venter, Robert L Strausberg, Sydney Brenner
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  ABSTRACT: Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.
  PLoS Biology 05/2007; 5(4):e101. · 11.45 Impact Factor
• Article: Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

  Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, [......], Peng Wang, Andy Peng Xiang, Fan Yang, Galt P. Barber, David Haussler, Donna Karolchik, Andy D. Kern, Robert M. Kuhn, Kayla E. Smith, Ann S. Zwieg
  [show abstract] [hide abstract]
  ABSTRACT: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
  Science 04/2007; 316(5822):222-234. · 31.20 Impact Factor