The Genome of Homo sapiens

Symposium Volume LXVIII Contents

 
             Symposium Participants v

              Foreword xxi 
			
            Human Genome Sequence
 The Finished Genome Sequence of Homo sapiens J. ROGERS 1

              The Human Genome: Genes, Pseudogenes, and Variation on Chromosome 
              7 R.H. WATERSTON, L.W. HILLIER, L.A. FULTON, R.S. FULTON, T.A. GRAVES, 
              K.H. PEPIN, P. BORK, M. SUYAMA, D. TORRENTS, A.T. CHINWALLA, E.R. 
              MARDIS, J.D. MCPHERSON, R.K. WILSON 13

              Mutational Profiling in the Human Genome R.K. WILSON, T.J. LEY, 
              F.S. COLE, J.D. MILBRANDT, S. CLIFTON, L. FULTON, G. FEWELL, P. 
              MINX, H. SUN, M. MCLELLAN, C. POHL, E.R. MARDIS 23

              Assessing the Quality of Finished Genomic Sequence J. SCHMUTZ, J. 
              WHEELER, J. GRIMWOOD, M. DICKSON, R.M. MYERS 31

              Human Subtelomeric DNA H. RIETHMAN, A. AMBROSINI, C. CASTANEDA, 
              J.M. FINKLESTEIN, X.-L. HU, S. PAUL, J. WEI 39

              Genome Research: The Next Generation F.S. COLLINS 49

Human Genetic Variation 
DNA Sequence Variation of Homo sapiens D.R. BENTLEY 55

              SNP Genotyping and Molecular Haplotyping of DNA Pools P.-Y. KWOK, 
              M. XIAO 65
            
              Highly Parallel SNP Genotyping J.-B. FAN, A. OLIPHANT, R. SHEN, 
              B.G. KERMANI, F. GARCIA, K.L. GUNDERSON, M. HANSEN, F. STEEMERS, 
              S.L. BUTLER, P. DELOUKAS, L. GALVER, S. HUNT, C. MCBRIDE, M. BIBIKOVA, 
              T. RUBANO, J. CHEN, E. WICKHAM, D. DOUCET, W. CHANG, D. CAMPBELL, 
              B. ZHANG, S. KRUGLYAK, D. BENTLEY, J. HAAS, P. RIGAULT, L. ZHOU, 
              et al. 69

              Structure of Linkage Disequilibrium in Humans: Genome Factors and 
              Population Stratification J. BERTRANPETIT, F. CALAFELL, D. COMAS, 
              A. GONZÁLEZ-NEIRA, A. NAVARRO 79

              Genome-wide Association of Haplotype Markers to Gene Expression 
              Levels . A. WINDEMUTH, M. KUMAR, K. NANDABALAN, B. KOSHY, C. XU, 
              M. PUNGLIYA, R. JUDSON 89

              Genetic Variation and the Control of Transcription C. COTSAPAS, 
              E. CHAN, M. KIRK, M. TANAKA, P. LITTLE 109

              Genome Structure and Evolution
Genome-wide Detection and Analysis of Recent Segmental Duplications 
              within Mammalian Organisms J.A. BAILEY, E.E. EICHLER 115

              The Effects of Evolutionary Distance on TWINSCAN, an Algorithm for 
              Pair-wise Comparative Gene Prediction M. WANG, J. BUHLER, M.R. BRENT 
              125

              Lineage-specific Expansion of KRAB Zinc-finger Transcription Factor 
              Genes: Implications for the Evolution of Vertebrate Regulatory Networks 
              A.T. HAMILTON, S. HUNTLEY, J. KIM, E. BRANSCOMB, L. STUBBS 131

              Sequence Organization and Functional Annotation of Human Centromeresn 
              M.K. RUDD, M.G. SCHUELER, H.F. WILLARD 141

Genomics of Non-human Species 
Evolutionary Strategies of Human Pathogens J. PARKHILL, N. THOMSON 
              151

              Gene Expression Profiling of Cells, Tissues, and Developmental Stages 
              of the Nematode C. elegans S.J. MCKAY, R. JOHNSEN, J. KHATTRA, 
              J. ASANO, D.L. BAILLIE, S. CHAN, N. DUBE, L. FANG, B. GOSZCZYNSKI, 
              E. HA, E. HALFNIGHT, R. HOLLEBAKKEN, P. HUANG, K. HUNG, V. JENSEN, 
              S.J.M. JONES, H. KAI, D. LI, A. MAH, M. MARRA, J. MCGHEE, R. NEWBURY, 
              et al. 159

              Building Comparative Maps Using 1.5x Sequence Coverage: Human Chromosome 
              1p and the Canine Genome R. GUYON, E.F. KIRKNESS, T.D. LORENTZEN, 
              C. HITTE, K.E. COMSTOCK, P. QUIGNON, T. DERRIEN, C. ANDRÉ, C.M. 
              FRASER, F. GALIBERT, E.A. OSTRANDER 171

              Positional Identification of Structural and Regulatory Quantitative 
              Trait Nucleotides in Domestic Animal Species M. GEORGES, L. ANDERSSON 
              179

              Evolving Methods for the Assembly of Large Genomes R.A. GIBBS, G.M. 
              WEINSTOCK 189

              Mouse Genome Encyclopedia Project Y. HAYASHIZAKI 195

Bioinformatics and Annotation 
            
DNA Sequence Assembly and Multiple Sequence Alignment by an Eulerian 
              Path Approach Y. ZHANG, M.S. WATERMAN 205

              Ensembl: A Genome Infrastructure E. BIRNEY, THE ENSEMBL TEAM 213

              Prediction, Annotation, and Analysis of Human Promoters M.Q. ZHANG 
              217 
 Ontologies for Biologists: A Community Model for the Annotation 
              of Genomic Data M. ASHBURNER, C.J. MUNGALL, S.E. LEWIS 227

              The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists 
              G. JOSHI-TOPE, I. VASTRIK, G.R. GOPINATH, L. MATTHEWS, E. SCHMIDT, 
              M. GILLESPIE, P. D'EUSTACHIO, B. JASSAL, S. LEWIS, G. WU, E. BIRNEY, 
              L. STEIN 237

              Comparing Genomes
The Share of Human Genomic DNA under Selection Estimated from Human–Mouse 
              Genomic Alignments F. CHIAROMONTE, R.J. WEBER, K.M. ROSKIN, M. DIEKHANS, 
              W.J. KENT, D. HAUSSLER 235

              Detecting Highly Conserved Regions of the Human Genome by Multispecies 
              Sequence Comparisons E.H. MARGULIES, NISC COMPARATIVE SEQUENCING 
              PROGRAM, E.D. GREEN 255 

              Comparative Analysis of Human Chromosome 22q11.1-q12.3 with Syntenic 
              Regions in the Chimpanzee, Baboon, Bovine, Mouse, Pufferfish, and 
              Zebrafish Genomes B.A. ROE, C. LAU, S. OOMMEN, J. LI, A. HUA, H.S. 
              LAI, S. KENTON, J. WHITE, H. WANG 265

              Genome-wide Analyses Based on Comparative Genomics O. JAILLON, J.-M. 
              AURY, H. ROEST CROLLIUS, M. SALANOUBAT, P. WINCKER, C. DOSSAT, V. 
              CASTELLI, N. BOUDET, S. SAMAIR, R. ECKENBERG, S. BONNEVAL, W. SAURIN, 
              C. SCARPELLI, V. SCHÄCHTER, J. WEISSENBACH 275

              Comparative Genomic Tools for Exploring the Human Genome I. OVCHARENKO, 
              G.G. LOOTS 283

              Evolution of Eukaryotic Gene Repertoire and Gene Structure: Discovering 
              the Unexpected Dynamics of Genome Evolution I.B. ROGOZIN, V.N. BABENKO, 
              N.D. FEDOROVA, J. D. JACKSON, A.R. JACOBS, D.M. KRYLOV, K.S. MAKAROVA, 
              R. MAZUMDER, S.L. MEKHEDOV, B.G. MIRKIN, A.N. NIKOLSKAYA, B.S. RAO, 
              S. SMIRNOV, A.V. SOROKIN, A.V. SVERDLOV, S. VASUDEVAN, Y.I. WOLF, 
              J.J. YIN, D.A. NATALE, E.V. KOONIN 293 
Comparative Functional Genomics

              Human–Mouse Comparative Genomics: Successes and Failures to Reveal 
              Functional Regions of the Human Genome L.A. PENNACCHIO, N. BAROUKH, 
              E.M. RUBIN 303

              High-Throughput Mouse Knockouts Provide a Functional Analysis of 
              the Genome C.J. FRIDDLE, A. ABUIN, R. RAMIREZ-SOLIS, L.J. RICHTER, 
              E.C. BUXTON, J. EDWARDS, R.A. FINCH, A. GUPTA, G. HANSEN, K.H. HOLT, 
              Y. HU, W. HUANG, C. JAING, B.W. KEY, P. KIPP, B. KOHLHAUFF, Z.-Q. 
              MA, D. MARKESICH, M. NEWHOUSE, T. PERRY, K.A. PLATT, D.G. POTTER, 
              N. QIAN, J. SHAW, J. SCHRICK, Z.-Z. SHI, M.J. SPARKS, D. TRAN, E.R. 
              WANN, et al. 311

              Identification of Novel Functional Elements in the Human Genome 
              Z. LIAN, G. EUSKIRCHEN, J. RINN, R. MARTONE, P. BERTONE, S. HARTMAN, 
              T. ROYCE, K. NELSON, F. SAYWARD, N. LUSCOMBE, J. YANG, J.-L. LI, 
              P. MILLER, A.E. URBAN, M. GERSTEIN, S. WEISSMAN, M. SNYDER 317

              High-resolution Human Genome Scanning Using Whole-genome BAC Arrays 
              J. LI, T. JIANG, B. BEJJANI, E. RAJCAN-SEPAROVIC, W.-W. CAI 323

              Annotation of Novel Proteins Utilizing A Functional Genome Shotgun 
              Coupled with High-Throughput Protein Interaction Mapping J.A. MALEK, 
              J.M. WIERZBOWSKI, G.A. DASCH, M.E. EREMEVA, P.J. MCEWAN, K.J. MCKERNAN 
              331 

              Global Predictions and Tests of Erythroid Regulatory Regions R.C. 
              HARDISON, F. CHIAROMONTE, D. KOLBE, HAO WANG, H. PETRYKOWSKA, L. 
              ELNITSKI, S. YANG, B. GIARDINE, Y. ZHANG, C. RIEMER, S. SCHWARTZ, 
              D. HAUSSLER, K.M. ROSKIN, R.J. WEBER, M. DIEKHANS, W. J. KENT, M.J. 
              WEISS, J. WELCH, W. MILLER 335

              Systems Approaches Applied to the Study of Saccharomyces cerevisiae 
              and Halobacterium sp. A.D. WESTON, N.S. BALIGA, R. BONNEAU, 
              L. HOOD 345 

              Genetic Variation and Disease
 Implications of Genomics for Public Health: The Role of Genetic 
              Epidemiology K.R. MERIKANGAS 359

              A Model System for Identifying Genes Underlying Complex Traits D. 
              DRAYNA, U.-K. KIM, H. COON, E. JORGENSON, N. RISCH, M. LEPPERT 365

              Genomic Variation in Multigenic Traits: Hirschsprung Disease A.S. 
              MCCALLION, E.S. EMISON, C.S. KASHUK, R.T. BUSH, M. KENTON, M.M. 
              CARRASQUILLO, K.W. JONES, G.C. KENNEDY, M.E. PORTNOY, E.D. GREEN, 
              A. CHAKRAVARTI 373

              Genetics of Schizophrenia and Bipolar Affective Disorder: Strategies 
              to Identify Candidate Genes D.J. PORTEOUS, K.L. EVANS, J.K. MILLAR, 
              B.S. PICKARD, P.A. THOMSON, R. JAMES, S. MACGREGOR, N.R. WRAY, P.M. 
              VISSCHER, W.J. MUIR, D.H. BLACKWOOD 383

              The Genetics of Common Diseases: 10 Million Times as Hard D.B. GOLDSTEIN, 
              G.L. CAVALLERI, K.R. AHMADI 395

              Genetics of Quantitative Variation in Human Gene Expression V.G. 
              CHEUNG, K.-Y. JEN, T. WEBER, M. MORLEY, J.L. DEVLIN, K.G. EWENS, 
              R.S. SPIELMAN 403

              Regulation of α-Synuclein Expression: Implications for Parkinson's 
              Disease O. CHIBA-FALEK, R.L. NUSSBAUM 409

              Genome Biology and Disease

              Genomic Perspective and Cancer D. BOTSTEIN 417

              Chromosome 21 and Down Syndrome: The Post-Sequence Era S.E. ANTONARAKIS, 
              A. REYMOND, R. LYLE, S. DEUTSCH, E.T. DERMITZAKIS 425

              Harvesting the Genome's Bounty: Integrative Genomics P. JORGENSEN, 
              B.-J. BREITKREUTZ, K. BREITKREUTZ, C. STARK, G. LIU, M. COOK, J. 
              SHAROM, J.L. NISHIKAWA, T. KETELA, D. BELLOWS, A. BREITKREUTZ, I. 
              RUPES, L. BOUCHER, D. DEWAR, M. VO, M. ANGELI, T. REGULY, A. TONG, 
              B. ANDREWS, C. BOONE, M. TYERS 431

              Genomic Disorders: Genome Architecture Results in Susceptibility 
              to DNA Rearrangements Causing Common Human Traits P. STANKIEWICZ, 
              K. INOUE, W. BI, K. WALZ, S.-S. PARK, N. KUROTAKI, C.J. SHAW, P. 
              FONSECA, J. YAN, J.A. LEE, M. KHAJAVI, J.R. LUPSKI 445

              Human Evolution
 
              Human Versus Chimpanzee Chromosome-wide Sequence Comparison and 
              Its Evolutionary Implication Y. SAKAKI, H. WATANABE, T. TAYLOR, 
              M. HATTORI, A. FUJIYAMA, A. TOYODA, Y. KUROKI, T. ITOH, N. SAITOU, 
              S. OOTA, C.-G. KIM, T. KITANO, H. LEHRACH, M.-L. YASPO, R. SUDBRAK, 
              A. KAHLA, R. REINHARDT, M. KUBE, M. PLATZER, S. TAENZER, P. GALGOCZY, 
              A. KEL, et al. 455

              Novel Transcriptional Units and Unconventional Gene Pairs in the 
              Human Genome: Toward a Sequence-level Basis for Primate-specific 
              Phenotypes? L. LIPOVICH, M.-C. KING 461

              Positive Selection in the Human Genome Inferred from Human–Chimp–Mouse 
              Orthologous Gene Alignments A.G. CLARK, S. GLANOWSKI, R. NIELSEN, 
              P. THOMAS, A. KEJARIWAL, M.J. TODD, D.M. TANENBAUM, D. CIVELLO, 
              F. LU, B. MURPHY, S. FERRIERA, G. WANG, X. ZHENG, T.J. WHITE, J.J. 
              SNINSKY, M.D. ADAMS, M. CARGILL 479

              mtDNA Variation, Climatic Adaptation, Degenerative Diseases, and 
              Longevity .C. WALLACE, E. RUIZ-PESINI, D. MISHMAR 471

              Inferring Human History: Clues from Y-Chromosome Haplotypes P.A. 
              UNDERHILL 487

              Summary: The New Quantitative Biology M.V. OLSON 495

              Author Index 503

              Subject Index 505