The Genom of Homo sapiens.pdf

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MOUSE KNOCKOUTS ILLUSTRATE FUNCTION 315S., Dow S., Lucau-Danila A., Anderson K., Andre B., ArkinA.P., Astromoff A., El-Bakkoury M., Bangham R., Benito R.,Brachat S., Campanaro S., Curtiss M., Davis K.,Deutschbauer A., Entian K.D., Flaherty P., Foury F.,Garfinkel D.J., and Gerstein M., et al. 2002. Functional profilingof the Saccharomyces cerevisiae genome. Nature 418:387.Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E.,Chen W., Burgess S., Haldi M., Artzt K., Farrington S., LinS.Y., Nissen R.M., and Hopkins N. 2002. Insertional mutagenesisin zebrafish rapidly identifies genes essential for earlyvertebrate development. Nat. Genet. 31: 135.Jorgensen E.M. and Mango S.E. 2002. The art and design of geneticscreens: Caenorhabditis elegans. Nat. Rev. Genet. 3: 356.Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C.,Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W.,Funke R., Gage D., Harris K., Heaford A., Howland J., KannL., Lehoczky J., LeVine R., McEwan P., McKernan K.,Meldrim J., Mesirov J.P., Miranda C., Morris W., and NaylorJ., et al. (International Human Genome Sequencing Consortium).2001. Initial sequencing and analysis of the humangenome. Nature 409: 860.Oh S.W., Kingsley T., Shin H.H., Zheng Z., Chen H.W., ChenX., Wang H., Ruan P., Moody M., and Hou S.X. 2003. A P-element insertion screen identified mutations in 455 novel essentialgenes in Drosophila. Genetics 163: 195.Rabitsch K.P., Toth A., Galova M., Schleiffer A., Schaffner G.,Aigner E., Rupp C., Penkner A.M., Moreno-Borchart A.C.,Primig M., Esposito R.E., Klein F., Knop M., and Nasmyth K.2001. A screen for genes required for meiosis and spore formationbased on whole-genome expression. Curr. Biol. 11: 1001.Sands A.T. 2003. The master mammal. Nat. Biotechnol. 21: 31.Sessions A., Burke E., Presting G., Aux G., McElver J., PattonD., Dietrich B., Ho P., Bacwaden J., Ko C., Clarke J.D., CottonD., Bullis D., Snell J., Miguel T., Hutchison D., KimmerlyB., Mitzel T., Katagiri F., Glazebrook J., Law M., and GoffS.A. 2002. A high-throughput Arabidopsis reverse geneticssystem. Plant Cell 14: 2985.Silver J. and Keerikatte V. 1989. Novel use of polymerase chainreaction to amplify cellular DNA adjacent to an integratedprovirus. J. Virol. 63: 1924.Skarnes W.C., Auerbach B.A., and Joyner A.L. 1992. A genetrap approach in mouse embryonic stem cells: The lacZ reportedis activated by splicing, reflects endogenous gene expression,and is mutagenic in mice. Genes Dev. 6: 903.Sorlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., JohnsenH., Hastie T., Eisen M.B., van de Rijn M., Jeffrey S.S.,Thorsen T., Quist H., Matese J.C., Brown P.O., Botstein D.,Eystein Lonning P., and Borresen-Dale A.L. 2001. Gene expressionpatterns of breast carcinomas distinguish tumor subclasseswith clinical implications. Proc. Natl. Acad. Sci. 98:10869.Thomas K.R. and Capecchi M.R. 1989. Site-directed mutagenesisby gene targeting in mouse embryo-derived stem cells.Cell 51: 503.Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., AbrilJ.F., Agarwal P., Agarwala R., Ainscough R., AlexanderssonM., An P., Antonarakis S.E., Attwood J., Baertsch R., BaileyJ., Barlow K., Beck S., Berry E., Birren B., Bloom T., BorkP., Botcherby M., Bray N., Brent M.R., Brown D.G., andBrown S.D., et al. (Mouse Genome Sequencing Consortium).2002. Initial sequencing and comparative analysis of themouse genome. Nature 420: 520.Zambrowicz B.P. and Friedrich G.A. 1998. Comprehensivemammalian genetics: History and future prospects of genetrapping in the mouse. Int. J. Dev. Biol. 42: 1025.Zambrowicz B.P. and Sands A.T. 2003. Knockouts model the100 best-selling drugs—Will they model the next 100? Nat.Rev. Drug Discov. 2: 38.Zambrowicz B.P., Friedrich G.A., Buxton E.C., Lilleberg S.L.,Person C., and Sands A.T. 1998. Disruption and sequenceidentification of 2,000 genes in mouse embryonic stem cells.Nature 392: 608.Zambrowicz B.P., Abuin A., Ramirez-Solis R., Richter L.J., PiggottJ., BeltrandelRio H., Buxton E.C., Edwards J., FinchR.A., Friddle C.J., Gupta A., Hansen G., Hu Y., Huang W.,Jaing C., Key B.W., Jr., Kipp P., Kohlhauff B., Ma X.Q.,Markesich D., Payne R., Potter D.G., Qian N., Shaw J., andSchrick H.J., et al. 2003. Wnk1 kinase deficiency lowersblood pressure in mice: A gene-trap screen to identify potentialtargets for therapeutic intervention. Proc. Natl. Acad. Sci.100: 14109.
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ForewordIn 2001, as we considered t
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The Finished Genome Sequence of Hom
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4 ROGERSFigure 2. Accumulation of h
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6 ROGERSFigure 4. Sequencing center
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8 ROGERSabcFigure 5. Ensembl view o
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10 ROGERS2000. Analysis of vertebra
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The Human Genome: Genes, Pseudogene
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VARIATION ON CHROMOSOME 7 15rived f
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VARIATION ON CHROMOSOME 7 17DNAs an
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VARIATION ON CHROMOSOME 7 19expecte
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VARIATION ON CHROMOSOME 7 21Drosoph
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Mutational Profiling in the Human G
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HUMAN MUTATIONAL PROFILING 25Anothe
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HUMAN MUTATIONAL PROFILING 27Figure
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HUMAN MUTATIONAL PROFILING 29Rieder
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32 SCHMUTZ ET AL.algorithm itself,
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34 SCHMUTZ ET AL.Figure 2. Genomic
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36 SCHMUTZ ET AL.compared. Some of
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Human Subtelomeric DNAH. RIETHMAN,
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HUMAN SUBTELOMERIC SEQUENCES 41The
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HUMAN SUBTELOMERIC SEQUENCES 43cate
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HUMAN SUBTELOMERIC SEQUENCES 45Figu
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HUMAN SUBTELOMERIC SEQUENCES 47pres
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50 COLLINSand expand the genomics r
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52 COLLINSFigure 2. A public-sector
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54 COLLINSdefine all the parts of t
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56 BENTLEYmon over many generations
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58 BENTLEYTable 1. Genetic Disease
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60 BENTLEY(Clark et al. 1998; Reich
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62 BENTLEYACKNOWLEDGMENTSThe author
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SNP Genotyping and Molecular Haplot
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GENETIC ANALYSIS OF DNA POOLS 67gen
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70 FAN ET AL.matrix is then mated t
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72 FAN ET AL.Figure 3. Views of gen
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74 FAN ET AL.including 32 duplicate
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76 FAN ET AL.Figure 7. Allele-speci
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78 FAN ET AL.microsphere-based assa
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80 BERTRANPETIT ET AL.function, may
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82 BERTRANPETIT ET AL.diversity in
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84 BERTRANPETIT ET AL.gree of block
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86 BERTRANPETIT ET AL.Figure 1. Dec
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88 BERTRANPETIT ET AL.1999. Populat
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90 WINDEMUTH ET AL.Expression data.
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92 WINDEMUTH ET AL.Table 1. A Summa
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94 WINDEMUTH ET AL.Table 2. Signifi
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96 WINDEMUTH ET AL.Table 3. Summary
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98 WINDEMUTH ET AL.Table 6. List of
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100 WINDEMUTH ET AL.Table 6. (Conti
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102 WINDEMUTH ET AL.Table 6. (Conti
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104 WINDEMUTH ET AL.much of a surpr
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106 WINDEMUTH ET AL.Given our resul
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Genetic Variation and the Control o
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GENETIC CONTROL OF TRANSCRIPTION 11
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GENETIC CONTROL OF TRANSCRIPTION 11
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Genome-wide Detection and Analysis
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RECENT SEGMENTAL DUPLICATIONS 117Fi
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RECENT SEGMENTAL DUPLICATIONS 119St
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RECENT SEGMENTAL DUPLICATIONS 121Co
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RECENT SEGMENTAL DUPLICATIONS 123Ho
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The Effects of Evolutionary Distanc
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EVOLUTIONARY DISTANCE AND GENE PRED
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EVOLUTIONARY DISTANCE AND GENE PRED
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Lineage-specific Expansion of KRAB
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EVOLUTION OF ZNF GENES 133Figure 2.
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EVOLUTION OF ZNF GENES 135Figure 4.
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EVOLUTION OF ZNF GENES 137get gene,
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EVOLUTION OF ZNF GENES 139Y., Goodw
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Sequence Organization and Functiona
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CENTROMERE ANNOTATION 143THE CENTRO
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CENTROMERE ANNOTATION 145Figure 4.
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CENTROMERE ANNOTATION 147CONCLUSION
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CENTROMERE ANNOTATION 149Schueler M
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152 PARKHILL AND THOMSONFigure 1. T
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154 PARKHILL AND THOMSONshow very h
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156 PARKHILL AND THOMSONGene Loss a
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158 PARKHILL AND THOMSONYersinia ad
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160 MCKAY ET AL.Choosing Candidate
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162 MCKAY ET AL.new comparative too
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164 MCKAY ET AL.rich. Based on a th
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166 MCKAY ET AL.Embryonic Muscle an
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168 MCKAY ET AL.native polyadenylat
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Building Comparative Maps Using 1.5
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HUMAN CHROMOSOME 1p IN THE DOG 1731
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HUMAN CHROMOSOME 1p IN THE DOG 175(
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HUMAN CHROMOSOME 1p IN THE DOG 177l
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180 GEORGES AND ANDERSSON5. There i
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182 GEORGES AND ANDERSSONplied to r
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184 GEORGES AND ANDERSSONbe common
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186 GEORGES AND ANDERSSONin humans
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Evolving Methods for the Assembly o
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ASSEMBLING LARGE GENOMES 191Figure
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ASSEMBLING LARGE GENOMES 193tant ad
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Mouse Genome Encyclopedia ProjectY.
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MOUSE GENOME ENCYCLOPEDIA PROJECT 1
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DNA Sequence Assembly and Multiple
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EULERIAN ASSEMBLY AND MULTIPLE ALIG
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Ensembl: A Genome InfrastructureE.
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ENSEMBL 215projects often submit th
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218 ZHANGthe majority of these are
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220 ZHANGFigure 2. Demonstration of
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222 ZHANG(G.X. Chen et al., in prep
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224 ZHANGWe are waiting for experim
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Ontologies for Biologists: A Commun
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ONTOLOGIES FOR BIOLOGISTS 229al. 20
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ONTOLOGIES FOR BIOLOGISTS 231TOPIC
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ONTOLOGIES FOR BIOLOGISTS 233a.b.Fi
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ONTOLOGIES FOR BIOLOGISTS 2352003.
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238 JOSHI-TOPE ET AL.Figure 1. The
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240 JOSHI-TOPE ET AL.state of knowl
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242 JOSHI-TOPE ET AL.and co-immunop
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The Share of Human Genomic DNA unde
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DNA UNDER SELECTION FROM HUMAN-MOUS
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Detecting Highly Conserved Regions
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DETECTING MULTISPECIES CONSERVED SE
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Page 273 and 274: 266 ROE ET AL.noncoding regions. On
Page 275 and 276: 268 ROE ET AL.a48 hpf embryos in Mi
Page 277 and 278: 270 ROE ET AL.aNovel gene KIAA0819[
Page 279 and 280: 272 ROE ET AL.aMouseRatAP00354.2 Hu
Page 281 and 282: 274 ROE ET AL.Tautz D. and Pfeifle
Page 283 and 284: 276 JAILLON ET AL.Detection of Evol
Page 285 and 286: 278 JAILLON ET AL.Table 1. Distribu
Page 287 and 288: 280 JAILLON ET AL.Table 3. Distribu
Page 289 and 290: 282 JAILLON ET AL.ecotig is a resul
Page 291 and 292: 284 OVCHARENKO AND LOOTSdivergent r
Page 293 and 294: 286 OVCHARENKO AND LOOTSmodulation
Page 295 and 296: 288 OVCHARENKO AND LOOTSsequencing
Page 297 and 298: 290 OVCHARENKO AND LOOTSments of cl
Page 300 and 301: Evolution of Eukaryotic Gene Repert
Page 302 and 303: EVOLUTION OF EUKARYOTIC GENES AND I
Page 308: EVOLUTION OF EUKARYOTIC GENES AND I
Page 311 and 312: 304 PENNACCHIO, BAROUKH, AND RUBINA
Page 313 and 314: 306 PENNACCHIO, BAROUKH, AND RUBINh
Page 315 and 316: 308 PENNACCHIO, BAROUKH, AND RUBINA
Page 318: High-Throughput Mouse Knockouts Pro
Page 321: 314 FRIDDLE ET AL.screen to lines o
Page 325 and 326: 318 LIAN ET AL.0 12 34 5 6 78 9 101
Page 327 and 328: 320 LIAN ET AL.90 minutes and the c
Page 329 and 330: 322 LIAN ET AL.Iyer V.I., Horak C.A
Page 331 and 332: 324 LI ET AL.Figure 1. Array-based
Page 333 and 334: 326 LI ET AL.Figure 4. Test of quan
Page 335 and 336: 328 LI ET AL.Figure 5. Comparison o
Page 338 and 339: Annotation of Novel Proteins Utiliz
Page 340 and 341: FUNCTIONAL SHOTGUN SEQUENCING 333Fi
Page 342 and 343: Global Predictions and Tests of Ery
Page 344 and 345: PREDICTING GENE REGULATORY REGIONS
Page 352 and 353: Systems Approaches Applied to the S
Page 354 and 355: SYSTEMS BIOLOGY IN S. CEREVISIAE AN
Page 364: SYSTEMS BIOLOGY IN S. CEREVISIAE AN
Page 367 and 368: 360 MERIKANGASidentification of gen
Page 369 and 370: 362 MERIKANGASDay 1984; Ottman 1990
Page 371 and 372: 364 MERIKANGASPrevention Research G
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366 DRAYNA ET AL.Figure 1. Distribu
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368 DRAYNA ET AL.Table 1. Summary o
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370 DRAYNA ET AL.Figure 5. Predicte
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Genomic Variation in Multigenic Tra
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GENOMIC VARIATION IN MULTIGENIC TRA
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384 PORTEOUS ET AL.of these devasta
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386 PORTEOUS ET AL.Figure 2. The t(
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388 PORTEOUS ET AL.Figure 3. DISC1
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390 PORTEOUS ET AL.cgi-bin/hgGatewa
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392 PORTEOUS ET AL.REFERENCESAshers
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394 PORTEOUS ET AL.Valles V., Van O
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396 GOLDSTEIN, CAVALLERI, AND AHMAD
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Genetics of Quantitative Variation
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HUMAN GENE EXPRESSION VARIATION 405
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HUMAN GENE EXPRESSION VARIATION 407
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410 CHIBA-FALEK AND NUSSBAUMconcent
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412 CHIBA-FALEK AND NUSSBAUMTable 4
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414 CHIBA-FALEK AND NUSSBAUMclein i
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Genomic Perspective and CancerD. BO
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GENOMIC PERSPECTIVE AND CANCER 419F
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GENOMIC PERSPECTIVE AND CANCER 421F
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GENOMIC PERSPECTIVE AND CANCER 423f
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Chromosome 21 and Down Syndrome: Th
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DOWN SYNDROME AND HUMAN CHROMOSOME
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DOWN SYNDROME AND HUMAN CHROMOSOME
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Harvesting the Genome’s Bounty: I
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INTEGRATIVE GENOMICS 433with high-d
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INTEGRATIVE GENOMICS 435497 baits3,
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INTEGRATIVE GENOMICS 437In contrast
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INTEGRATIVE GENOMICS 439Fly19,912Ye
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INTEGRATIVE GENOMICS 441IMPLICATION
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INTEGRATIVE GENOMICS 443gene intera
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446 STANKIEWICZ ET AL.Table 1. Sele
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448 STANKIEWICZ ET AL.al. 2002; Wal
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450 STANKIEWICZ ET AL.ate DNA rearr
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452 STANKIEWICZ ET AL.Figure 5. Sch
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454 STANKIEWICZ ET AL.Legius E. 200
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456 SAKAKI ET AL.determined. We pai
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458 SAKAKI ET AL.Table 2. Base Subs
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460 SAKAKI ET AL.D.R. 2003. Genomic
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462 LIPOVICH AND KINGtions that cre
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464 LIPOVICH AND KINGto-tail antise
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466 LIPOVICH AND KINGFigure 2. Perl
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468 LIPOVICH AND KINGtions. In inte
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470 LIPOVICH AND KINGOlson M.V. and
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472 WALLACE, RUIZ-PESINI, AND MISHM
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480 CLARK ET AL.Table 1. Derivation
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482 CLARK ET AL.Table 3. Biological
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484 CLARK ET AL.be under adaptive e
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Inferring Human History: Clues from
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Y-CHROMOSOME HAPLOTYPES AND GEOGRAP
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496 OLSONTable 1. Talks Grouped by
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498 OLSONbacterial lineages prosper
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500 OLSONwill respond to perturbati
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502 OLSONIn short, much remained to
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