The Genom of Homo sapiens.pdf

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Human Versus Chimpanzee Chromosome-wide SequenceComparison and Its Evolutionary ImplicationY. 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, § H. BLÖECKER,** M. SCHARFE,** G. NORDSIEK,**I. HELLMANN, †† P. KHAITOVICH, †† S. PÄÄBO, †† Z. CHEN, ‡‡ S.-Y. WANG, ‡‡ S.-X. REN, ‡‡X.-L. ZHANG, ‡‡ H.-J. ZHENG, ‡‡ G.-F. ZHU, ‡‡ B.-F. WANG, ‡‡ G.-P. ZHAO, ‡‡ S.-F. TSAI, K. WU, T.-T. LIU, §§ K.-J. HSIAO,*** H.-S. PARK, ††† Y.-S. LEE, ††† J.-E. CHEONG, †††AND S.-H. CHOI ††† (THE CHIMPANZEE CHROMOSOME 22 SEQUENCING CONSORTIUM)*RIKEN, Genomic Sciences Center, Yokohama 230-0045, Japan; † National Institute of Genetics, Japan;‡ Max-Planck-Institut for Molekulare Genetik, Germany; Institute of Molecular Biotechnology, Germany;§ BIOBASE GmbH, Germany; German Research Centre for Biotechnology, Germany; †† Max-Planck-Institutof Evolutionary Anthropology, Germany; ‡‡ Chinese National Human Genome Center at Shanghai, China; National Health Research Institutes, Taiwan; §§ Veterans General Hospital-Taipei, Taiwan;***National Yang-Ming University, Taiwan; and ††† Genome Research Center, KRIBB, KoreaHomo sapiens is a unique organism characterized by itshighly developed brain, use of complex languages,bipedal locomotion, and so on. These unique featureshave been acquired by a series of mutation and selectionevents during evolution in the human lineage and aremainly determined by genetic factors encoded in the humangenome. It is of great interest and also of great importancefrom biological and medical viewpoints to understandwhat kind of genetic factors are involved inthese complex human features and how they have beenestablished during human evolution (Carrol 2003). Recentcompletion of the human genome sequence provideda solid platform for addressing these issues. However, theinformation obtained from the human genome alone is insufficientto discover genetic changes specific to human.The genomes of several experimental organisms such asmouse, fly, and nematode have successfully been used tocharacterize the human genome, but they are evolutionarilytoo distant to zoom in on the human-specific changes.Therefore, we definitely need the genome sequence of theclosest organism to human. Detailed molecular anthropologicalstudies have now established that the chimpanzee(and bonobo) is the closest organism to human, followedby the gorilla (see, e.g., Sibley and Ahlquist 1984; Saitou1991; Chen and Li 2001; Wildman et al. 2003). Thechimpanzee genome is thus the best for comparison withthe human genome to elucidate the genetic changes thathave occurred on the human lineage in the past 5–6 millionyears, providing us with important clues to addressthe above issues.A number of pilot studies have already been done comparinghuman and chimpanzee genomes (see Olson andVarki 2003). For example, we previously showedthrough chimpanzee BAC end sequencing that the genomicdifference between human and chimpanzee interms of nucleotide substitution is 1.23% (Fujiyama et al.2002). Frequent insertions and deletions were detected(Frazer et al. 2003). When insertions and deletions (indels)were compared, about 5% of the genome was shownto differ between human and chimpanzee (Britten 2002).Duplication, translocation, and transposition events havebeen also reported (Bailey et al. 2002). However, thesedata were obtained from various parts of the genomes byusing several different technologies including sequencebasedcomparison, chip technology, and cytogeneticanalysis, so that it is difficult to draw an integrated pictureof dynamic changes of the genome to evaluate the overallconsequence of these genetic changes to human evolution.For these reasons, we conducted a human–chimpanzeewhole-chromosome comparison at the nucleotidesequence level. We chose human chromosome 21 and itsgenomic ortholog in chimpanzee, namely chromosome22, because human chromosome 21 is one of the mostwell-characterized human chromosomes (Hattori et al2000) and contains regions and units representing characteristicfeatures of the human genome such as GCrich/gene-richregions and AT-rich/gene-poor regions,many repeated structures, duplications, housekeepinggenes and tissue-specific genes, genes with a variety offunctions such as transcriptional factors and receptors,members of large gene families and singleton genes.RESULTS AND DISCUSSIONMapping and SequencingAt first, a BAC clone map of chimpanzee chromosome22 was constructed based on the sequence similarity ofBAC end sequences to human chromosome 21. Somegaps were then filled by screening chromosome-22-specificlibraries or by PCR amplification. Finally, only twoclone gaps remained at positions corresponding to gaps inhuman chromosome 21 (Hattori et al. 2000). A nucleotidesequence totaling 32.7 Mb of the mapped clones was thenCold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII. © 2003 Cold Spring Harbor Laboratory Press 0-87969-709-1/04. 455
456 SAKAKI ET AL.determined. We paid special attention to the data quality,because high-quality data are essential for comparisonbetween human and chimpanzee genomic sequences inorder to avoid false-positive differences and to identifyeven subtle differences within the sequences that mayrepresent functionally and evolutionarily significantchanges between the species. For quality assessment ofthe finished sequence, we first counted actual errors in theoverlapping regions between sequenced chimpanzeeclones. Overlaps ranged in size from 6 bp to 129 kb. In249 overlaps, of which the total length was 9,890,299bases (both clones) representing about 15% of the entirenon-redundant sequence, errors totaling 165 bp includingsubstitutions and indels were found and corrected. Fromthis result, the accuracy of the overlapping sequence wasestimated to be 99.9983%. These high-quality data enabledus for the first time to conduct a chromosome-widesequence comparison between human and chimpanzee.Overall ComparisonThe high-quality chimp sequence was compared to thehuman chromosome 21 sequence essentially by using thelocal alignment algorithm BLAST. Since there are manytandem duplications in the chromosome, global alignmentalgorithms are not suitable for this study. Figure 1shows a so-called Harrplot analysis for overall comparison,demonstrating that there are no large rearrangementsbetween human chr. 21 and chimp chr. 22, except for a200-kb duplication that was found at the pericentromericregion in human chr. 21 but is missing in chimp chr. 22.To identify genetic changes of smaller sizes, we conductedmore regional analyses as summarized below:1. Base substitutions: The rate of overall base substitutionsin comparable regions (except the centromericand telomeric regions) is about 1.69%, which isslightly higher than the previously reported averagesubstitution rate (1.23%) with the human genome (Fujiyamaet al 2002). Interestingly, a significant bias wasobserved between A+T/L1-rich regions (1.62%) andG+C/Alu-rich regions (1.77%). This A+T vs. G+Cbias may be partly explained by different substitutionrates of some sequence units such as L1 (1.53%), Alu(2.69%), and CpG islands (3.83%). Centromeric andtelomeric regions seem more unstable because of theirrepeated structures and show higher substitution rates.These regional differences in base substitution ratemay reflect some structural and also some physiologicaldifferences of each unit, element, and region, butthis remains to be resolved.2. Insertion/deletions: Detailed comparisons also revealedthe presence of many insertion/deletions (indels),ranging from one base to more than 5 kb. PCRamplification verification using an out group as a referencecan distinguish whether these indels are insertionsor deletions that occurred in the human or chimpanzeelineages. As shown in Figure 2, there arehuman-specific insertions and deletions as well aschimpanzee-specific insertions and deletions. In someFigure 1. Harrplot between HSA21q and PTR 22q. Humanchromosome 21 sequence (Hattori et al. 2000) was used forcomparison by BLAST.cases, more complex combinations of insertions anddeletions were found. Most indels seem to be derivedfrom the length differences of simple repeats, buttransposable elements also comprise a considerableportion of indels. Interestingly, some subfamilies oftransposable elements were preferentially found inone lineage as insertions. For example, L1Hs (11 vs.2), MER83B (11 vs. 0), AluYa5 (23 vs. 3), andAluYb8 (37 vs. 2) are preferentially found as insertionsin the human lineage (Table 1). On the otherhand, LTR/ERV1 and LTR/MaLR are found preferentiallyin chimpanzee. In addition to transposable elements,some large human-specific (or chimp-specific)“insertion” sequences were observed. For instance, alarge (nearly 18 kb) insertion in a GRIk1 gene first intronwas found in human, potentially affecting the expressionprofile of this gene (data not shown). The originof this sequence is obscure as no homologoussequence was found in all the known sequences in thepublic database.Gene StructureThe above-described study demonstrated that there area large number and variety of genetic changes betweenhuman and chimpanzee. The average rate of thosechanges suggested that almost every gene (including pro-Table 1. Significantly Deviated Distribution of RepeatsFamily Subfamily HS21 PTR22LINE/L1 L1HS 11 2LTR/ERV1 HERVIP10FH 14 5MER41A-int 10 2MER4A1-int 5 0MER83B-int 11 0MER87 32 12SINE/Alu AluYa5 23 3AluYb8 37 2AluYb9 7 1DNA/MER2 Tigger3 42 67LTR/ERV1 LTR49-int 11 23LTR/MaLR MLT1E-int 0 5
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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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266 ROE ET AL.noncoding regions. On
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268 ROE ET AL.a48 hpf embryos in Mi
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270 ROE ET AL.aNovel gene KIAA0819[
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272 ROE ET AL.aMouseRatAP00354.2 Hu
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274 ROE ET AL.Tautz D. and Pfeifle
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276 JAILLON ET AL.Detection of Evol
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278 JAILLON ET AL.Table 1. Distribu
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280 JAILLON ET AL.Table 3. Distribu
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282 JAILLON ET AL.ecotig is a resul
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284 OVCHARENKO AND LOOTSdivergent r
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286 OVCHARENKO AND LOOTSmodulation
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288 OVCHARENKO AND LOOTSsequencing
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290 OVCHARENKO AND LOOTSments of cl
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Evolution of Eukaryotic Gene Repert
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EVOLUTION OF EUKARYOTIC GENES AND I
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304 PENNACCHIO, BAROUKH, AND RUBINA
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306 PENNACCHIO, BAROUKH, AND RUBINh
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308 PENNACCHIO, BAROUKH, AND RUBINA
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High-Throughput Mouse Knockouts Pro
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314 FRIDDLE ET AL.screen to lines o
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Identification of Novel Functional
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100 bp ladder68G1168G1168H1168H6100
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FUNCTIONAL ELEMENTS IN HUMAN DNA 32
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High-resolution Human Genome Scanni
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HUMAN GENOME SCANNING 325false-posi
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HUMAN GENOME SCANNING 327affecting
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HUMAN GENOME SCANNING 329methods fo
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332 MALEK ET AL.Figure 1. The bacte
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334 MALEK ET AL.J., Vincent S., and
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336 HARDISON ET AL.reflect blocks o
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338 HARDISON ET AL.plain the region
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340 HARDISON ET AL.CALIBRATION OF T
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342 HARDISON ET AL.PositionRP2.3noE
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344 HARDISON ET AL.cific chromosoma
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346 WESTON ET AL.these differences
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348 WESTON ET AL.els controlled by
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350 WESTON ET AL.ures prominently i
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352 WESTON ET AL.nal and Bop, which
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354 WESTON ET AL.ablp 1466 bopbcrtB
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356 WESTON ET AL.like fold (Fig. 6)
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Implications of Genomics for Public
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GENETIC EPIDEMIOLOGY 361lytic epide
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GENETIC EPIDEMIOLOGY 363curate risk
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A Model System for Identifying Gene
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PTC TASTE GENETICS 367Figure 2. Hap
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PTC TASTE GENETICS 369Table 2. Hapl
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PTC TASTE GENETICS 371the emergence
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374 MCCALLION ET AL.Figure 1. Schem
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376 MCCALLION ET AL.lier (Carrasqui
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378 MCCALLION ET AL.Table 3. HSCR A
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380 MCCALLION ET AL.Figure 3. Trans
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Genetics of Schizophrenia and Bipol
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SCHIZOPHRENIA AND BIPOLAR AFFECTIVE
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The Genetics of Common Diseases: 10
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GENETICS OF COMMON DISEASES 397with
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GENETICS OF COMMON DISEASES 399SELE
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GENETICS OF COMMON DISEASES 401F.,
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Page 433 and 434: 426 ANTONARAKIS ET AL.1316192225283
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Page 437 and 438: 430 ANTONARAKIS ET AL.POPULATION VA
Page 439 and 440: 432 JORGENSEN ET AL.tive small mole
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Page 495 and 496: 488 UNDERHILLorigin episodes, each
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Page 504 and 505: NEW QUANTITATIVE BIOLOGY 497alone.
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