The Genom of Homo sapiens.pdf

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HUMAN SUBTELOMERIC SEQUENCES 45Figure 3. Human subterminal sequence organization. The shaded region is low-copy subtelomeric repeat (Srpt) DNA; unshaded issingle-copy DNA. The terminal (TTAGGG)n tracts are depicted by the arrows, with a 3´-end overhang as shown. The cross-hatchedportion of the Srpt regions in b and c are the TelBam11 and TelBam3.4 segments, respectively. The subterminal regions from whichsingle-copy and low-copy hybridization probes can be derived are shown, as are regions from which allele-specific primers (A_sp)can be selected.telomere-specific and allele-specifc primers. The Tel-Bam3.4 class of subterminal low-copy repeat sequence(Brown et al. 1990) has properties similar to the Tel-Bam11 class, including a low-copy DNA hybridizationprobe specific for this subtelomeric repeat and sufficientdivergence for development of single-telomere-specificand allele-specific telomere-oriented primers (Fig. 3c).Completed reference telomeres that include TelBam3.4family members are those for 9ptel, 15qtel, 16ptel, andXq/Yqtel.Individual-specific telomere-length typing of all 92telomeres in a given genome would have a dramatic impacton basic studies of human telomere capping/uncapping,end-resection and 3´-overhang processing, andtelomere replication and maintenance. In addition, thiscapability may reveal inborn individual-specific differencesin telomere lengths that could affect susceptibilityto aging and cancer phenotypes. The completion of thehuman genome telomere regions and the ongoing analysisof variation in human subtelomeric regions will enableprogress toward this goal.CONCLUSIONSAs shown in Table 1 and Figure 2, there are still verylarge gaps in our understanding of human subtelomericDNA sequence content, organization, and structure. Thecomplete sequencing of these regions is absolutely essentialfor an accurate picture of the human genome. Evenfrom the little that is currently known, it is clear thatlarge-scale subtelomeric variation can have importantfunctional consequences in terms of mutations that causehuman disease (van Deutekom et al. 1996), relative susceptibilityof telomere regions to chromosome rearrangement/instability(Bailey et al. 2002), and subtelomericgene dosage, gene variation, and gene evolution (Trask etal. 1998; Mah et al. 2001; Bailey et al. 2002). It is verylikely that the specific sequence content and organizationof subtelomere regions will have an impact on telomereposition effects, telomeric chromatin/heterochromatinstructure, and DNA replication near telomeres. Telomeremaintenance pathways, particularly those influenced byrecombination, may likewise be affected by differentialsubtelomeric structure and sequence organization. Littleis currently known of possible recombination within andadjacent to large variant regions, and how the haplotypestructure of subtelomeric regions might be affected byspecific subtelomeric sequence content and organizationduring human evolution.Current “finished” reference sequences for most subtelomericregions are amalgams of sequenced BAC,PAC, and half-YAC clones from separate alleles, and theonly cases where some certainty exists with respect to thesequence organization of single, specific subtelomeric al-
46 RIETHMAN ET AL.leles are those where DNA from entire half-YACs hasbeen sequenced. Most subtelomeric variants have yet tobe characterized, cloned, and sequenced in their entirety,and perhaps many are still undetected. This gap in our understandingof the structure and sequence content of thesedynamic and rapidly evolving chromosome regions mustbe filled in order to complete the human genome sequenceand to develop reagents for understanding itsfunction and evolution. Sequencing of representatives ofall common large-scale variants of chromosome ends willprovide a comprehensive picture of the occurrence andfrequency of different subtelomeric length variants in humanpopulations, and will permit development of sequence-basedmarker sets for more facile analysis of variantregions using PCR-based methods. These aims areachievable and essential for understanding the structureand function of the human genome.ACKNOWLEDGMENTSWe thank the members of the International HumanGenome Sequencing Consortium, many of whom participatedin the sequencing of subtelomeric regions. BobMoyzis, Jonathan Flint, and William Brown collaboratedor provided reagents for the earlier stages of this work,and Uma Mudunuri provided technical support. John Ruxand the Wistar Bioinformatics Facility provided programmingand computational support. Financial supportwas provided by National Institutes of Health grants HG-00567 and CA-25874, and by the Commonwealth UniversalResearch Enhancement Program, PennsylvaniaDepartment of Health.REFERENCESAltschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z.,Miller W., and Lipman D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.Nucleic Acids Res. 25: 3389.Azzalin C.M., Nergadze S.G., and Giulotto E. 2001. Human intrachromosomaltelomeric-like repeats: Sequence organizationand mechanisms of origin. Chromosoma 110: 75.Bailey J.A., Gu Z., Clark R.A., Reinert K., Samonte R.V.,Schwartz S., Adams M.D., Myers E.W., Li P.W., and EichlerE.E. 2002. Recent segmental duplications in the humangenome. Science 297: 1003.Baird D.M., Rowson J., Wynford-Thomas D., and Kipling D.2003. Extensive allelic variation and ultrashort telomeres insenescent human cells. Nat. Genet. 33: 203.Blasco M.A., Gasser S.M., and Lingner J. 1999. Telomeres andtelomerase. Genes Dev. 13: 2353.Brown W.R., MacKinnon P.J., Villasante A., Spurr N., BuckleV.J., and Dobson M.J. 1990. Structure and polymorphism ofhuman telomere-associated DNA. Cell 63: 119.Cook G.P., Tomlinson I.M., Walter G., Carter N.G., RiethmanH.C., Winter G., and Rabbitts T.H. 1994. A map of the humanimmunoglobulin V H locus completed by analysis of thetelomeric region of chromosome14q. Nat. 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Sequencecomparison of human and yeast telomeres identifiesstructurally distinct subtelomeric domains. Hum. Mol. Genet.6: 1305.Forstemann K., Hoss M., and Lingner J. 2000. Telomerase-dependentrepeat divergence at the 3´ ends of yeast telomeres.Nucleic Acids Res. 28: 2690.Griffith J.D., Comeau L., Rosenfield S., Stansel R.M., BianchiA., Moss H., and de Lange T. 1999. Mammalian telomeresend in a large duplex loop. Cell 97: 503.Hemann M.T., Strong M.A., Hao L.Y., and Greider C.W. 2001.The shortest telomere, not average telomere length, is criticalfor cell viability and chromosome stability. Cell 107: 67.Ijdo J.W., Lindsay E.A., Wells R.A., and Baldini A. 1992. Multiplevariants in subtelomeric regions of normal karyotypes.Genomics 14: 1019.International Human Genome Sequencing Consortium(IHGSC). 2001. Initial sequencing and analysis of the humangenome. Nature 409: 860.Koob M., Burkiewicz A., Kur J., and Szybalski W. 1992. 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Page 6 and 7: ForewordIn 2001, as we considered t
Page 8: The Finished Genome Sequence of Hom
Page 11 and 12: 4 ROGERSFigure 2. Accumulation of h
Page 13 and 14: 6 ROGERSFigure 4. Sequencing center
Page 15 and 16: 8 ROGERSabcFigure 5. Ensembl view o
Page 17 and 18: 10 ROGERS2000. Analysis of vertebra
Page 20 and 21: The Human Genome: Genes, Pseudogene
Page 22 and 23: VARIATION ON CHROMOSOME 7 15rived f
Page 24 and 25: VARIATION ON CHROMOSOME 7 17DNAs an
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Page 32 and 33: HUMAN MUTATIONAL PROFILING 25Anothe
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Page 39 and 40: 32 SCHMUTZ ET AL.algorithm itself,
Page 41 and 42: 34 SCHMUTZ ET AL.Figure 2. Genomic
Page 43 and 44: 36 SCHMUTZ ET AL.compared. Some of
Page 46 and 47: Human Subtelomeric DNAH. RIETHMAN,
Page 48 and 49: HUMAN SUBTELOMERIC SEQUENCES 41The
Page 50 and 51: HUMAN SUBTELOMERIC SEQUENCES 43cate
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Page 57 and 58: 50 COLLINSand expand the genomics r
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Page 63 and 64: 56 BENTLEYmon over many generations
Page 65 and 66: 58 BENTLEYTable 1. Genetic Disease
Page 67 and 68: 60 BENTLEY(Clark et al. 1998; Reich
Page 69 and 70: 62 BENTLEYACKNOWLEDGMENTSThe author
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Page 77 and 78: 70 FAN ET AL.matrix is then mated t
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Page 81 and 82: 74 FAN ET AL.including 32 duplicate
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Page 87 and 88: 80 BERTRANPETIT ET AL.function, may
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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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404 CHEUNG ET AL.netic analysis. Ex
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406 CHEUNG ET AL.Figure 3. The expr
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Regulation of α-Synuclein Expressi
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α-SYNUCLEIN EXPRESSION AND PD 411T
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1. The levels of α-synuclein prote
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α-SYNUCLEIN EXPRESSION AND PD 415g
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418 BOTSTEINFigure 1. (A) Blectron
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420 BOTSTEINFigure 3. Cluster diagr
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422 BOTSTEINFigure 6. Kaplan-Meier
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424 BOTSTEINGarber M.E., Troyanskay
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426 ANTONARAKIS ET AL.1316192225283
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428 ANTONARAKIS ET AL.Figure 5. Sam
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430 ANTONARAKIS ET AL.POPULATION VA
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432 JORGENSEN ET AL.tive small mole
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434 JORGENSEN ET AL.FLAG-tagged pro
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436 JORGENSEN ET AL.visualization t
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438 JORGENSEN ET AL.AArp2/3 Complex
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Pathway40S440 JORGENSEN ET AL.ANutr
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442 JORGENSEN ET AL.Giaever G., Chu
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Genomic Disorders: Genome Architect
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GENOME ARCHITECTURE AND GENOMIC DIS
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Human Versus Chimpanzee Chromosome-
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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Novel Transcriptional Units and Unc
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TRANSCRIPTIONAL UNITS AND GENE PAIR
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mtDNA Variation, Climatic Adaptatio
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mtDNA VARIATION 473Figure 3. Region
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ANALYSIS OF ADAPTIVE SELECTION FORR
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mtDNA VARIATION 477Figure 8. Temper
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Positive Selection in the Human Gen
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HUMAN-SPECIFIC EVOLUTIONARY CHANGES
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488 UNDERHILLorigin episodes, each
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490 UNDERHILLhaplogroups C through
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492 UNDERHILLO (Fig. 2e) that share
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The New Quantitative BiologyM.V. OL
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NEW QUANTITATIVE BIOLOGY 497alone.
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NEW QUANTITATIVE BIOLOGY 499There w
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NEW QUANTITATIVE BIOLOGY 501ceded,
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