Initial sequencing and analysis of the human genome - Vitagenes

articlesWe also searched for sets of four chromosomes where there aremultiple genes with homologues on each of the four. The strongestexample was chromosomes 2, 7, 12 and 17, containing the HOXclusters as well as additional genes. These four chromosomes appearto have an excess of quadruplicated genes. The genes are not allclustered in a single region; this may re¯ect intrachromosomalrearrangement since the duplication of these genes, or it mayindicate that they result from several independent events. Of thegenes with homologues on chromosomes 2, 12 and 17, many ofthose missing on chromosome 7 are clustered on chromosome 3,suggesting a translocation. Several additional examples of groups offour chromosomes were found, although they were connected byfewer homologous genes.Although the analyses are sensitive to the imperfect quality of thegene predictions, our results so far are insuf®cient to settle whethertwo rounds of WGD occurred around 500 Myr ago. It may bepossible to resolve the issue by systematically estimating the time ofeach of the many gene duplication events on the basis of sequencedivergence, although this is beyond the scope of this report. Anotherapproach to determining whether a widespread duplicationoccurred at a particular time in vertebrate evolution would be tosequence the genomes of organisms whose lineages diverged fromvertebrates at appropriate times, such as amphioxus.Recent history from human polymorphismThe recent history of genomic segments can be probed by studyingthe properties of SNPs segregating in the current human population.The sequence information generated in the course of thisproject has yielded a huge collection of SNPs. These SNPs wereextracted in two ways: by comparing overlapping large-insert clonesderived from distinct haplotypes (either different individuals ordifferent chromosomes within an individual) and by comparingrandom reads from whole-genome shotgun libraries derived frommultiple individuals. The analysis con®rms an average heterozygosityrate in the human population of about 1 in 1,300 bp (ref. 97).More than 1.42 million SNPs have been assembled into agenome-wide map and are analysed in detail in an accompanyingpaper 97 . SNP density is also displayed across the genome in Fig. 9.The SNPs have an average spacing of 1.9 kb and 63% of 5-kbintervals contain a SNP. These polymorphisms are of immediateutility for medical genetic studies. Whereas investigators studying agene previously had to expend considerable effort to discoverpolymorphisms across the region of interest, the current collectionnow provides then with about 15 SNPs for gene loci of average size.The density of SNPs (adjusted for ascertainmentÐthat is, polymorphismsper base screened) varies considerably across theFrequency1,4001,2001,0008006004002000Human(x):Fly(1):Worm(1)1 2 3 4 5 6 7 8 9 10 11+No. of human paraloguesFigure 49 Number of human paralogues of genes having single orthologues in worm and¯y.genome 97 and sheds light on the unique properties and history ofeach genomic region. The average heterozygosity at a locus willtend to increase in proportion to the local mutation rate and the`age' of the locus (which can be de®ned as the average number ofgenerations since the most recent common ancestor of two randomlychosen copies in the population). For example, positiveselection can cause a locus to be unusually `young' and balancingselection can cause it to be unusually `old'. An extreme example isthe HLA region, in which a high SNP density is observed, re¯ectingthe fact that diverse HLA haplotypes have been maintained formany millions of years by balancing selection and greatly predatethe origin of the human species.SNPs can also be used to study linkage disequilibrium in thehuman genome 376 . Linkage disequilibrium refers to the persistenceof ancestral haplotypesÐthat is, genomic segments carrying particularcombinations of alleles descended from a common ancestor. Itcan provide a powerful tool for mapping disease genes 377,378 and forprobing population history 379±381 . There has been considerablycontroversy concerning the typical distance over which linkagedisequilibrium extends in the human genome 382±387 . With thecollection of SNPs now available, it should be possible to resolvethis important issue.Applications to medicine and biologyIn most research papers, the authors can only speculate about futureapplications of the work. Because the genome sequence has beenreleased on a daily basis over the past four years, however, we canalready cite many direct applications. We focus on a handful ofapplications chosen primarily from medical research.Disease genesA key application of human genome research has been the ability to®nd disease genes of unknown biochemical function by positionalcloning 388 . This method involves mapping the chromosomal regioncontaining the gene by linkage analysis in affected families and thenscouring the region to ®nd the gene itself. Positional cloning ispowerful, but it has also been extremely tedious. When theapproach was ®rst proposed in the early 1980s 9 , a researcher wishingto perform positional cloning had to generate genetic markers totrace inheritance; perform chromosomal walking to obtain genomicDNA covering the region; and analyse a region of around 1 Mb byeither direct sequencing or indirect gene identi®cation methods.The ®rst two barriers were eliminated with the development in themid-1990s of comprehensive genetic and physical maps of thehuman chromosomes, under the auspices of the Human GenomeProject. The remaining barrier, however, has continued to beformidable.All that is changing with the availability of the human draftgenome sequence. The human genomic sequence in public databasesallows rapid identi®cation in silico of candidate genes, followedby mutation screening of relevant candidates, aided byinformation on gene structure. For a mendelian disorder, a genesearch can now often be carried out in a matter of months with onlya modestly sized team.At least 30 disease genes 55,389±422 (Table 26) have been positionallycloned in research efforts that depended directly on the publiclyavailable genome sequence. As most of the human sequence hasonly arrived in the past twelve months, it is likely that many similardiscoveries are not yet published. In addition, there are many casesin which the genome sequence played a supporting role, such asproviding candidate microsatellite markers for ®ner genetic linkageanalysis.The genome sequence has also helped to reveal the mechanismsleading to some common chromosomal deletion syndromes. Inseveral instances, recurrent deletions have been found to result fromhomologous recombination and unequal crossing over betweenlarge, nearly identical intrachromosomal duplications. ExamplesNATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com © 2001 Macmillan Magazines Ltd911