Proc. Natl. Acad. Sci. USAVol. 92, pp. 10841-10848, November 1995

Review

How is the Human Genome Project doing, and what have we learnedso far?Mark S. Guyer and Francis S. CollinsNational Center for Human Genome Research, National Institutes of Health, Bethesda, MD 20892

ABSTRACT In this paper, we de-scribe the accomplishments of the initialphase of the Human Genome Project, withparticular attention to the progress madetoward achieving the defined goals forconstructing genetic and physical maps ofthe human genome and determining thesequence of human DNA, identifying thecomplete set of human genes, and analyz-ing the need for adequate policies forusing the information about human ge-netics in ways that maximize the benefitsfor individuals and society.

The purpose of the Human GenomeProject (HGP) is to generate a set ofinformation, material, and technology re-sources that will be readily available to theentire scientific community. This "scien-tific infrastructure" will vastly improve theability of investigators from a variety offields to apply molecular approaches tothe study of a wide range of biologicalproblems as we enter the 21st century.Specifically, the HGP is intended to de-velop, efficiently and cost-effectively, de-tailed genetic and physical maps of thehuman genome, determine the completenucleotide sequence of human DNA, anddevelop the new technology necessary toachieve these ambitious goals. This infor-mation will lead, in turn, to the locationsof the estimated 50,000-100,000 geneswithin the human genome. The goals ofthe HGP also include the construction ofdetailed genetic and physical maps and ac-quisition of DNA sequence informationcharacterizing the genomes of several non-human organisms used extensively in re-search laboratories as model systems. Thisreview focuses on progress on the charac-terization of the genome of Homo sapiens;progress on the characterization of the ge-nomes of several model organisms is dis-cussed in the accompanying set of papers.Among the many issues raised in the

early discussions of the genome project inthe late 1980s was its feasibility. There wasconsiderable skepticism that technologyadequate to the challenge of buildingdense maps and sequencing billions ofbase pairs of DNA was available or couldbe developed in a reasonable period oftime. Thus, perhaps the most importantlesson that has been learned from theHGP is that it can be done.

Indeed, from the beginning, progress ingenomics research has been remarkablyrapid (Fig. 1). In part, this has been due tothe strategic planning that has been anintegral part of the HGP. In 1990, the U.S.agencies involved [the National Institutesof Health (NIH) National Center for Hu-man Genome Research (NCHGR) andthe Department of Energy (DOE) Officeof Health and Environmental Research]publicly presented a plan that describedthe scientific and other goals for the firstphase of the project (2). Even in 1990, thegathering pace of genome research was be-ginning to be evident, and the NIH/DOEplan noted that the general plan that hadbeen described just two years earlier by theNational Research Council (3) was "stillappropriate, but some of the details must bechanged as improvements in the technologyhave occurred in the past two years." As forthe 1990 plan, it was refined and extendedjust three years later (4) "because a muchmore sophisticated and detailed under-standing of what needs to be done and howto do it is now available." And in 1995, thesigns are rapidly emerging that the 1993 planis similarly being superseded by scientificdevelopments, so that a new plan will likelybe needed by 1997.

Genetic Mapping

In late 1994, the human genetic linkage mapbecame the first of the major goals of theHGP to be reached, when an internationalgroup of investigators, representing contri-butions from >100 laboratories, published acomprehensive human linkage map (5). Themap contains 5826 loci covering 4000 cen-timorgans (cM) on a sex-averaged map,representing an average marker density of0.7 cM. This is well beyond the initial HGPgoal of a 2- to 5-cM map. The rapid successin genetic linkage mapping was the result, inlarge part, of the introduction of microsat-ellite-based genetic markers (6, 7) and thedevelopment of large-scale, semiautomatedmethods for marker isolation, typing, andanalysis (8, 9).

This map is much more detailed thanany previous human linkage map; yet, it isstill far from ideal. Only 908 of the mark-ers on it are ordered with high confidence(odds of >1000:1) (5). These constitute a"framework map" of about 4-cM resolu-tion. The additional 4500 markers are

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localized with respect to the markers ofthe framework map with odds for orderbetween 10:1 and 1000:1. There also arecertain technical problems with microsat-ellites that make them more difficult touse than one would like, especially forhighly automated approaches to genotyp-ing (10). Continued improvement in thetechnology for genetic mapping and geno-typing, giving more reliable order infor-mation, improved markers, and bettermethods for genotyping on a large scalewould make the human genetic linkagemap even more useful.

Physical Mapping

Considerable progress has also been madein constructing physical maps of the hu-man genome. The current 5-year HGPgoal for physical mapping calls for com-pletion of maps based on sequence-taggedsite (STS)* markers, with an average spac-ing of 100 kb. STS-based physical mapswere taken as the HGP goal because STSsprovide a "common mapping language";since they can be used as markers in avariety of mapping techniques, STSs canbe used to integrate and compare physicalmaps constructed by different techniques(11). For the same reason, STSs can alsobe used to integrate genetic and physicalmaps. STSs have rapidly gained accep-tance as the markers of choice for mapconstruction (Fig. 1B; most of the PCRprobes in the GDB are STSs), and the goalof a physical map of the human genomewith a resolution of 100 kb-i.e., 30,000STSs-is well within sight. Already, morethan 23,000 STSs (mapped at least to achromosome) have been deposited inGDBt (as of June 1, 1995).By using a variety of mapping strategies,

long-range clone contiguity has beenachieved for several individual chromo-

Abbreviations: HGP, Human Genome Project;NCHGR, National Center for Human GenomeResearch; cM, centimorgan(s); STS, sequence-tagged site; ELSI, ethics, legal, and social im-plications; CF, cystic fibrosis; GDB, GenomeData Base; EST, expressed sequence tag.*STSs, or sequenced-tagged sites, are "shorttracts of single-copy DNA sequence that caneasily be recovered by PCR as the landmarksthat define the physical map" (11).

tInformation about access and use ofGDB maybe obtained by e-mail at help@gdb.org.

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FIG. 1. Genomic information in public data bases, 1972-1995. In the cases of polymorphisms (A), PCR probes (B), and mapped genes (D), thenumber of each data type shown is the number in the Genomic Data base (GDB) as of September 30 of each year from 1990 to 1994; for 1995,the number is as of March 31. For the years 1972-1989, data were taken from the report of the DNA Committee at Human Gene Mapping Workshop11 (1); for these years, the number of polymorphisms was approximated by the number of polymorphic D-segments, while the number of mappedgenes was approximated by the number of genes. In the case of DNA sequences (C), the number shown is the amount of sequence in GenBankand is based on the earliest date of a published reference for each entry.

somes. Clone/STS maps of the entire eu-

chromatic regions of chromosomes 21 (12)and Y (13) were published in 1992, andmaps for several other chromosomes, in-cluding 3, 4, 7, 11, 12, 16, 19, 22, and Xt are

nearing completion. On this set of chromo-somes, between 50% and >100% of theSTSs needed to achieve 100-kb average res-olution have been isolated, from 5% to>75% of those STSs have been ordered,and between 70% and 80% of each of thechromosomes have been isolated in over-lapping clone sets. Some very large contigshave been constructed: 50 Mb on the X

*Of these, only the chromosome 22 map hasbeen published (14). The others are availableelectronically: chromosome 3, http://mars.uthscsa.edu/; chromosome 4, http://shgc.stanford.edu; chromosome 7, http://www.nchgr.nih.gov; chromosome 11, http://mcdermott.swmed.edu; chromosome 12, http://paella.med.yale.edu/chrl2/Home.html;chromosome 16, http://www-ls.lanl.gov/mas-terhgp.html; chromosome 19, http://www-bio.llnl.gov/bbrp/genome/chrommap.html;chromosome X, http://ibc.wustl.edu:70/1/GCM.

chromosome, 42 Mb on chromosome 4, 34Mb on chromosome 3, >28 Mb on the Ychromosome, 24 Mb on chromosome 11,and >20 Mb on chromosome 22 (14).As an alternative to the chromosome-

specific approaches that have led to theseindividual maps, a few groups have pur-sued genome-wide assembly strategies forconstructing physical maps. In 1994,French scientists published a low-resolu-tion physical map of the entire humangenome (15) which was based on datafrom STS screening (STS content map-ping), restriction digestion of individualyeast artificial chromosome (YAC)clones, and Alu-PCR fingerprinting to as-semble contigs. Although much of thismap needs additional confirmation, manyof the smaller contigs appear to be reli-able. These data have been useful in build-ing the large, more highly characterizedcontigs of several of the chromosomesreported above. The genome-wide STScontent mapping strategy has also beenemployed by a U.S. group that has recentlyachieved significant increases in the effi-

ciency of STS typing and has alreadyreleased data on more than 10,000 STSs.§

Radiation hybrid (RH) mapping is adifferent approach to physical mapping(16) that determines marker order anddistance by a statistical analysis of markerdistribution in a series of chromosomalfragments generated from one or morechromosomes by x-irradiation. Recently,the feasibility of a "whole-genome" ap-proach to RH mapping has been demon-strated by using a set of radiation hybridsmade from the entire human genome toconstruct maps of 100 markers on chro-mosome 4 and 300 markers on chromo-some 7 (D. R. Cox, D. Vollrath, and R. M.Myers, personal communication).None of the first-generation maps is error

free. Errors in physical maps come from atleast two sources. In most clone libraries, afraction of the individual clones are rear-

§Data may be obtained by anonymous filetransport protocol (ftp) (genome.wi.mit.edu),Internet e-mail (genome database@genome.-mit.edu), or World-Wide Web (http://www-genome.wi.mit.edu).

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ranged relative to the genome from whichthe clones were derived. Furthermore, cur-rent map assembly procedures do not alwaysproduce the correct order. Some of theproblems with the initial physical maps willresolve themselves; as the density of mark-ers on the physical maps increases, many ofthe internal inconsistencies will become ev-ident and will be corrected upon reexami-nation of the data. This has already hap-pened in the case of one well-mapped chro-mosome: chromosome 21 (17).

Quality control in mapping will also beaided by the use of multiple, independentmapping methods. Comparison of inde-pendently generated maps which arebased on different ordering algorithms,such as radiation hybrid maps and STScontent maps, will allow differences inwhat should be the same map to be readilyidentified. In most cases, further analysiswill allow the differences to be resolvedand the correct map to be determined.The use of a comtnon subset of markers inthe different mapping efforts is necessaryfor such a comparison. Criteria for theassessment and reporting of map qualityand mapping progress have been pro-posed by two groups (18, 19).With approximately 20,000 of the 30,000

STSs needed to reach the original goalalready in hand, an STS-based physical mapof the human genome, with some regionsmapped in more detail than others and anaverage interval of approximately 150 kbbetween markers, is expected to be availablein the next year. A more detailed map, withSTSs at an average resolution of 100 kb, wasoriginally expected no later than the end of1998 (4) but may be achieved sooner.

In spite of these impressive advances,further improvements in mapping technol-ogy will be essential to facilitate cost-effective construction of maps of other ge-nomes and maps that comprise sequencingsubst-rates. New vectors and better methodsfor library construction will be necessary totake full advantage of the power of genomicapproaches. It is likely that physical maps ofgreater than 100-kb resolution (20-23) willultimately be needed, both as substrates forDNA sequencing and for use in other typesof biological research. However, it is alsoprobable that different uses (in particular,different sequencing strategies) will havedifferent requirements in terms of the na-ture and degree of detail of the very-high-resolution physical maps. Thus, it will beimportant for the development of new strat-egies and reagents for very-high-resolutionphysical mapping to be well integrated withthe proposed use(s) of such maps.

DNA Sequencing

From the beginning, the sequencing com-ponent of the HGP seemed the mostdaunting. Of all the areas of genomicresearch in which new technology wasneeded, DNA sequencing was probably

the one in which the greatest advanceswere needed. In many ways that is stilltrue. During the initial phase of the HGP,there has been (by budget necessity) arelative underinvestment in sequencingtechnology in favor of map development.Nevertheless, during the past severalyears, substantial improvements in gel-based methods have led to a significantincrease in the capacity to sequence largecontiguous regions of genomic DNA.Three paths have been taken to increase

the capacity for genomic DNA sequenc-ing. The first has attempted to maximizethe capacity of current sequencing tech-nology. A second has focused on the "evo-lutionary" development of new methodsfor high-throughput, electrophoresis-based sequencing, while a third has beendirected to the development of entirelynew, "revolutionary," technologies fornonelectrophoresis-based sequencing.Improvement in the throughput of cur-

rent sequencing methods has been steadyover the past several years and has led toa rather striking increase in sequencingcapacity. For example, over the last 2 years,the throughput of automated sequencinginstruments has improved by about 2- to3-fold. This improvement has come fromexpansion in the number of electrophoresislanes per gel, lengthening of the sequencinggel, and increases in the number of dailyruns of which such instruments are capable.New sequencing strategies have also been

developed. The most commonly employedstrategy for large-scale sequencing remainsthe "shotgun" approach, in which eachmember of a set of randomly-generatedsubclones of the target region is completelysequenced and the sequence of the targetregion is reconstructed by a computer-basedassembly process that compares the se-quences of the subclones and finds the over-lapping regions. However, for statistical rea-sons, a pure shotgun approach requires avery large amount ofrandom sequencing (toat least a 10-fold redundancy) to obtain thecomplete target sequence and is, therefore,quite expensive. To reduce this cost, mostsequencing efforts have employed modifi-cations of the basic shotgun approach, in-volving random sequencing to a lower re-dundancy, partial sequence assembly, andcompletion by a more directed strategy.Other approaches to reducing redundancy(24, 25) promise to lead to further increasesin overall efficiency.

Alternatives involving completely di-rected strategies for large-scale sequenc-ing have also been developed. Transpo-son-based sequencing strategies (refs. 26and 27; P. Cartwright, R. Gesteland, andR. Weiss, personal communication) whichinvolve using mapped transposon inser-tions within the region to be sequenced assites for initiating sequencing reactionspromise to reduce both the amount ofsequence redundancy needed to achieveclosure and the difficulty of sequence as-

sembly. New approaches to primer walk-ing, involving the use of short oligonucle-otides to construct sequencing primers insitu (28, 29) or inexpensive oligonucleo-tide synthesis (T. Brennan, D. Lashkari &R. W. Davis, personal communication)are also being tested. Yet another se-quencing strategy is "multiplex" sequenc-ing (30), which employs a different ap-proach to sample preparation that theo-retically offers improvement in efficiencyin combination with either shotgun ordirected approaches.Combined with increased attention to

issues of laboratory organization andmanagement, these developments have al-lowed throughput of as many as severalmegabases of sequence per year to beachieved in a small number of laborato-ries. The highest output to date has comefrom the collaborative effort of the labo-ratories of R. Waterston and J. Sulston tosequence the 100-Mb genome of the nem-atode Caenorhabditis elegans (see accom-panying article). Together, these twogroups have already finished, and submit-ted to the sequence databases more than16.5 Mb (sequence submission in Gen-Bank) of sequence data. Other laborato-ries have generated the sequence of mega-base regions of the DNA of other organ-isms, including Haemophilus influenzae,Escherichia coli, Myobacterium leprae, andDrosophila melanogaster (sequence sub-missions are in GenBank), while three labshave each sequenced at least 1 Mb ofmammalian DNA. L. Hood's group hascompleted the sequence of >1 Mb of theT-cell receptor region from human andmouse DNA (ref. 31; L. Rowen, personalcommunication). In B. Roe's laboratory,the sequence of >1.5 Mb of human DNAfrom chromosomes 9 and 22 has been de-termined (ref. 32; B. Roe, personal commu-nication). Finally, the sequencing group atthe Sanger Center has determined the se-quence of - 1.5 Mb of human DNA, pri-marily in the region of the Huntington dis-ease (HD) gene on chromosome 4.

Order-of-magnitude improvements inDNA sequencing capability are promisedby the next generation of electrophoresis-based automated sequencing instrumentsnow under development. The expectationis based on "evolutionary" advances, in-cluding new geometries for electrophore-sis (such as ultrathin gels and capillaries),new matrices for DNA-fragment resolu-tion, improved detection technologies,and improvements in process automation,all of which will lead to increased through-

IA total of 0.5 Mb of sequence from the HDregion and 0.1 Mb from Xq28 have beensubmitted to the public nucleic acid sequencedata bases; additional data, representing se-quence that is largely finished, is availableby ftp from ftp.sanger.ac.uk pub/human/sequences or by mosaic from http://www.sanger.ac.uk.

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put by increased parallelization of sampleprocessing, increased electrophoresisspeed, and decreased sample size.

In particular, the miniaturization ofelectrophoresis-based sequencing holdsgreat promise. Recent work in ultrathin(capillary or slab) gel electrophoresis (33-35) has shown that the advantageous heat-transfer properties afford by the ultrathingeometry allows the greatly increased sep-aration speed predicted for this technique.Ultrathin gels also have the advantage ofallowing greatly reduced sample size. Fur-ther reductions in scale and increases inthroughput can be anticipated through theapplication of technologies for microfab-rication (36) and microelectronic mechan-ical systems to DNA sequencing. Consid-erable technological challenges remainbefore miniaturized systems for DNA se-quencing become routinely available, buttheir potential is enormous.Also under development are a number

of different approaches to DNA sequenc-ing that are "revolutionary" in that theydo not rely on the electrophoresis of sets("ladders") of DNA fragments. Massspectrometric methods forDNA sequenceanalysis are being investigated in severallaboratories. Although the application ofthis technology to large-scale genomicDNA sequence analysis is considered tobe at least several years away, recentprogress suggests that these approacheshave a chance for ultimate success insequencing and/or mapping applications.For example, the recent identification of amatrix, 3-hydroxypicolinic acid, that al-lows very reproducible volatilization of anucleic acid sample without fragmenta-tion (37) increases prospects for the ap-plication of matrix-assisted laser desorp-tion/time of flight mass spectrometry inDNA sequencing. Single-base resolutionof oligonucleotides in the length range of40-50 nt has been achieved (C. Becker,personal communication); recently, re-sults have been obtained that demonstrateresolution of the products of Sanger se-quencing reactions up to 35 nt in length(C. Becker, personal communication).

Sequencing by hybridization (SBH) isanother nonelectrophoresis-based ap-proach in which the sequence of a DNAfragment is determined by hybridizing theDNA to a known set of oligomers arrayedon a surface (38, 39). In principle, thepattern of annealing to the oligonucleo-tide array allows the sequence of the tar-get DNA to be determined. Challenges indeveloping this technique include effi-cient synthesis of high density arrays, bet-ter understanding of hybridization reac-tion kinetics, and improved detectionschemes and methods for data analysis.The utility of this approach for detectionof specific gene sequences, as well assingle-base mutations, has recently beendemonstrated (40). A particular challengefor the SBH approach is the determina-

tion of the sequence of large regions ofDNA containing repeated sequences. Thecombination of the sequence-checking ca-pabilities ofSBH with rapid sequencing byother methods is potentially a very pow-erful approach to de novo sequencing.Over the past 3 years, progress in se-

quencing technology development hasbeen steady. Current sequencing technol-ogy appears to be capable of accomplish-ing the complete sequencing of the ge-nomes of several model organisms beforethe end of the century. Recently, it hasbeen argued that current technology iseven capable of being used to generate afirst-pass sequence of the human genomein a reasonable period of time and for areasonable cost (41). This presents a cru-cial strategic question to the HGP. Shouldthe complete genomic sequencing of hu-man DNA be begun with current technol-ogy (and whatever technological improve-ments occur in the course of doing so) orshould "production sequencing" be de-layed for some time in favor of continuedemphasis on development of further im-provements in sequencing technology?

This is not a question of whether con-tinued development of improved technol-ogy for DNA sequencing is important.Vast reductions in DNA sequencing costsand increases in DNA sequencing rateswill be required to elucidate the enormousamount of biological information aboutindividual traits that will come from mak-ing correlations between the variation inparticular traits among many individualsand differences among those individualsin the sequence of relevant, large (mega-base) regions of the genome. Similarly, anuntold amount of useful information willbe obtained by knowing the sequences ofthe genomes of many other organisms,ranging from infectious microorganismsto agriculturally important plants. Tech-nology far beyond today's will be requiredto achieve the necessary sequencing capa-bility. Therefore, even if revolutionarynew sequencing technologies were un-likely to be sufficiently developed in thenext few years to contribute to the firsthuman genome sequence, their continueddevelopment will continue to be an im-portant activity of the HGP. Rather, thequestions currently demanding answersare how best to stimulate the developmentof new sequencing technology andwhether acquisition of large amounts ofhuman DNA sequence sooner rather thanlater will be a stimulus or deterrent tofurther technology development.Another dilemma facing the HGP in-

volves attracting new groups to large-scalesequencing. It is important to involve asmany groups as possible in the developmentof production-sequencing capability to pro-vide competition and innovative approachesto this problem. At the same time, doing sohas a cost, the cost of the learning curve. Ithas been the experience in large genome

centers that efficiency increases with expe-rience. Among the groups that have focusedtheir attention on production, the efficiencyof data generation has increased in thecourse of confronting and solving the prob-lems that have arisen as their productioncapacity (for either mapping or sequencing)has increased. There remains a questionabout how efficiency scales with size. Willefficiency continue to increase as the groupsize increases, or is there an optimal groupsize in terms of efficiency (Fig. 2)? Atpresent, we do not have a good sense ofwhatthe trade-offs and costs will be in paying thecosts for new groups to move up the learn-ing curve compared with increasing the sizeof the few existing groups.

Gene Identification

Starting from contigs of large-insertclones, a number of gene isolation andlocalization techniques, such as cDNAselection and enrichment methods (42)and exon amplification methods (43-45),have been used in the positional cloning ofa number of human genes. So far, how-ever, none of the methods has been shownto be sufficiently robust to support large-scale gene identification; in Fig. 1D, forexample, it can be seen that the rate ofidentification of new genes is still rela-tively low. Thus, there is not yet confi-dence that the cataloging and mapping ofthe complete collection of human genescan be done with the kind of complete-ness, efficiency, and cost-effectiveness de-manded by the HGP (46). An optimaltechnology or combination of technolo-gies for identifying genes in large clonedregions remains to be formulated.

= c13

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FIG. 2. Hypothetical curves of cost-efficiencyinDNA sequencing. Current experience indicatesthat economies of scale reduce the cost per basepair of sequencing up to a production level of 10Mb per year; however, no group has thus farpushed beyond this level, so we do not know atwhat point such economies become overwhelmedby the managerial problems of running a verylarge-scale sequencing center. Three possiblecurves are shown, without any information atpresent to determine which will apply to large-scale mammalian DNA sequencing. The ultimatedivision of labor in accomplishing the sequencingcomponent of the HGP will depend critically onwhich of these curves applies, as that is likely toplay a major role in determining the optimalnumber of centers to complete the sequence forthe most reasonable cost.

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The term "expressed sequence tag"(EST) has been used to refer to a shortDNA sequence derived from a cDNA cloneand used to identify a genomic coding se-quence (47). A considerable number ofESTs have been collected in a public repos-itory, dbEST (188,122 as of June 15, 1995;ref. 48), and a much larger number willbecome publicly available by the end of 1995through an effort supported by the pharma-ceutical company Merck; over 100,000 ESTsfrom this effort have been put into dbEST inthe first few months of operation. STSsderived from these ESTs will rapidly beincorporated into physical maps through theefforts of an international mapping consor-tium (49). These projects lend confidencethat the slope of the curve in Fig. 1D willsoon increase significantly and that half ormore of the genes in the human genome willbe localized on physical maps within thenext few years. However, the actual numberof genes that can be identified and mappedby this approach cannot be predicted, norcan the proportion of the total number ofhuman genes they will represent. The num-ber ofgenes that can be identified in this waydepends entirely on the quality of the cDNAlibraries from which the ESTs are obtained,and cDNA libraries that represent the com-plete set of human genes have not beenconstructed.

Medical Applications

The term "gene identification" is alsoused more broadly to describe the isola-tion of the gene(s) underlying a particularphenotype or trait, such as a disease. Inthis sense, gene identification is a biolog-ical problem with considerable medicalsignificance that HGP resources are al-ready helping to solve. It is one measure ofthe success of the HGP to date that,through the use of these new tools, thespeed with which disease genes are beingfound is rapidly increasing. New diseasegenes are being found and reported at arate of several per month, compared witha few per year not so long ago (50).

During the past 2 years, many genes forhuman diseases have been isolated by usingthe powerful methods of positional cloning(51), where no prior knowledge of the gene'sfunction is available. In contrast to posi-tional cloning, functional cloning or candi-date-gene strategies make use of informa-tion that is known about the gene productand/or the function of the gene of interestthat suggest it as a particularly good candi-date for the affected gene in a particulardisease. For example, keratins are the majorclass of proteins found in skin cells. Theeffects of mutations on the properties ofcertain keratin proteins and the observationthat mice in which such mutant genes areexpressed exhibit features of epidermolysisbullosa simplex (EBS) led to the discoverythat mutations in the human K5 and K14

keratin genes are responsible for the sever-est forms of EBS in humans (52).The candidate-gene methods have also

taken advantage of the improvement ingenomic maps, resources, and technolo-gies, and, as genomic maps improve andbecome more populated with gene se-quences, a new strategy is emerging.Known as "positional candidate" cloning(50, 53), this approach begins with map-ping the disease gene to a small chromo-somal interval. All genes located in thatinterval can then be tested for their in-volvement, starting with any whose prod-uct functions in a way that suggests pos-sible involvement. In other words, a genebecomes a candidate not only by virtue ofthe properties of its protein product but byits map location as well.As more human genes have been iden-

tified and cloned, new insights are alreadybeing gained into human biology and dis-ease. Some of these might not be surpris-ing in that they show that many aspects ofhuman molecular genetics are familiarand similar to those seen in more well-studied organisms. For instance, as elab-orated below, different phenotypes havenow been found to arise from differentmutations in a single human gene, andsimilar phenotypes have been found toarise from mutations in different (related)genes. Yet, this similarity is itself impor-tant because it confirms once more thatmany of the lessons we have learned aboutthe biology of nonhuman organisms willbe directly applicable to our understand-ing of human biology.

Several human genes have been ana-lyzed sufficiently thoroughly that analysisof mutational spectra has been possible.Mutations in the receptor tyrosine kinasegene RET can give rise to any of fourdifferent syndromes: familial medullarythyroid carcinoma (54), multiple endo-crine neoplasia types 2A (54, 55) and 2B(56), and Hirschsprung disease (57, 58).There is no reported cancer associationwith the latter condition. Similarly, whilea large number of mutations in the CFTRgene cause cystic fibrosis (CF) (of varyingdegrees of severity) (59), mutations inCFTR have also been found in patientswho do not exhibit the standard pulmo-nary symptoms of CF. A significant frac-tion of otherwise healthy males who areinfertile due to a congenital bilateral ab-sence of the vas deferens (CBAVD) carryone or two known CFTR mutations (60),although recent evidence indicates thatthe CBAVD condition itself is geneticallyheterogeneous (61).

Genetic analyses of inherited conditionsare also beginning to give the anticipatedleads into better understanding of humanbiology. A number of examples illustratethat mutations in members of a genefamily can give rise to a set of relatedpathologies. For instance, several rare andoften diagnostically confusing craniosyn-

ostosis syndromes [Crouzon syndrome(62-64), Jackson-Weiss syndrome (63),Pfeiffer syndrome (65-68), Apert syn-drome (64), and achondroplasia (69)]have been found to be caused by muta-tions in one of several fibroblast growthfactor receptor genes. Similarly, as notedabove, several blistering skin diseases arecaused by mutations in different keratingenes. Other skin diseases, however, af-fecting different cell types within the epi-dermis, are caused by mutations in genesrepresenting other gene families (70, 71).Kallmann syndrome is a condition char-

acterized by an unusual constellation ofseemingly unrelated features: hypogo-nadism resulting from an endocrinologicalproblem (deficiency of hypothalamic gona-dotropin-releasing hormone) and anosmia(inability to smell). Isolation of the KALgene (72, 73) led to the recognition that thepredicted KAL gene product was related toneural-adhesion molecules. This is consis-tent with a role of the gene product inembryonic neural migration and with theobservation of a common developmentalpathway of two types of neurons that orig-inate in the olfactory placode: the olfactoryneurons and the neurons that produce go-nadotropin-releasing hormone.

Analysis of other genetic diseases inhumans has led to the identification of apreviously unobserved mutational mech-anism. Fragile X syndrome (74), spinaland bulbar muscular atropy (75), myo-tonic dystrophy (76-78), Huntington dis-ease (79), and several others have beenfound to be caused by trinucleotide-expansion mutations in which the numberof copies of a trinucleotide repeat se-quence is significantly increased in af-fected compared with nonaffected indi-viduals.

Charcot-Marie-Tooth disease type 1A(CMT1A) represents another unique (todate) genetic situation, in that it mostfrequently results from duplication of theregion of chromosome 17 containing thePMP22 gene (80). Hypotheses suggestingthat this is a gene dosage effect are beingtested. Point mutations in PMP22 havealso been found in patients with CMT1A(80) and, as in the case ofRET and CFTR,other mutations in PMP22 have beenfound to be responsible for other clinicalconditions: Dejerine-Sottas syndrome(81) and, possibly, hereditary neuropathywith liability to pressure palsies (82).

Informatics

With respect to genomics, informatics is-sues range from the algorithmic and data-management needs of mapping and se-quencing projects to the dissemination ofdata to the scientific community, and thedevelopment of adequate informatics ap-proaches to this variety of issues has beenan important area of research since theinception of the HGP. Data analysis and

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data management are actually open-endedproblems in that today's solutions will, ingeneral, have a limited lifetime as new ap-proaches to genomic analysis and more dataare developed. Nonetheless, much progresshas been made in genome informatics in thepast 5 years. A considerable number ofindividual laboratories have developed andare using computer-based systems for au-tomating the acquisition, management,analysis, and distribution of experimentaldata. Similarly, a number of new databases have been created for the purpose ofallowing the rapid distribution of the find-ings of genome research.

In fact, the number of data sources andprograms of interest is too large to sum-marize in this article, but informationabout many may be obtained electroni-cally from http://www.nchgr.nih.gov. Thecurrent state of genome informatics isdriven by the rapidly expanding capabili-ties afforded by the increased capacity ofcomputers and networks. Through the useof ftp sites and the World Wide Web, forexample, many genome centers provideelectronic access to much larger amountsof data and less refined data than could bepublished. While this system has the ad-vantage of allowing those who generategenome data to take the responsibility forits rapid provision to the research com-munity, it can sometimes appear to beoverly anarchic. More seriously, it canpose some serious challenges to the usersof the data as they attempt to locatediverse information sources and integratedata in diverse formats. Recently, both thecentral data bases and independent soft-ware developers have made significantprogress on data-access systems and tools.

Ethical, Legal, and Social Implications(ELSI)

It was recognized almost from the outsetof the HGP that the increased knowledgeof human biology and human disease thatwould come from application of genomicinformation would raise a number of sub-stantive ethical and policy issues for indi-viduals and for society. Accordingly, anELSI research program has been an inte-gral element of genome programs aroundthe world. In the U.S., the ELSI researchprogram has focused on identifying andaddressing a few high priority areas raisedby the most immediate potential applica-tions or consequences of genome re-search. These are ethical issues surround-ing genetics research, responsible clinicalintegration of new genetic technologies,privacy and fair use of genetic informa-tion, and professional and public educa-tion about these issues.

Research and education projects havebeen funded in each of these priority areas.In pursuing these goals, there has been anemphasis on the integration of sound scien-tific knowledge with an understanding of

the many historical, ethnocultural, social,and psychological factors that influence pol-icy development and service delivery inhuman genetics. The first of these projectsare now beginning to be completed, and theresearch results are leading to the identifi-cation of policy options intended to ensurethat genetic information is used for thebenefit of individuals and society.One of the first examples is a coordi-

nated set of studies that examined issuessurrounding genetic testing and counsel-ing of patients for CF mutations. Theinvestigators participating in these studieswere organized into a consortium to con-duct the studies more efficiently and pro-ductively, to allow a broader range ofissues to be addressed, and to pursue acoordinated approach to the developmentof policy recommendations related to CFtesting. These studies found that interestin the general population for CF testingwas much lower than anticipated. Thedemand for CF testing was found to beinfluenced by a number of variables, in-cluding the cost of the test, the timing, thesetting, and even the manner in which thetesting was offered. It was also found that,although people can be educated aboutCF testing (with the goal of allowing themto make informed choices about testing),doing so is difficult because of the com-plexity of the information to be commu-nicated, the lack of incentives on the partof some providers to teach people aboutthe information, and the lack of motiva-tion on the part of consumers to learn it.The results of this research have also led toproposals about optimal methods to pro-vide CF testing to those who desire it.These and other results of the studies havebeen discussed in professional societymeetings, and it is anticipated that clinicalpolicy recommendations will emerge fromthese organizations.A second major effort in the area of

introduction of genetic tests was initiated inthe autumn of 1994 and consists of a set ofprojects to examine issues surrounding test-ing and counseling for heritable breast,ovarian, and colon cancer risks. Questionsto be addressed in these studies include theinterest and demand for testing, the impactof testing, and alternative ways to providesuch services. As with the CF studies, theinvestigators involved in these projects willform a consortium to pool resources, reduceduplication of effort, and increase coordi-nation of some aspects of the studies. Bypooling initial findings where possible andfollowing the results of this set of researchprojects, it may be feasible to identifyemerging themes and develop some policyrecommendations sooner than if theprojects were conducted and assessed inde-pendently.

In another approach to addressing is-sues associated with the use and regula-tion of new genetic tests, the joint NIH/

DOE ELSI Working Groupll has created aGenetic Testing Task Force that will re-view the "state of the art" of genetictesting, examine the strengths and weak-nesses of current practices and policiesrelating to testing, and, if needed, recom-mend changes or policy options that willensure that the public is protected, suchthat only the appropriate tests are done,and these by qualified laboratories. TheTask Force will report its findings throughthe ELSI Working Group and the Na-tional Advisory Council for Human Ge-nome Research to the Directors of theNCHGR and the NIH and eventually tothe Secretary of the Department ofHealth and Human Services.

Finally, in 1994, the Institute of Medi-cine published a study of professional pol-icy issues in the clinical integration of newgenetic tests (83). This report offers anumber of recommendations for the lab-oratory quality control of DNA diagnos-tics and the provision of genetic testing inthe clinical setting.With the advent of new technologies to

identify more genetic information aboutindividuals, concerns arise about the pri-vacy and fair use of the information. Oneof the initial products of the discovery ofa variant gene that underlies a particularcondition is information that can be usefulin predicting the likelihood that an indi-vidual will develop that condition. Thiscan potentially serve the individual well byopening the door to preventative inter-ventions, including more informed pre-symptomatic screening or lifestylechanges involving diet, exercise patterns,or environment. At the same time, how-ever, this information may also have un-welcome effects, such as increased anxi-ety, altered family relationships, stigmati-zation, and discrimination on the basis ofgenotype. Concerns about stigmatizationand discrimination are cited as particu-larly troubling, especially in relation toemployability and insurability. The TaskForce on Genetic Information and Insur-ance, established by the joint NIH/DOEELSI Working Group, assessed the poten-tial impact of advances in human geneticson the current system of health-care cov-erage in the U.S. The Task Force re-port,** issued in 1993, contained recom-mendations for managing that impactwithin a reformed health-care system.Model legislation dealing with genetic pri-vacy has been drafted by G. Annas, L.Glantz, and P. Roche (G. Annas, personal

l1The joint NIH/DOE ELSI Working Groupwas established to explore and propose optionsfor the development of sound professional andpublic policies related to human genome re-search and its applications.**Genetic Information and Health Insurance:Report of the Task Force on Genetic Informa-tion and Insurance, is available from the ELSIBranch, NCHGR, Building 38A, Room 613,NIH, Bethesda, MD 20817.

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communication)tt and is being reviewedat both the federal and state levels.A recent gratifying development is the

ruling by the U.S. Equal EmploymentOpportunities Commission (EEOC) thatgenetic discrimination in employment de-cisions is illegal. The EEOC has formallyruled that the Americans with DisabilitiesAct (ADA), passed in 1991, does extendcoverage to individuals who are at risk forfuture illness and who are discriminatedagainst in employment decisions on thatbasis. The argument is that these individ-uals are 'regarded as' having a disability bytheir employer, even though they are cur-rently well, and therefore the protectionsof the ADA should be extended to them.The need to provide legal protectionsagainst genetic discrimination in hiringpractices was considered a high priority bythe ELSI Working Group from its veryfirst deliberations, and the resolution ofthis problem by the EEOC is seen by manyas a landmark development. Its signifi-cance even extends beyond employmentdiscrimination because it establishes thegeneral principle that discriminationagainst individuals on the basis of theirgenetic inheritance is unjust.While much research in human genetics

is focused on the causes of human diseaseand disability, genes and genetic markersthat appear to be associated with otherhuman characteristics are being reportedon an increasingly frequent basis. Reportsthat associate genes with human traits thatexhibit a wide range of variation in thegeneral population, from stature, weight,and metabolism to learning ability, behav-ior, and sexual orientation, raise very dif-ferent and potentially controversial socialissues (84, 85). Typically, such geneticstudies provide only introductory and in-complete clues about the interplay of bi-ological, psychological, and socioculturalfactors that influence the developmentand expression of these complex humantraits. However, the results of such re-search can be misinterpreted in two im-portant ways. First, they can be inter-preted to imply that such traits can bereduced to the expression of particulargenes; this has the effect of deemphasizingthe important role of psychosocial andother environmental factors. Second, theresults can also be interpreted in a waythat narrows the range of variation con-sidered to be "normal" or "healthy." Suchoverly deterministic interpretations can,in turn, be misused to undercut the respectowed to individuals as responsible moralagents or to inappropriately label individ-uals as sick or abnormal. Both forms ofmisinterpretation can have untoward con-sequences, such as devaluing human ge-netic diversity or fostering social discrim-

ttAvailable from http://www-busph.bu.edu/Depts/HealthLaw/.

ination on the basis of genotype. As itproceeds, the HGP will need to foster abetter understanding of the meaning ofhuman genetic variation among membersof the public and the professions and expandits efforts to propose policy initiatives de-signed to prevent genetic stigmatization, dis-crimination, and other misinterpretation ormisuses of genetic information.

Conclusion

The beginning phase of the HGP has beenremarkably successful. The amount of ge-nome data describing human DNA andthe DNA of other organisms that is avail-able in public data bases has increasedenormously, and the information is beingused at an increasing rate. The contribu-tions that the HGP has already made toadvance the study of inherited disease andother biological phenomena are, by now,widely recognized in the scientific com-munity. The community is no longer ar-guing whether the HGP is a good idea butis now debating the most effective ways toreap its rewards.These achievements are attributable to

several decisions that were made early inthe life of the program. One was to basethe implementation of the program on avisionary, flexible, and on-going planningprocess. Over the years, the program hasbenefitted from advice from a large num-ber of members of the scientific commu-nity, both from those directly involved ingenome research and from those who arenot but who will be the ultimate users ofthe products of the HGP. Second, theHGP has been highly dependent upon theintroduction of new technology for map-ping and sequencing, the development ofwhich has been emphasized as part of theresearch program from the beginning.Further technology development will con-tinue to be critical, not only to achievingthe long-range goals of the HGP (whichare, in fact, rather circumscribed), but alsoto the ability to take advantage of the(virtually unlimited) promise offered bythe sequence-based approach to biologicalresearch that will be opened up by theHGP. Third, large research centers, bothpublicly and privately financed, havemoved rapidly along the "learning curve"and have achieved significant efficienciesof scale that have allowed them to gener-ate large amounts of data in relativelyshort periods of time. Fourth, the consen-sus that genomic information should bepublicly available has led to policies on thepart of the funding agencies and practiceson the part of the genome research com-munity that have resulted in an exemplaryrecord for rapid publication of the data inaccessible formats with the result that thisvaluable information is available to thescientific community much more rapidlythan through conventional publicationmeans. Finally, the international aspects of

the HGP have been a demonstration of thepower of an intemational collaboration inachieving a very ambitious set of goals.We are rapidly approaching the time

when we will have the initial products of theHGP, including maps, genomic DNA se-quences, and the improved technology forgenomic analysis, in hand. That will repre-sent the true point of initiation for the era ofsequence-based biological investigation.

Note Added in Proof. After this manuscript wassubmitted, several significant publications ap-peared addressing issues discussed in this pa-per. These included YAC contig maps of hu-man chromosomes 3 (86), 12 (87), and 22 (88);an integrated physical map of chromosome16(89); and an improved version (90) of thewhole genome map originally published by theCentre d'Etude du Polymorphisme Humain-Genethon group (15). Investigators from TheInstitute of Genome Research (TIGR) andHuman Genome Sciences, Inc., reported a setof 174,472 ESTs which, when combined withother 188,406 ESTs from the public data basedbEST (48), allowed the definition of 87,983distinct sequences (91), consisting of 29,599merged sequences and 58,384 nonoverlappingESTs. Finally, investigators from TIGR alsopublished the complete DNA sequence ofHae-mophilus influenzae (92).

The ideas discussed in this paper have ben-efitted from the long and productive collabo-ration that we have had with our colleagues atthe NCHGR. We particularly want to thankElke Jordan, David Benton, Carol Dahl, BettieGraham, Jane Peterson, and Bob Strausbergfor their helpful critiques and suggestions dur-ing preparation of the manuscript.

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