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Experimental Cell Research 253, 305–307 (1999)Article ID excr.1999.4724, available online at http://www.idealibrary.com on

REVIEW

Technology and the Evolution of Human GeneticsRay White

Huntsman Cancer Institute and Department of Oncological Science, University of Utah, Salt Lake City, Utah 84112

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TECHNOLOGY AND COMPLEXITY

Analysis of human genetic inheritance has providedemarkable insights into the molecular specifics byhich human and individual characteristics are en-

oded by genes. In early research, genetic traits tendedo be defined largely on the basis of simply “running inamilies.” Familiality is not a sufficient basis for aesignation of genetic, however, as the familial traitay result from cultural, rather than genetic inheri-

ance. Persuasive evidence requires matching the pat-erns of inheritance with the probabilistic expectationsf specific models. In practice, only highly penetrantlleles for rather rare traits segregating in large fam-lies will reveal statistically convincing associations. Inddition to the traits that seemed to run in families,here was reason to suspect that a significant fractionf developmental anomalies, e.g., retardation and dys-orphologies, might also have a genetic basis. Because

he majority of dysmorphologies were not usuallyransmitted in families over multiple generations,lear evidence was hard to obtain. Tracing the somaticnheritance of cell lineages in tissues was similarlyhallenging. Although chromosomal anomalies wereeen early in the observation of cancer cells, it was notossible, when all the chromosomes looked alike, toink specific anomalies with specific forms of cancer.

The rapid evolution of human genetics from a pri-arily descriptive science into our current, highly de-

ailed molecular mechanistic understanding of humannd cellular inheritance has been strongly driven byechnology. Advances that have subdivided the chro-osomes more and more finely have improved our

bility to create statistical associations with diseaseyndromes and have ultimately led to our ability toctually identify, clone, and sequence the specific genengaged in the pathological process. The analysis of theuman genome, its variation and phenotypes, is aranch of genetic science that has been driven by tech-ology development perhaps more than any other. Inetrospect, we realize how daunting the challenge re-lly was; we now understand that .100,000 genes

istributed over 23 randomly assorting chromosomes c

305

arry the genetic information. The hard problem ofomplexity had to be addressed head on, as the neces-ary restrictions on genetic manipulation in humansoreclosed other approaches—inbred lines, mutagene-is, etc. that have been so successful in other geneticystems. The crucial problem that had to be solved washat of scale; how to parse the human chromosomesnto smaller pieces, of reduced complexity, that coulde analyzed and understood.

THE CASPERSSON DISCOVERY—CHROMOSOMETECHNOLOGY

It was the work of Caspersson that brought the firstajor breakthrough in genomic analysis (Caspersson,

970 #1515]. Caspersson had discovered a technology,method for staining human chromosomes, that gavenique patterns for virtually every chromosome. Theolecular basis for the region-specific, differential

taining remains incompletely understood. Casperssonaw clearly, however, that here was a method thatould distinguish the individual human chromosomes.enetic functions, activities and components could bessigned to individual chromosomes and even to thendividual bands of specific chromosomes. With thisechnology, an ;100-fold reduction in complexity hadeen obtained—each chromosome carried, on average,pproximately 2000 genes distributed over several dis-inct bands. A gene or a function could now be mappedo the single band level. The number of human chro-osomes could be counted easily with accuracy. With

his new technology, two areas virtually exploded withrogress: analysis of congenital chromosomal anoma-ies and analysis of tumor cell rearrangements.

ANALYSIS OF CONGENITAL ANOMALIES

Trisomy 21 had been discovered and linked to men-al retardation many years earlier by Lejeune; yet ac-urate diagnosis was still challenging—even accurate

hromosome counts were challenging prior to chromo-

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306 RAY WHITE

ome banding. Furthermore, the door had been openedo connect many human congenital syndromes withpecific, smaller chromosomal anomalies. Cri-du-chatyndrome, for example, results from inheritance of aeletion of the short arm of chromosome 5; a smalleletion of chromosome 15 (15q11-13) results inrader-Willi syndrome [McKusick, 1992 #1516]. Thebility to identify specific chromosomes and even sub-hromasomal regions was essential to the identifica-ion of the genetic basis for these disorders. The abilityo accurately predict an outcome of severe mental re-ardation and/or developmental anomaly based on ex-mination of chromosomes also made it possible toetect such genetic accidents in utero by examinationf fetal cells in amniotic fluid. This new power forrenatal diagnosis has had widespread clinical appli-ations but has also introduced profound ethical issues.hese issues continue to be associated with our in-reasing ability to measure human genetic potentials.

ANALYSIS OF TUMOR CELLS

With banding, the chromosomes of tumor cells couldlso be analyzed in much greater detail, now revealingpecific chromosome rearrangements to be associatedith specific tumor types. The Philadelphia chromo-

ome, originally reported as an anonymous microchro-osome associated with chronic myelogenous leuke-ia [Nowell, 1960 #1512] for example, was identified

y banding analysis as one product of a reciprocal 9:22ranslocation [Rowley, 1973 #1511]. This informationed to the realization that the translocation might beirectly affecting a single gene and ultimately to thedentification of the specific genes broken and rejoinedy the translocation. Many translocations and dele-ions have now been associated with both blood tumorsnd solid tumors [Mitelman, 1991 #1513].

IN SITU HYBRIDIZATION—CHROMOSOME LOCATIONSOF INDIVIDUAL GENES

Through the study of rearrangements with banding,ndividual and cellular phenotypes could be associatedith specific chromosome regions. The next major ad-ance came from the development of technology thatllowed precise chromosomal localization of specificenes through in situ hybridization [Harper, 19811514]. The idea was that dissociated strands of DNAight be able to hybridize to the chromosomal DNA ofxed chromosomes; if the DNA carried an isotopic la-el, it might be detectable through overlay of a photo-raphic emulsion. It worked; individual genes couldow be localized within specific regions defined byanding or, very importantly, by chromosome translo-ations, deletions, and duplications. Individual genes

ould be mapped to the regions of chromosomal anom- n

ly, which were in turn associated with specific humanathologies. Genes which mapped to the region ofnomaly now became “candidates,” each potentiallyeing the genetic target of the rearrangement. In thease of deletion syndromes, for example, overlappingeletion sets could be developed which would narrowhe range of location of the target gene. The specificene could, in some cases, be selected from among theandidates. A new way to link specific genes with dis-ase syndromes had been created. These new technol-gies now enabled a new level of association, not just ofegions, but of individual genes, with human pheno-ypes. As before, this more precise mapping has, inost cases, allowed the identification of the specific

ene involved.

GENETIC MARKERS

Mapping based on chromosomal anomalies, how-ver, did not address the analysis of genetic syndromesased on the inheritance of “small” mutations withinpecific genes. Again, a new technology came to the foreo reduce complexity. This technology was based on thedea that there might exist enough DNA sequence vari-tion in the human genome to alter restriction enzymeleavage sites at frequent intervals within the humanenome [Botstein, 1980 #11]. If the variation existednd were stable, Southern blot technology with specificrobes would enable the development of a large set ofapped markers that could be used for linkage analy-

is in human families. Genes that mapped to the regionf linkage would become candidates for the gene whoseutations were causing the disease. Analysis of the

andidates for the presence of small mutations thatad destroyed or altered their activity would identifyhe specific gene from among the candidates. This sys-em has proven remarkably effective and resulted inhe mapping and identification of literally hundreds ofegions and genes that underlay inherited genetic pre-ispositions [McKusick, 1992 #1516]. The philosophy isssentially identical to that described above for dele-ion mapping—by placing the genetic location of theyndrome, as determined by phenotype, in a specifichromosomal region and identifying the specific genesn that region, the gene causing the phenotype can beiscovered.

GENOMICS: THE HUMAN GENOME TODAY

From these roots, a new discipline, genomics, hasmerged. The gestalt of genomics is based on principles ofnstrumentation and large-scale parallel processing ofamples. Sequencing of genes is an obviously parallelctivity—the sequence of one gene does not depend on theequence of any other. The most effective practitioners,

ot surprisingly given its production orientation, have

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307HUMAN GENETICS

urned out to be companies, such as Incyte and Humanenome Sciences, which have raised and committed the

esources necessary for large scale implementations ofequencing technology. The result is that the great ma-ority of expressed human genes have likely been se-uenced. Many important discoveries are coming fromimply searching for sequence similarities among theene sequences in computerized databases. Many genesre members of multigene families, and specific func-ional domains conserve amino acid sequence, allowingheir discovery by sequence analysis. Large-scaleenomic sequencing of the human is being implementedn both the public and the private sector. It is likely thathe great majority of human chromosomal sequence, inddition to the expressed sequences, will be availableithin just a few years. This will transform our approach

o human genetic analysis, as this extremely fine-grainedata (down to the single nucleotide) will support associ-tion of single nucleotide changes with phenotypic com-onents.Human genomic analysis is thus undergoing a new

evolution, again driven by technological advances. It willemain necessary to map human phenotypes to a specifichromosomal region. The candidate genes located in theegion, however, will largely be discoverable by examin-ng the DNA sequence of the region, greatly simplifyingnd speeding up the process of candidate gene identifica-ion. Furthermore, a new approach, which might bealled the genetics of genes, can now be applied. We nownow that the majority of human genes are polymorphic

n the human population. We expect that many, if notost, of these variants may be truly silent, conferring no

pecial properties or risks on the individual carrier.ome, however, may have implications for the humanondition and some of these may be discoverable by com-aring cohorts that carry the polymorphic variant withhose that do not. Precisely which traits to look for isften a mystery, but in other cases, in which some aspectsf gene function may be known, there are attractive hy-otheses as to phenotypic expression which can beeadily examined. In addition, the development of mi-roarray technologies for the display of DNA sequencesxpressed into mRNAs makes possible a further refine-ent of our search for the genetic basis of human pathol-

gies—candidate genes should in general be expressed inhe target tissue. This knowledge should also simplify

nd speed up the process of gene identification. m

PRIVATE SECTOR AND PUBLIC SECTOR

Large-scale DNA sequencing has also opened up newhallenges for the sociology of science. One novel fea-ure of the genomic approach to human genetic analy-is is the capital-intensive nature of the productionngineering and instrumentation necessary to gener-te large-scale DNA sequence. A second is the per-eived potential economic value of the findings. Theseeatures combine to attract investment from the pri-ate sector for the development of large databases ofNA sequence, first cDNA sequences and, more re-

ently, genomic sequences. Although there have beenarge investments in sequencing from the public sector,he current situation is that much more sequence isresent in the private databases, not generally avail-ble to researchers, than in the public databases.Private ownership of such large blocks of humanNA sequence has led to expressions of concern in the

esearch community that important knowledge of theuman genome is now controlled by the private sector.he questions raised are often phrased in terms of “tohom does the Human Genome rightfully belong?” and

is it appropriate for such knowledge to be controlledy for-profit corporations?” The response of the privateector is straightforward and in keeping with tradi-ion—they have paid for the research that has led tohese discoveries and, therefore, have a right to com-ensation. Without that right they would not haveeen able to make the investments that have led to theiscoveries. Furthermore, the private sector supportsell-developed pathways to the development of newedical treatments that will be for the benefit of hu-anity.These are intriguing issues that will be the subject of

mportant debate for some time to come, along with thessues of the patenting of specific genes. Perhaps the

ost important conclusion in the current context, how-ver, is that the interest of the private sector stronglynderscores the importance of human genome analy-is. As we have seen, this approach, initiated by aajor technological advance in chromosome imaging

hat allowed individual chromosomes and subchromo-omal regions to be distinguished and correlated withuman characteristics, has been carried and driven byngoing technological development. The scientific and

edical payouts are outstanding.