The Candidate Gen e App ro a c h Jennifer M. Kwon, M.D., and Alison M. Goate, D.Phil. Alcoholism has a significant genetic basis, and identifying genes that confer a susceptibility to alcoholism will aid clinicians in preventing and effectively treating the disease. One commonly used technique to identify genetic risk factors for complex disorders such as alcoholism is the candidate gene approach, which directly tests the effects of genetic variants of a potentially contributing gene in an association study. These studies, which may include members of an affected family or unrelated cases and controls, can be performed relatively quickly and inexpensively and may allow identification of genes with small effects. However, the candidate gene approach is limited by how much is known of the biology of the disease being investigated. As researchers identify potential candidate genes using animal studies or linking them to DNA regions implicated through other analyses, the candidate gene approach will continue to be commonly used. KEY WO R D S : genetic theory of AODU (AOD [alcohol or other drug] use, abuse, and dependence); genetic linkage; genetic polymorphism; nucleotides; apolipoproteins; quantitative trait locus; alcohol dehydrogenases; aldehyde dehydrogenases; Alzheimer’s disease am i l y , twin, and adoption studies families, investigators can identify genetic Wh e r eas the linkage mapping ha v e indicated that alcoholism regions associated or “in linkage” with ap p r oach is an unbiased search of the Fhas a strong genetic component the disease by observing that affected en t i r e genome without any prec o n c e p - (R eich et al. 1999). Although res e a rc h e r s family members share certain marke r tions about the role of a certain gene, ar e still investigating its exact nature, variants (i.e., alleles) located in those the candidate gene approach allows se v eral genes of var ying effect that con- regions more frequently than would be res e a r chers to investigate the validity of fer a susceptibility to alcoholism (i.e., expected by chance. These regions can an “educated guess” about the genetic susceptibility genes) likely play a rol e . then be isolated, or cloned, for furth e r basis of a disorde r . This approach invol ve s Identification of these genes will aid analysis and characterization of the assessing the association between a par- res e a r chers and clinicians in preve n t i n g responsible genes. Linkage mapping ticular allele (or set of alleles) of a gene and effectively treating this disorde r . techniques have already resulted in the that may be invol v ed in the disease (i . e . , The search for alcoholism suscepti- identification of several potential DNA a candidate gene) and the disease it s e l f . bility genes centers on two major tech- regions that may contain susceptibility In other words, this type of association niques, linkage mapping and the can- genes for alcoholism (Reich et al. 19 9 9 ) . didate gene approach. Linkage mapping, (F or a rev i e w of the analogous approa c h also called positional cloning, is the pro- in mice, see the article in this issue on JEN N I F E R M. KWO N , M.D., is an assistant cess of systematically scanning the entire qu a n t i t a t i v e trait locus [QTL] analysis pr ofessor of neurol o g y and ALI S O N M. DNA contents (i.e., the genomes) of by Grisel, pp. 169–174.) The primary GOATE , D.PHI L ., is a professor of genetics various members of families affected by ad v antage of linkage mapping is that in psych i a t r y at Washington Uni ve r s i t y the disorder using regularly spaced, in v estigators need no prior knowledge of School of Medicine, St. Louis, Mis s o u r i . highly variable (i.e., polymorphic) DNA the physiology or biology underlying the Both authors are res e a r chers in the segments whose exact position is known dis o r der being studied, which is importa n t Co l l a b o ra t i v e Study of the Genetics of (i.e., genetic markers). Using those for complex disorders, such as alcoholism. Alc o h o l i s m . 164 Alcohol Research & Health TheWhat Candidate Is Moderate Gene Drinking?Approach study tries to answer the question, se v eral variants, or alleles, allowing for functions that might influence the trait “I s one allele of a candidate gene more its use in the candidate gene approach. of interes t . 1 (F or more information on fr equently seen in subjects with the dis- In alcoholism, as in other addictive the relationship betwee n mutations in ease than in subjects without the dis- di s o r ders, the pathways through which the DNA and variations in prot e i n ease?” The major difficulty with this brain chemicals (i.e., neurot r a n s m i t t e r s ) function, see the sidebar, p. 167.) In the ap p r oach is that in order to choose a and other signaling molecules act may case of ALDH, several wel l - k n ow n potential candidate gene, res e a rc h e r s polymorphisms result in the substitution must already have an understanding of of certain protein building blocks (i.e., the mechanisms underlying the disease Candidate gene studies amino acids) and thus can lead to pro- (i.e., disease pathophysiology). In con- teins with biologically rel e v ant changes trast with linkage mapping studies, how- ar e better suited for in function. In many cases, howeve r , eve r , studies of candidate genes do not detecting genes res e a r chers may know a gene’s DNA req u i r e large families with both affected sequence but may not have any infor- and unaffected members, but can be un d e r lying common mation about functional variation in pe r formed with unrelated cases and the gene. co n t r ol subjects or with small families and more complex Detecting genetic variants is a labo- (e.g., a prob a n d and parents). Furt h e r - diseases where the risk rious process that often invol ve s mo r e, candidate gene studies are better sequencing—that is, determining the suited for detecting genes underlying associated with any sequence of DNA building blocks (i.e., common and more complex diseases nucleotides)—for the entire gene in wh e r e the risk associated with any given gi v en candidate gene both affected and unaffected individu- candidate gene is rel a t i v ely small (Collins is rel a t i v ely small. als to look for consistent differen c e s . 2 et al. 1997; Risch and Mer i k a n g a s Al t e r n a t i ve l y , res e a r chers can employ 1996). This article describes the methods sc re e n i n g pro c e d u r es during which they used in candidate gene studies, including also play a role in the development and isolate small gene sections from many associated methodological and technical maintenance of addictive behaviors. individuals and compare their mobility considerations, and rev i e ws examples of For example, res e a r chers using the frui t in a gelatinous material. Dif f e r ences in this approach that are both related and fly Dr osophila melanogaster as an animal mobility in these analyses may indicate un r elated to alcoholism. Because many model of alcohol sensitivity found that nucleotide variations (Malhotra and of the best known examples of this a fly mutant called ch e a p d a t e ex h i b i t e d Goldman 1999).3 To confirm that a ap p r oach have been conducted in enhanced vulnerability to alcohol (Moo r e potential nucleotide variation exists and humans, these studies have been high- et al. 1998). This mutant carries a spe- to determine its exact location in the lighted. Howeve r , the overall approa c h cific allele of a gene important in cellu- genome, investigators then must con- is similar in other model organisms, lar signaling pathways; co n s e q u e n t l y , duct additional studies, typically on the and the differences will be rev i e wed at genes invol v ed in this and other signaling di r ect sequencing of the DNA section the end of this article. pa t h w a y s would be reasonable choices in question. This information also for candidate genes influencing alcohol al l o ws res e a r chers to determine Strategies Used sensitivity and possibly alcoholism. (For whether the nucleotide variation is in the Candidate mo r e information on alcohol-rel a t e d likely to have functional significance, Gene Approach studies in Dro s o p h i l a , see the ar ticle in either because it actually results in this issue by Heberlein, pp. 185–188.) amino acid changes in the resulting pro- The selection of pa r ticular genes for tein or because it occurs in DNA reg i o n s Selecting a Candidate Gene fu r ther analysis as candidate genes could co n t r olling the gene’s activity.