The objective of this article is to provide a nontechnical and intuitive introduction to the basic concepts and techniques that are used to establish statistical connections between genetic variants and human phenotypes. Depressive symptoms and delinquent behaviors that are of interest to sociologists are a subset of such human phenotypes. This article focuses on basic linkage analysis and association studies, the essential ideas behind the methods, and a very limited amount of molecular genetics needed for understanding the ideas. The article is written with those social scientists in mind who are interested in the topic but not yet ready to engage the vast and rapidly developing primary literature (journal articles).
Allison, D.B.1997. ``Transmission-Disequilibrium Tests for Quantitative Traits .'' American Journal of Human Genetics60:676-90.
2.
Allison, D.B. and M.C. Neale.2001. ``Joint Tests of Linkage and Association for Quantitative Traits.'' Theoretical Population Biology60:239-51.
3.
Barker, D., E. Wright, K. Nguyen, L. Cannon, P. Fain, D. Goldgar, et al. 1987. ``Gene for von Recklinghausen Neurofibromatosis Is in the Pericentromeric Region of Chromosome 17.'' Science236:1100-1102.
4.
Benjamini, Y., D. Drai, G. Elmer, N. Kafkafi, and I. Golani.2001. ``Controlling the False Discovery Rate in Behavior Genetics Research.'' Behavioural Brain Research125:279-84.
5.
Cardon, L.R. and G.R. Abecasis.2003. ``Using Haplotype Blocks to Map Human Complex Trait Loci.'' Trends in Genetics19 (3): 135-40.
6.
Cardon, L.R. and L.J. Palmer.2003. ``Population Stratification and Spurious Allelic Association.'' Lancet361:598-604.
7.
Cargill, M., D. Altshuler, J. Ireland, P. Sklar, K. Ardlie, N. Patil, et al. 1999. ``Characterization of Single-Nucleotide Polymorphisms in Coding Regions of Human Genes.'' Nature Genetics22:231-38.
8.
Claverie, J.M.2001. ``Gene Number: What If There Are Only 30,000 Human Genes?''Science291:1255-57.
9.
Collins, A. and N.E. Morton.1998. ``Mapping a Disease Locus by Allelic Association.''Proceedings of the National Academy of Sciences of the United States of America95:1741-45.
10.
Devlin, B., S.A. Bacanu, and K. Roeder.2004. ``Genomic Control to the Extreme. '' Nature Genetics36:1129-30.
11.
Devlin, B. and K. Roeder.1999. ``Genomic Control for Association Studies .'' Biometrics55:997-1004.
12.
Edgington, E.1980. Randomization Tests. New York: Marcel Dekker.
13.
Ewens, W.J. and R.S. Spielman.1995. ``The Transmission Disequilibrium Test: History, Subdivision, and Admixture.'' American Journal of Human Genetics57:455-64.
14.
Hall, J.M., M.K. Lee, B. Newman, J.E. Morrow, L.A. Anderson, B. Huey, et al. 1990. ``Linkage of Early-Onset Familial Breast Cancer to Chromosome 17q21.''Science250:1684-89.
15.
Hamer, D. and L. Sirota.2000. ``Beware the Chopsticks Gene. '' Molecular Psychiatry5:11-13.
16.
Hochberg, Y.1988. ``A Sharper Bonferroni Procedure for Multiple Tests of Significance.'' Biometrika75:800-802.
17.
International HapMap Consortium.2003. ``The International HapMap Project.''Nature426:789-96.
18.
--- 2005. ``A Haplotype Map of the Human Genome. ''Nature437:1299-320.
19.
Lander, E.S. and N.J. Schork.1994. ``Genetic Dissection of Complex Traits .'' Science265:2037-48.
20.
Lifton, R.P. and X. Jeunemaitre.1993. ``Finding Genes That Cause Human Hypertension .'' Journal of Hypertension11:231-36.
21.
Mackay, T.F.C.1996. ``The Nature of Quantitative Genetic Variation Revisited: Lessons from Drosophila bristles.'' Bioessays18:113-21.
22.
Mange, E.J. and A.P. Mange.1999. Basic Human Genetics. 2d ed. Sunderland, MA: Sinauer Associates.
23.
Morton, N.E.1955. ``Sequential Tests for the Detection of Linkage. '' American Journal of Human Genetics7:277-318.
24.
Nichols, T.E. and A.P. Holmes.2002. ``Nonparametric Permutation Tests for Functional Neuroimaging: A Primer With Examples.'' Human Brain Mapping15:1-25.
25.
O'Callaghan, F.J.K.1999. ``Tuberous Sclerosis: Epidemiological Research Is Needed to Complement New Findings in Genetics.''British Medical Journal318:1019-20.
26.
Penrose, L.S.1935. ``The Detection of Autosomal Linkage in Data Which Consists of Pairs of Brothers and Sisters of Unspecified Parentage. '' Annals of Eugenics6:133-38.
27.
Price, A.L., N.J. Patterson, R.M. Plenge, M.E. Weinblatt, N.A. Shadick, and D. Reich.2006. ``Principal Components Analysis Corrects for Stratification in Genome-wide Association Studies.''Nature Genetics38:904-9.
28.
Pritchard, J.K., M. Stephens, and P. Donnelly.2000. ``Inference of Population Structure Using Multilocus Genotype Data.'' Genetics155:945-59.
29.
Pritchard, J.K., M. Stephens, N.A. Rosenberg, and P. Donnelly.2000. ``Association Mapping in Structured Populations.''American Journal of Human Genetics67:170-81.
30.
Reich, D.E. and D.B. Goldstein.2001. ``Detecting Association in a Case-Control Study While Correcting for Population Stratification.'' Genetic Epidemiology20:4-16.
31.
Risch, N. and K. Merikangas.1996. ``The Future of Genetic Studies of Complex Human Diseases.'' Science273:1516-17.
32.
Schork, N.J., D. Fallin, and J.S. Lanchbury.2000. ``Single Nucleotide Polymorphisms and the Future of Genetic Epidemiology.'' Clinical Genetics58:250-64.
33.
Spielman, R.S., R.E. McGinnis, and W.J. Ewens.1993. ``Transmission Test for Linkage Disequilibrium: The Insulin Gene Region and Insulin-Dependent Diabetes Mellitus (IDDM). '' American Journal of Human Genetics52:506-16.
34.
Strachan, T. and A.P. Read.1999. Human Molecular Genetics. 2d ed. New York: John Wiley.
35.
Tang, H., T. Quertermous, B. Rodriguez, S.L.R. Kardia, X. Zhu, A. Brown, et al. 2005. ``Genetic Structure, Self-Identified Race/Ethnicity, and Confounding in Case-Control Association Studies.'' American Journal of Human Genetics76:268-75.
36.
Tennyson, C.N., H.J. Klamut, and R.G. Worton.1995. ``The Human Dystrophin Gene Requires 16 Hours to Be Transcribed and Is Cotranscriptionally Spliced. '' Nature Genetics9:184-90.
37.
van den Oord, E. and P.F. Sullivan.2003. ``False Discoveries and Models for Gene Discovery.'' Trends in Genetics19:537-42.
38.
Weiss, K.M. and J.D. Terwilliger .2000. ``How Many Diseases Does It Take to Map a Gene With SNPs?'' Nature Genetics26:151-57.
39.
Zuckerkandl, E.2002. ``Why So Many Noncoding Nucleotides? The Eukaryote Genome as an Epigenetic Machine.'' Genetica115:105-29.
