OS_refs

References from Statistical Genetics: Gene Mapping Through Linkage and Association

A-C D-F G-K L-N O-R S-T U-Z Online Material

O’Connell, J. R., & Weeks, D. E. (1995). The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet, 11(4), 402-408 Abstract

O’Connell, J. R., & Weeks, D. E. (1998). PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet, 63(1), 259-266 Abstract

O’Connell, J. R. (2000). Zero-recombinant haplotyping: applications to fine mapping using SNPs. Genet Epidemiol, 19 Suppl 1, S64-70 Abstract

Odeberg, J., Holmberg, K., Eriksson, P., & Uhlen, M. (2002). Molecular haplotyping by pyrosequencing. Biotechniques, 33(5), 1104, 1106, 1108 Abstract

Ogura, Y., Bonen, D. K., Inohara, N., Nicolae, D. L., Chen, F. F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R. H., Achkar, J. P., Brant, S. R., Bayless, T. M., Kirschner, B. S., Hanauer, S. B., Nunez, G., & Cho, J. H. (2001). A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature, 411(6837), 603-606 Abstract

Olson, J. M. (1999). Relationship estimation by Markov-process models in a sib-pair linkage study. Am J Hum Genet, 64(5), 1464-1472 Abstract

Olson, J. M., Witte, J. S., & Elston, R. C. (1999). Genetic mapping of complex traits. Stat Med, 18, 2961-2981

Open Source Initiative. (2005). http://opensource.org.

Ott, J. (1976). A computer program for linkage analysis of general human pedigrees. Am J Hum Genet, 28(5), 528-529 Abstract

Ott, J. (1991). Analysis of human genetic linkage. Baltimore, MD.: Johns Hopkins University Press.

Ott, J. (1993). Detecting marker inconsistencies in human gene mapping. Hum Hered, 43(1), 25-30 Abstract

Owerbach, D., Naya, F. J., Tsai, M. J., Allander, S. V., Powell, D. R., & Gabbay, K. H. (1997). Analysis of candidate genes for susceptibility to type I diabetes: a case-control and family-association study of genes on chromosome 2q31-35. Diabetes, 46(6), 1069-1074 Abstract

Ozaki, K., Ohnishi, Y., Iida, A., Sekine, A., Yamada, R., Tsunoda, T., Sato, H., Sato, H., Hori, M., Nakamura, Y., & Tanaka, T. (2002). Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat Genet, 32(4), 650-654 Abstract

Palmer, L. J., Jacobs, K. B., & Elston, R. C. (2000). Haseman and Elston revisited: the effects of ascertainment and residual familial correlations on power to detect linkage. Genet Epidemiol, 19(4), 456-460 Abstract

Palmer, L. J. (2003). Loosening the cuff: important new advances in modeling antihypertensive treatment effects in genetic studies of hypertension. Hypertension, 41(2), 197-198 Abstract

Palmer, L. J., & Cardon, L. R. (2005). Shaking the tree: mapping complex disease genes with linkage disequilibrium. Lancet, 366(9492), 1223-1234 Abstract

Parra, E. J., Marcini, A., Akey, J., Martinson, J., Batzer, M. A., Cooper, R., Forrester, T., Allison, D. B., Deka, R., Ferrell, R. E., & Shriver, M. D. (1998). Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet, 63(6), 1839-1851 Abstract

Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., Nguyen, B. T., Norris, M. C., Sheehan, J. B., Shen, N., Stern, D., Stokowski, R. P., Thomas, D. J., Trulson, M. O., Vyas, K. R., Frazer, K. A., Fodor, S. P., & Cox, D. R. (2001). Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 294(5547), 1719-1723 Abstract

Peacock, M., Koller, D. L., Lai, D., Hui, S., Foroud, T., & Econs, M. J. (2005). Sex-specific quantitative trait loci contribute to normal variation in bone structure at the proximal femur in men. Bone, 37(4), 467-473 Abstract

Pearson, K., & Lee, A. (1901). On the inheritance of characteristics not capable of exact quantitative measurement. Philos. Trans. R. Soc. Lond. Ser. A, 195, 79-150

Peltonen, L., Palotie, A., & Lange, K. (2000). Use of population isolates for mapping complex traits. Nat Rev Genet, 1(3), 182-190 Abstract

Penrose, L. (1935). The detection of autosomal linkage in data which consist of pairs of brothers and sisters of unspecified parentage. Ann. Eugen., 6, 133-138

Penrose, L. (1953). The general purpose sib-pair linkage test. Ann. Eugen, 18, 120-124

Plomin, R., DeFries, J. C., & Loehlin, J. C. (1977). Genotype-environment interaction and correlation in the analysis of human behavior. Psychol Bull, 84(2), 309-322 Abstract

Posthuma, D., & Boomsma, D. I. (2000). A note on the statistical power in extended twin designs. Behav Genet, 30(2), 147-158 Abstract

Posthuma, D., de Geus, E. J., & Boomsma, D. I. (2001). Perceptual speed and IQ are associated through common genetic factors. Behav Genet, 31(6), 593-602 Abstract

Posthuma, D., Beem, A. L., de Geus, E. J., van Baal, G. C., von Hjelmborg, J. B., Iachine, I., & Boomsma, D. I. (2003). Theory and practice in quantitative genetics. Twin Res, 6(5), 361-376 Abstract

Posthuma, D., de Geus, E. J., Boomsma, D. I., & Neale, M. C. (2004). Combined linkage and association tests in mx. Behav Genet, 34(2), 179-196 Abstract

Posthuma, D., Luciano, M., Geus, E. J., Wright, M. J., Slagboom, E., Montgomery, G. W., Boomsma, D. I., & Martin, N. G. (2005). A genomewide scan for intelligence identifies quantitative trait loci on 2q and 6 Am J Hum Genet, 77(2), 318-326 Abstract

Presson, A. P., Sobel, E., Lange, K., & Papp, J. C. (2006). Merging microsatellite data. J Comput Biol, 13(6), 1131-1147 Abstract

Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet, 38(8), 904-909 Abstract

Pritchard, J. K., & Rosenberg, N. A. (1999). Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet, 65(1), 220-228 Abstract

Pritchard, J. K., Stephens, M., & Donnelly, (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959 Abstract

Pritchard, J. K., Stephens, M., Rosenberg, N. A., & Donnelly, (2000). Association mapping in structured populations. Am J Hum Genet, 67(1), 170-181 Abstract

Pritchard, J. K., & Donnelly, (2001). Case-control studies of association in structured or admixed populations. Theor Popul Biol, 60(3), 227-237 Abstract

Pritchard, J. K., & Przeworski, M. (2001). Linkage disequilibrium in humans: models and data. Am J Hum Genet, 69(1), 1-14 Abstract

Purcell, S., Cherny, S. S., Hewitt, J. K., & Sham, C. (2001). Optimal sibship selection for genotyping in quantitative trait locus linkage analysis. Hum Hered, 52(1), 1-13 Abstract

Purcell, S. (2002). Variance components models for gene-environment interaction in twin analysis. Twin Res, 5(6), 554-571 Abstract

Purcell, S., & Sham, (2002). Variance components models for gene-environment interaction in quantitative trait locus linkage analysis. Twin Res, 5(6), 572-576 Abstract

Purcell, S., Cherny, S. S., & Sham, C. (2003). Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics, 19(1), 149-150 Abstract

Purcell, S., & Sham, (2004). Properties of structured association approaches to detecting population stratification. Hum Hered, 58(2), 93-107 Abstract

Purcell, S., Daly, M. J., & Sham, C. (2007). WHAP: haplotype-based association analysis. Bioinformatics, 23(2), 255-256 Abstract

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, I., Daly, M. J., & Sham, C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet, 81(3), 559-575 Abstract

Putter, H., Sandkuijl, L. A., & van Houwelingen, J. C. (2002). Score test for detecting linkage to quantitative traits. Genet Epidemiol, 22(4), 345-355 Abstract

Putter, H., Lebrec, J., & van Houwelingen, H. C. (2003). Selection strategies for linkage studies using twins. Twin Res, 6(5), 377-382 Abstract

Qian, D., & Beckmann, L. (2002). Minimum-recombinant haplotyping in pedigrees. Am J Hum Genet, 70(6), 1434-1445 Abstract

Qin, Z. S., Niu, T., & Liu, J. S. (2002). Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet, 71(5), 1242-1247 Abstract

R Development Core Team. (2005). R. Vienna: R Foundation for Statistical Computing.

Rabinowitz, D. (1997). A transmission disequilibrium test for quantitative trait loci. Hum Hered, 47(6), 342-350 Abstract

Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., Gonzalez, J. R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K. W., Scherer, S. W., & Hurles, M. E. (2006). Global variation in copy number in the human genome. Nature, 444(7118), 444-454 Abstract

Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S. F., Ward, R., & Lander, E. S. (2001). Linkage disequilibrium in the human genome. Nature, 411(6834), 199-204 Abstract

Reich, D. E., & Lander, E. S. (2001). On the allelic spectrum of human disease. Trends Genet, 17(9), 502-510 Abstract

Reich, D. E., Schaffner, S. F., Daly, M. J., McVean, G., Mullikin, J. C., Higgins, J. M., Richter, D. J., Lander, E. S., & Altshuler, D. (2002). Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet, 32(1), 135-142 Abstract

Rice, K. M., & Holmans, (2003). Allowing for genotyping error in analysis of unmatched case-control studies. Ann Hum Genet, 67(Pt 2), 165-174 Abstract

Rietveld, M. J., Posthuma, D., Dolan, C. V., & Boomsma, D. I. (2003). ADHD: sibling interaction or dominance: an evaluation of statistical power. Behav Genet, 33(3), 247-255 Abstract

Rijsdijk, F. V., Hewitt, J. K., & Sham, C. (2001). Analytic power calculation for QTL linkage analysis of small pedigrees. Eur J Hum Genet, 9(5), 335-340 Abstract

Rijsdijk, F. V., & Sham, C. (2002). Estimation of sib-pair IBD sharing and multipoint polymorphism information content by linear regression. Behav Genet, 32(3), 211-220 Abstract

Riordan, J. R., Rommens, J. M., Kerem, B., Alon, N., Rozmahel, R., Grzelczak, Z., Zielenski, J., Lok, S., Plavsic, N., Chou, J. L., & et al. (1989). Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science, 245(4922), 1066-1073 Abstract

Risch, N. (1990a). Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. Am J Hum Genet, 46(2), 242-253 Abstract

Risch, N. (1990b). Linkage strategies for genetically complex traits. II. The power of affected relative pairs. Am J Hum Genet, 46(2), 229-241 Abstract

Risch, N. (1990c). Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet, 46(2), 222-228 Abstract

Risch, N. (1992). Corrections to “Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs”. Am J Hum Genet, 51(3), 673-675 Abstract

Risch, N., & Zhang, H. (1995). Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science, 268(5217), 1584-1589 Abstract

Risch, N., & Merikangas, K. (1996). The future of genetic studies of complex human diseases. Science, 273(5281), 1516-1517 Abstract

Risch, N., & Teng, J. (1998). The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling. Genome Res, 8(12), 1273-1288 Abstract

Risch, N., & Teng, J. (1999). The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases II. Individual genotyping. Genome Res, 9, 234-241 Abstract

Risch, N. J., & Zhang, H. (1996). Mapping quantitative trait loci with extreme discordant sib pairs: sampling considerations. Am J Hum Genet, 58(4), 836-843 Abstract

Risch, N. J. (2000). Searching for genetic determinants in the new millennium. Nature, 405(6788), 847-856 Abstract

Roberts, S. B., MacLean, C. J., Neale, M. C., Eaves, L. J., & Kendler, K. S. (1999). Replication of linkage studies of complex traits: an examination of variation in location estimates. Am J Hum Genet, 65(3), 876-884 Abstract

Robin, E. D., & Wong, R. (1988). Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol, 136(3), 507-513 Abstract

Roeder, K., Bacanu, S. A., Sonpar, V., Zhang, X., & Devlin, B. (2005). Analysis of single-locus tests to detect gene/disease associations. Genet Epidemiol, 28(3), 207-219 Abstract

Roeder, K., Bacanu, S. A., Wasserman, L., & Devlin, B. (2006). Using linkage genome scans to improve power of association in genome scans. Am J Hum Genet, 78(2), 243-252 Abstract

Rohde, K., & Fuerst, R. (2001). Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. Hum Mutat, 17(4), 289-295 Abstract

Rommens, J. M., Iannuzzi, M. C., Kerem, B., Drumm, M. L., Melmer, G., Dean, M., Rozmahel, R., Cole, J. L., Kennedy, D., Hidaka, N., & et al. (1989). Identification of the cystic fibrosis gene: chromosome walking and jumping. Science, 245(4922), 1059-1065 Abstract

Rothman, K. J. (1986). Modern Epidemiology. Boston, MA.: Little Brown and Company.