Abstract
Linkage analysis is a powerful tool for identifying and characterizing the genetic basis for human disease. Most successes have been in the localization of diseases whose inheritance is known to follow simple patterns of Mendelian inheritance like X-linked hypophosphatemic rickets, neurofibromatosis, and Duchenne muscular dystrophy. For these diseases, linkage analysis follows a standard approach — identifying the chromosomal location of the disease gene, determining the minimum candidate interval by the identification of critical recombination events, and systematically narrowing the interval to as small a region as possible by typing additional markers and individuals. This approach is well established: if enough informative meioses are available, the diagnosis is correctly assigned and the power of the available pedigree material is sufficient, the locus will be mapped.
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Roessler, E., Belloni, E., Gaudenz, K., Vargas, F., Scherer, S. W., Tsui, L.-C., and Muenke, M. (1997) Mutations in the C-terminal domain of Sonic Hedgehog cause holoprosencephaly. Hum. Mol. Genet. 6, 1847–1853.
Martin, N., Boomsma, D., and Machin, G. (1997) A twin-pronged attack on complex traits. Nat. Genet. 17, 387–392.
Lalouel, J. M. (1984) Segregation analysis: a gene or not a gene, in Genetic Epidemiology of Coronary Heart Disease: Past, Present, and Future, Alan R. Liss, pp. 217–243.
Morton, N. E. (1982) Segregation and linkage analysis, in Human Genetics, Part B: Medical Aspects ( Rao, D. C., et al., eds.), Alan R. Liss, pp. 3–14.
Elston, R. C. (1981) Segregation analysis. Adv. Hum. Genet. 11, 63–120.
Rutter, M., Yule, W., Berger, M., Yule, B., Morton, J., and Bagley, C. (1974) Children of West Indian immigrants. I. Rates of behavioural deviance and of psychiatric disorder. J. Child Psychol. Psychiatr. Allied Disciplines, 15, 241–262.
Greenberg, D. A. (1986) The effect of proband designation on segregation analysis. Am. J. Hum. Genet. 39, 329–339.
Goldin, L. R., Elston, R. C., Graham, J. B., and Miller, C. H. (1980) Genetic analysis of von Willebrand’s disease in two large pedigrees: a multivariate approach. Am. J. Med. Genet. 6, 279–293.
Go, C. P., Lamiell, J. M., Hsia, Y. E., and Yuen, W.-M. P. Y. (1984) Segregation and linkage analyses of von Hippel Lindau disease among 220 descendants from one kindred. Am. J. Hum. Genet. 36, 142
Elston, R. C., Namboordiri, K. K., and Nino, H. V. P. W. S. (1974) Studies on blood and urine glucose in Seminole Indians: Indications for segregation of a major gene. Am. J. Hum. Genet. 26, 13–33.
Bonney, G. E., Elston, R. C., Correa, P., Haenszel, W., Zavala, S. E., Zarama, G., et al. (1986) Genetic etiology of gastric carcinoma: chronic atrophic gastritis. Genet. Epidemiol. 3, 213–224.
Pericak-Vance, M. A., Vance, J. M., Elston, R. C., Namboodiri, K. K., and Fogle, T. A. (1985) Segregation and linkage analysis of alpha-N-acetyl-D-glucosaminidase (NAG) levels in a black family. Am. J. Med. Genet. 20, 295–306.
Lalouel, J. M. and Morton, N. E. (1981) Complex segregation analysis with pointers. Hum. Hereditary. 31, 312–321.
MacLean, C. J., Morton, N. E., and Yee, S. (1984) Combined analysis of genetic segregation and linkage under an oligogenic model. Comput. Biomed. Res. 17, 471–4806.
Elston, R. C. and Stewart, J. (1971) A general model for the genetic analysis of pedigree data. Hum. Hered. 21, 523–542.
Lalouel, J. M., Rao, D. C., Morton, N. E., and Elston, R. C. (1983) A unified model for complex segregation analysis. Am. J. Hum. Genet. 35, 816–826.
Bonney, G. E. (1984) On the statistical determination of major gene mechanisms in continuous human traits: regressive models. Am. J. Hum. Genet. 18, 731–749.
Vieland, V. J. and Hodge, S. E. (1995) Inherent intractability of the ascertainment problem for pedigree data: a general likelihood framework. Am. J. Hum. Genet. 56, 33–43.
Elston, R. C. (1995) Invited editorial. Twixt cup and lip: how intractable is the ascertainment problems? Am..1. Hum. Genet. 56, 15–17.
Risch, N. (1990) Linkage strategies for genetically complex traits I. Multilocus models. Am. J. Hum. Genet. 46, 222–228.
Worton, R. G. and Thompson, M. W. (1988) Genetics of Duchenne muscular dystrophy, in Annual Review of Genetics ( Campbell, A., Baker, B. S., and Herskowitz, I. eds.), Annual Reviews Inc., Palo Alto, CA, pp. 601–630.
Easton, D. F., Bishop, D. T., Ford, D., Crockford, G. P., and Breast Cancer Linkage Consortium. (1993) Genetic linkage analysis in familial breast and ovarian cancer: results from 217 families. Am. J. Hum. Genet. 52, 678–701.
Bowcock, A. M., Anderson, L.A., Friedman, L. S., Black, D. M., Osborne-Lawrence, S., Rowell, S. E., et al. (1993) THRA1 and D17S183 flank an interval of < 4 cM for the breast-ovarian cancer gene (BRCA1) on chromosome 17g21. Am. J. Hum. Genet. 52, 718–722.,.
Baraitser, M. and Pallon, M. A. (1985) Reduced penetrance in tuberous sciensis. J. Med. Genet. 22, 29–31.
Folstein, M. F. (1989) Heterogeneity in Alzheimer’s disease. Neurobiol. Aging. 10, 434–435.
Faner, L. A. and Conneally, P. M. (1985) A genetic model for age at onset in Huntington disease. Am. J. Hum. Genet. 37, 350–357.
Pericak-Vance, M. A., Elston, R. C., Conneally, P. M., and Dawson, D. V. (1983) Ageof-onset heterogeneity in Huntington disease families Am. J. Med. Genet. 14, 49–59.
Futreal, P. A., Liu, Q., Shattuck-Eidens, D., Cochran, C., Harshman, K., Tavtigian, S., et al. (1994) BRCA1 Mutations in Primary Breast and Ovarian Carcinomas. Science 266, 120–126.
Wooster, R., Bignell, G., Lancaster, J., Swift, S., Seal, S., Mangion, J., et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378, 789–792.
Tavtigian, S. V., Simard, J., Rommens, J., Couch, F., Shattuck-Eidens, D., Neuhausen, S., et al. (1996) The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds. Nature Genet. 12, 333–337.
Pericak-Vance, M. A., Bebout, J. L., Gaskell, P. C., Yamaoka, L. H., Hung, W.-Y., Alberts, M. J., et al. (1991) Linkage studies in familial Alzheimer’s disease: evidence for chromosome 19 linkage. Am. J. Hum. Genet. 48, 1034–1050.
Leal, S. M. and Ott, J. (1990) Expected lod scores in linkage analysis of autosomal recessive traits for affected and unaffected offspring. Am. J. Hum. Genet. 47, A188.
Hauser, E. R., Boehnke, M., Guo, S. W., and Risch, N. (1996) Affected-sib-pair interval mapping and exclusion for complex genetic traits-sampling considerations. Genet Epidemiol. 13, 117–137.
Hacia, J. G., Brody, L. C., Chee, M. S., Fodor, S. P. A., and Collins, F. S. (1996) Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat. Genet. 14, 441–447.
Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human disorders. Science 273, 1516–1517.
Ott, J. (1989) Computer simulation methods in human linkage analysis. Proc. Natl. Acad. Sci. USA 86, 4175–4178.
Weeks, D. E., Ott, J., and Lathrop, G. M. (1990) SLINK: A general simulation program for linkage analysis. Am..1. Hum. Genet. 47, A204
Boehnke, M. (1986) Estimating the power of a proposed linkage study: a practical computer simulation approach. Am. J. Hum. Genet. 39, 513–527.
Ploughman, L. M. and Boehnke, M. (1989) Estimating the power of a proposed linkage study for a complex genetic trait. Am. J. Hum. Genet. 44, 543–551.
Ott, J. (1991) Analysis of Human Genetic Linkage. Johns Hopkins University Press, Baltimore.
Ott, J. (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. Am. J. Hum. Genet. 51, 283–290.
Weeks, D. E., Lehner, T., Squires-Wheeler, E., Kaufmann, C., and Ott, J. (1990) Measuring the inflation of the lod score due to its maximization over model parameter values in human linkage analysis. Genet. Epidemiol. 7, 237–243.
Bernstein, F. (1931) Zur grundlegung der chromosomentheorie der vererbung beim menschen. Z. Abst. Vererb. 57, 113–138.
Weinberg, W. (1912) Zur verebung der anlage der bluterkrankheit mit methodologischen ergaenzungen meiner geschwistermethode. Arch. Rass. Ges. Biol. 6, 694–709.
Penrose, L. S. (1935) The detection of autosomal linkage in data which consists of pairs of brothers and sisters of unspecified parentage. Ann. Eugen. 6, 133–138.
Haseman, J. K. and Elston, R. C. (1972) The investigation of linkage between a quantitative trait and a marker locus. Behay.Genet. 2, 3–19.
Haldane, J. B. S. and Smith, C. A. B. (1947) A new estimate of the linkage between the genes for color blindness and hemophilia in man. Ann. Eugen. 14, 10–31.
Morton, N. E. (1955) Sequential tests for the detection of linkage. Am. J. Hum. Genet.7, 277–318.
Wald, A. (1947) Sequential Analysis John Wiley, New York.
Lange, K. and Elston, R. C. (1975) Extension to pedigree analysis. I. Likelihood calculations for simple and complex pedigrees. Hum. Hered. 25, 95–105.
Lander, E. S. and Kruglyak, L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 11, 241
Edwards, A. W. F. (1992) Likelihood (expanded ed.), Johns Hopkins University Press, Baltimore.
Conneally, P. M., Edwards, J. H., and Kidd, K. K. (1985) Report of the commitee on methods of linkage analysis reporting. Eighth International Workshop on Human Gene Mapping. Cytogenet. Cell Genet. 40, 356–359.
Lathrop, G.M., Lalouel, J. M., Julier, C., and Ott, J. (1984) Strategies for multilocus linkage analysis in humans. Proc. Natl. Acad. Sci. USA 81, 3443–3446.
Lander, E. S. and Botstein, D. (1986) Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms. Proc. Natl. Acad. Sci. USA 83, 7357
Lander, E. S. and Botstein, D. (1987) Homozygostiy mapping: a way to map human recessive traits with the DNA of inbred children. Science 236, 1567–1570.
Risch, N. and Giuffra, L. (1992) Model misspecification and multipoint linkage analysis. Hum. Hered. 42, 77–92.
Knowles, J. A., Vieland, V. J., and Gilliam, T. C. (1992) Perils of gene mapping with microsatellite markers. Am. J. Hum. Genet. 51, 905–909.
Dausset, J., Cann, H., Cohen, D., Lathrop, M., Lalouel, J. M., and White, R. (1990) Centre d’ etude du polymorphisme humanin (CEPH): collaborative genetic mapping of the human genome. Genomics 6, 575–577.
Bird, T. D., Ott, J., and Giblett, E. F. (1982) Evidence for linkage of Charcot-MarieTooth neuropathy to the Duffy locus on chromosome 1. Am. J. Hum. Genet. 34, 388–394.
Fryer, A. E., Connor, J. M., Povey, S., Yates, J. R. W., Chalmer, A., Fraser, I., et al. (1987) Evidence that the gene for tuberous sclerosis is on chromosome 9. Lancet 1, 659–661.
Kandt, R. S., Haines, J. L., Smith, M., Northrup, H., Gardner, R. J., Short, M. P., et al. (1992) Linkage of an important gene locus for tuberous sclerosis to a chromosome 16 marker for polycystic kidney disease. Nat. Genet. 2, 37–41.
Van Camp, G., Willems, P. J., and Smith, R. J. H. (1997) Nonsyndromic hearing impairment: unparalleled heterogeneity. Am. J. Hum. Genet. 60, 758–764.
Reeders, S. T., Breuning, M. H., Ryynaenen, M. A., Wright, A. F., Davies, K. E., King, A. W., et al. (1987) A study of genetic linkage heterogeneity in adult polycystic kidney disease. Hum. Genet. 76, 348–351.
Morton, N. E. (1956) The detection and estimation of linkage between the genes for elliptocytosis and the Rh blood type. Am. J. Hum. Genet. 8, 80–96.
Ott, J. (1983) Linkage analysis and family classification under heterogeneity. Ann. Hum. Genet. 47, 311–320.
Smith, C. A. B. (1961) Homogeneity test for linkage data. Proc. Sec. Int. Cong. Hum. Genet. 212–213.
Terwilliger, J. D. and Ott, J. (1994) Handbook of Genetic Linkage, Johns Hopkins University Press, Baltimore.
Clerget-Darpoux, F., Babron, M., and Bonaiti-Pellie, C. (1987) Power and robustness of the linkage homogeneity test in genetic analysis of common disorders. J. Psychiatr. Res. 21, 625–630.
Hodge, S. E. (1984) The information contained in multiple sibling pairs. Genet. Epidemiol. 1, 109–122.
Clerget-Darpoux, F., Bonaiti-Pellie, C., and Hochez, J. (1986) Effects of mis-specifying genetic parameters in lod score analysis. Biometrics 42, 393–399.
Smith, C. A. B. (1963) Testing for heterogeneity of recombination fractions values in human genetics. Ann. Hum. Genet. 27, 175–182.
Berrettini, W. H., Ferraro, T. N., Goldin, L. R., Weeks, D. E., Detera-Wadleigh, S., Nurnberger, J. I., Jr., and Gershon, E. S. (1994) Chromosome 18 DNA markers and manic-depressive illness: evidence for a susceptibility gene. Proc. Natl. Acad. Sci.USA 91, 5918–5921.
Lathrop, G. M. and Ott, J. (1990) Analysis of complex diseases under oligogenic models and intrafamilial heterogeneity by the LINKAGE program. Am. J. Hum. Genet. 47, A188.
Schork, N. J., Boehnke, M., Terwilliger, J. D., and Ott, J. (1993) Two trait locus linkage analysis: a powerful strategy for mapping complex genetic traits. Am. J. Hum. Genet. 53, 1127–1136.
Weeks, D. E. and Lange, K. (1988) The affected-pedigree member method of linkage analysis. Am. J. Hum. Genet. 42, 315–326.
Davis, S., Schroeder, M., Goldin, L. R., and Weeks, D. E. (1996) Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am. J. Hum. Genet. 58, 867–880.
Econs, M. J. and Speer, M. C. (1998) Genetic studies of complex diseases: let the reader beware. J Bone Miner. Res. 11, 1835–1839.
Spielman, R. S., McGinnis, R. E., and Ewens, W. J. (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52, 506–516.
Schaid, D. J. and Sommer, S. S. (1994) Comparison of statistics for candidate-gene association studies using cases and parents. Am. J. Hum. Genet. 55, 402–409.
Terwilliger, J. D. and Ott, J. (1992) A haplotype-based “haplotype relative risk” approach to detecting allelic associations. Hum. Heredity 42, 337–346.
Falk, C. T. and Rubinstein, P. (1987) Haplotype relative risks: an easy reliable way to construct a proper control sample for risk calculations. Ann. Hum. Genet. 51, 227–233.
Kaplan, N. L., Martin, E. R., and Weir, B. S. (1997) Power studies for the transmission/disequilibrium tests with multiple alleles. Am. J. Hum. Genet. 60, 691–702.
Monks, S. A., Martin, E. R., Weir, B. S., and Kaplan, N. L. (1997) A sibship test of linkage in the absence of parental information. Am. J. Hum. Genet. 61, A286 (Abstract).
Boehnke, M. and Langefeld, C. D. (1998) Genetic association mapping based on discordant sib pairs: the discordant alleles test (DAT). Am. J. Hum. Genet. 62, 950–961.
Cottingham, R. W. Jr., Idury, R. M., and Schaffer, A. A. (1993) Faster sequential genetic linkage computations. Am. J. Hum. Genet. 53, 252–263.
O’Connell, J. R. and Weeks, D. E. (1995) The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recording and fuzzy inheritance. Nat. Genet. 11, 402–408.
Kruglyak, L., Daly, M. J., Reeve-Daly, M. P., and Lander, E. S. (1996) Parametric and nonparametric linkage analysis:— a unified multipoint approach. Am. J. Hum. Genet. 58, 1347–1363.
Blackwelder, W. C. and Elston, R. C. (1985) A comparison of sib-pair linkage tests for disease susceptibility loci. Genet. Epidemiol. 2, 85–98.
Knapp, M., Seuchter, S., and Bauer, M. (1994) Linkage analysis in nuclear families. 1. Optimality criteria for affected sib—pair test. Hum. Heredity 44, 37–43.
Davis, S. and Weeks, D. E. (1997) Comparison of nonparametric statistics for detection of linkage analysis in nuclear families: single marker evaluation. Am. J. Hum. Genet. 61, 1431–1444.
Kruglyak, L. and Lander, E. S. (1995) Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am. J. Hum. Genet. 57, 439–454.
Curtis, D. and Sham, P. C. (1994) Using risk calculation to implement an extended relative pair analysis. Am. J. Hum. Genet. 58, 151–162.
Speer, M. C. (1998) Sample size and power, in Gene Mapping in Complex Human Disease ( Haines, J. L. and Pericak-Vance, M., eds.), Wiley-Liss, New York, pp. 161–200.
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Leal, S.M., Speer, M.C. (2000). Genetic Linkage Analysis in Human Disease. In: Econs, M.J. (eds) The Genetics of Osteoporosis and Metabolic Bone Disease. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-033-9_20
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