6 Identity by Descent in the Mapping of Genetic Traits
157
References
Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin – rapid analysis of dense
genetic maps using sparse gene flow trees. Nat Genet 30:97–101
Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees.
Am J Hum Genet 62:1198–1211
Balding DJ, Moltke I, Marioni J (eds) (2019) Handbook of statistical genomics, 4th edn. Wiley,
Oxford, UK
Blangero J, Williams JT, Almasy L (2000) Robust LOD scores for variance component-based
linkage analysis. Genet Epidemiol 19(Suppl. 1):S8–S14
Brown MD, Glazner CG, Zheng C, Thompson EA (2012) Inferring coancestry in population
samples in the presence of linkage disequilibrium. Genetics 190:1447–1460
Browning SR, Browning BL (2010) High-resolution detection of identity by descent in unrelated
individuals. Am J Hum Genet 86:526–539
Browning SR, Thompson EA (2012) Detecting rare variant associations by identity by descent
mapping in case-control studies. Genetics 190:1521–1531
Chapman NH, Nato AQ Jr, Bernier R, Ankeman K, Sohi H, Munson J, Patowary A, Archer M,
Blue EM, Webb SJ, Coon H, Raskind WH, Brkanac Z, Wijsman EM (2015) Whole exome
sequencing in extended families with autism spectrum disorder implicates four candidate genes.
Hum Genet 134:1055–1068
Cox DR (1962) Renewal theory. Methuen and Co., London, UK
Day-Williams, AG, Blangero J, Dyer TD, Lange K, Sobel EM (2011) Linkage analysis without
defined pedigrees. Genet Epidemiol 35:360–370
Donnelly KP (1983) The probability that related individuals share some section of genome
identical by descent. Theor Popul Biol 23:34–63
Elston RC, Stewart J (1971) A general model for the analysis of pedigree data. Hum Hered 21:523–
542
Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3:87–112
Glazner CG, Thompson EA (2015) Pedigree-free descent-based gene mapping from population
samples. Hum Hered 80:21–35
Haldane JBS (1919) The combination of linkage values and the calculation of distances between
the loci of linked factors. J Genet 8:229–309
Haseman JK, Elston RC (1972) The investigation of linkage between a quantitative trait and a
marker locus. Behav Genet 2:3–19
Hayes BJ, Visscher PM, Goddard ME (2009) Increased accuracy of artificial selection by using the
realized relationship matrix. Genome Res 91:47–60
Hill WG, Weir BS (2011) Variation in actual relationship as a consequence of Mendelian sampling
and linkage. Genet Res Camb 93:47–64
Karigl G (1981) A recursive algorithm for the calculation of gene identity coefficients. Ann Hum
Genet 45:299–305
Koepke HA, Thompson EA (2013) Efficient testing operations on dynamic graph structures using
strong hash functions. J Comput Biol 20:551–570
Lander ES, Botstein D (1987) Homozygosity mapping: a way to map human recessive traits with
the DNA of inbred children. Science 236:1567–1570
Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl
Acad Sci (USA) 84(8):2363–2367
Lange K, Sobel E (1991) A random walk method for computing genetic location scores. Am J
Hum Genet 49:1320–1334
Lauritzen SJ (1992) Propagation of probabilities, means and variances in mixed graphical
association models. J Am Stat Assoc 87:1098–1108
Leutenegger A, Prum B, Genin E, Verny C, Clerget-Darpoux F, Thompson EA (2003) Estimation
of the inbreeding coefficient through use of genomic data. Am J Hum Genet 73:516–523
157
References
Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin – rapid analysis of dense
genetic maps using sparse gene flow trees. Nat Genet 30:97–101
Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees.
Am J Hum Genet 62:1198–1211
Balding DJ, Moltke I, Marioni J (eds) (2019) Handbook of statistical genomics, 4th edn. Wiley,
Oxford, UK
Blangero J, Williams JT, Almasy L (2000) Robust LOD scores for variance component-based
linkage analysis. Genet Epidemiol 19(Suppl. 1):S8–S14
Brown MD, Glazner CG, Zheng C, Thompson EA (2012) Inferring coancestry in population
samples in the presence of linkage disequilibrium. Genetics 190:1447–1460
Browning SR, Browning BL (2010) High-resolution detection of identity by descent in unrelated
individuals. Am J Hum Genet 86:526–539
Browning SR, Thompson EA (2012) Detecting rare variant associations by identity by descent
mapping in case-control studies. Genetics 190:1521–1531
Chapman NH, Nato AQ Jr, Bernier R, Ankeman K, Sohi H, Munson J, Patowary A, Archer M,
Blue EM, Webb SJ, Coon H, Raskind WH, Brkanac Z, Wijsman EM (2015) Whole exome
sequencing in extended families with autism spectrum disorder implicates four candidate genes.
Hum Genet 134:1055–1068
Cox DR (1962) Renewal theory. Methuen and Co., London, UK
Day-Williams, AG, Blangero J, Dyer TD, Lange K, Sobel EM (2011) Linkage analysis without
defined pedigrees. Genet Epidemiol 35:360–370
Donnelly KP (1983) The probability that related individuals share some section of genome
identical by descent. Theor Popul Biol 23:34–63
Elston RC, Stewart J (1971) A general model for the analysis of pedigree data. Hum Hered 21:523–
542
Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3:87–112
Glazner CG, Thompson EA (2015) Pedigree-free descent-based gene mapping from population
samples. Hum Hered 80:21–35
Haldane JBS (1919) The combination of linkage values and the calculation of distances between
the loci of linked factors. J Genet 8:229–309
Haseman JK, Elston RC (1972) The investigation of linkage between a quantitative trait and a
marker locus. Behav Genet 2:3–19
Hayes BJ, Visscher PM, Goddard ME (2009) Increased accuracy of artificial selection by using the
realized relationship matrix. Genome Res 91:47–60
Hill WG, Weir BS (2011) Variation in actual relationship as a consequence of Mendelian sampling
and linkage. Genet Res Camb 93:47–64
Karigl G (1981) A recursive algorithm for the calculation of gene identity coefficients. Ann Hum
Genet 45:299–305
Koepke HA, Thompson EA (2013) Efficient testing operations on dynamic graph structures using
strong hash functions. J Comput Biol 20:551–570
Lander ES, Botstein D (1987) Homozygosity mapping: a way to map human recessive traits with
the DNA of inbred children. Science 236:1567–1570
Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl
Acad Sci (USA) 84(8):2363–2367
Lange K, Sobel E (1991) A random walk method for computing genetic location scores. Am J
Hum Genet 49:1320–1334
Lauritzen SJ (1992) Propagation of probabilities, means and variances in mixed graphical
association models. J Am Stat Assoc 87:1098–1108
Leutenegger A, Prum B, Genin E, Verny C, Clerget-Darpoux F, Thompson EA (2003) Estimation
of the inbreeding coefficient through use of genomic data. Am J Hum Genet 73:516–523