Relatedness Coefficients in Pedigrees with Inbred Founders

Overview

Journal J Math Biol

Date 2020 Jun 10

PMID 32514944

Citations 6

Authors

Magnus Dehli Vigeland

Affiliations

Soon will be listed here.

Abstract

We study an extension of the standard framework for pedigree analysis, in which we allow pedigree founders to be inbred. This solves a number of practical challenges in calculating coefficients of relatedness, including condensed identity coefficients. As a consequence we expand considerably the class of pedigrees for which such coefficients may be efficiently computed. An application of this is the modelling of background inbreeding as a continuous effect. We also use inbred founders to shed new light on constructibility of relatedness coefficients, i.e., the problem of finding a genealogy yielding a given set of coefficients. In particular, we show that any theoretically admissible coefficients for a pair of noninbred individuals can be produced by a finite pedigree with inbred founders. Coupled with our computational methods, implemented in the R package ribd, this allows for the first time computer analysis of general constructibility solutions, thus making them accessible for practical use.

Citing Articles

Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale.

Horne J, Frey A, Gaos A, Martin S, Dutton P R Soc Open Sci. 2023; 10(5):221547.

PMID: 37206959 PMC: 10189603. DOI: 10.1098/rsos.221547.

Two-locus identity coefficients in pedigrees.

Vigeland M G3 (Bethesda). 2022; 13(2).

PMID: 36525359 PMC: 9911075. DOI: 10.1093/g3journal/jkac326.

Causal inference for the covariance between breeding values under identity disequilibrium.

Cantet R, Angarita-Barajas B, Forneris N, Munilla S Genet Sel Evol. 2022; 54(1):64.

PMID: 36138346 PMC: 9502921. DOI: 10.1186/s12711-022-00750-6.

QuickPed: an online tool for drawing pedigrees and analysing relatedness.

Vigeland M BMC Bioinformatics. 2022; 23(1):220.

PMID: 35672681 PMC: 9175388. DOI: 10.1186/s12859-022-04759-y.

Linkage analysis identifies novel genetic modifiers of microbiome traits in families with inflammatory bowel disease.

Sharma A, Szymczak S, Ruhlemann M, Freitag-Wolf S, Knecht C, Enderle J Gut Microbes. 2022; 14(1):2024415.

PMID: 35129060 PMC: 8820822. DOI: 10.1080/19490976.2021.2024415.

References

Lacy R . Extending pedigree analysis for uncertain parentage and diverse breeding systems. J Hered. 2012; 103(2):197-205. DOI: 10.1093/jhered/esr135. View

Weeks D, Lange K . A multilocus extension of the affected-pedigree-member method of linkage analysis. Am J Hum Genet. 1992; 50(4):859-68. PMC: 1682645. View

Lange K, Sinsheimer J . Calculation of genetic identity coefficients. Ann Hum Genet. 1992; 56(4):339-46. DOI: 10.1111/j.1469-1809.1992.tb01162.x. View

Weeks D, Lange K . The affected-pedigree-member method of linkage analysis. Am J Hum Genet. 1988; 42(2):315-26. PMC: 1715269. View

Pemberton T, Rosenberg N . Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Hum Hered. 2014; 77(1-4):37-48. PMC: 4154368. DOI: 10.1159/000362878. View

Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S . The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2013; 505(7481):43-9. PMC: 4031459. DOI: 10.1038/nature12886. View

Garcia-Cortes L . A novel recursive algorithm for the calculation of the detailed identity coefficients. Genet Sel Evol. 2015; 47:33. PMC: 4414392. DOI: 10.1186/s12711-015-0108-6. View

Thompson E . Two-locus and three-locus gene identity by descent in pedigrees. IMA J Math Appl Med Biol. 1988; 5(4):261-79. DOI: 10.1093/imammb/5.4.261. View

Kardos M, Akesson M, Fountain T, Flagstad O, Liberg O, Olason P . Genomic consequences of intensive inbreeding in an isolated wolf population. Nat Ecol Evol. 2017; 2(1):124-131. DOI: 10.1038/s41559-017-0375-4. View

10.

Thompson E . The gene identity states of a descendant. Theor Popul Biol. 1980; 18(1):76-93. DOI: 10.1016/0040-5809(80)90041-6. View

11.

Hossjer O . Modeling the effect of inbreeding among founders in linkage analysis. Theor Popul Biol. 2006; 70(2):146-63. DOI: 10.1016/j.tpb.2006.05.004. View

12.

Hill W, Weir B . Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genet Res (Camb). 2011; 93(1):47-64. PMC: 3070763. DOI: 10.1017/S0016672310000480. View

13.

Thompson E . A restriction on the space of genetic relationships. Ann Hum Genet. 1976; 40(2):201-4. DOI: 10.1111/j.1469-1809.1976.tb00181.x. View

14.

Kirkpatrick B, Ge S, Wang L . Efficient computation of the kinship coefficients. Bioinformatics. 2018; 35(6):1002-1008. DOI: 10.1093/bioinformatics/bty725. View

15.

Cheng E, Elliott B, Ozsoyoglu Z . Efficient computation of kinship and identity coefficients on large pedigrees. J Bioinform Comput Biol. 2009; 7(3):429-53. DOI: 10.1142/s0219720009004175. View

16.

Abney M . A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics. 2009; 25(12):1561-3. PMC: 2687941. DOI: 10.1093/bioinformatics/btp185. View

17.

Karigl G . A recursive algorithm for the calculation of identity coefficients. Ann Hum Genet. 1981; 45(3):299-305. DOI: 10.1111/j.1469-1809.1981.tb00341.x. View

18.

Kaplanis J, Gordon A, Shor T, Weissbrod O, Geiger D, Wahl M . Quantitative analysis of population-scale family trees with millions of relatives. Science. 2018; 360(6385):171-175. PMC: 6593158. DOI: 10.1126/science.aam9309. View

19.

Thompson E . Gene identities and multiple relationships. Biometrics. 1974; 30(4):667-80. View

20.

Thompson E . Identity by descent: variation in meiosis, across genomes, and in populations. Genetics. 2013; 194(2):301-26. PMC: 3664843. DOI: 10.1534/genetics.112.148825. View