Abstract
In this paper we provide a mathematical model that describes genetic inheritance. In terms of our framework, we describe two commonly used algorithms that calculate the set of founder allele assignment that are compatible with some genotype information and a given inheritance pattern. These calculations cater for the first step in the multi point linkage analysis. The first algorithm we investigate is a part of the Genhunter software package developed at the Whitehead Institute at MIT and is developed by Kruglyak et al [8]; the second one occurs in the software package Allegro provided by Gudbjartsson et al [5] at DeCode Genetics in Reykjavik. We also state and prove formally the correctness of these algorithms.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abecasis, G.R., Cherny, S.S., Cookson, W.O., Cardon, L.R.: Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics 30, 97–101 (2001)
Aceto, L., Hansen, J.A., Ingólfsdóttir, A., Johnsen, J., Knudsen, J.: Checking consistency of pedigree information is NP-complete (Preliminary report) BRICS Report Series RS-02-42 (October 2002), Available at http://www.brics.dk/RS/02/42/
Elston, R.C., Stewart, J.: A general model for the genetic analysis of pedigree data. Hum Hered 21, 523–542 (1971)
Gudbjartsson, D.F., Gunnarsson, G., Ingólfsdóttir, A., Stefansson, S., Thorvaldsson, T.: BDDbased algorithms in genetic linkage analysis. BRICS Report Series RS-03-??, Available at http://www.brics.dk/RS/03
Gudbjartsson, D.F., Jonasson, K., Frigge, M., Kong, A.: Allegro, a new computer program for multipoint linkage analysis. Nature Genetics 25, 12–13 (2000)
Jorde, L.B., Carey, J.C., Bamshad, M.J., White, R.L.: MedicalGenetics. Mosby (1999)
Klug, W.S., Cummings, M.R.: Concepts of genetics, 5th edn. Prentice-Hall, Englewood Cliffs (1997)
Kruglyak, L., Daly, M.J., Reeve-Daly, M.P., Lander, E.S.: Parametric and nonparametric linkage analysis: A unified multipoint approach. Am. J. Hum. Genet. 58, 1347–1363 (1996)
Kruglyak, L., Lander, E.S.: Faster multipoint linkage analysis using fourier transforms. Journal of Computational Biology 5(1), 7 (1998)
Markianos, K., Daly, M.J., Kruglyak, L.: Efficient multipoint linkage analysis through reduction of inheritance space. American journal of human genetics 68, 963–977 (2001)
Lange, K.: Mathematical and statistical methods for genetic analysis. Springer, Heidelberg (1997)
Lander, E.S., Green, P.: Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. 84, 2363–2367 (1987)
Ott, J.: Analysis of human genetic linkage,third edition. The Johns Hopkins University Press (1999)
O’Connell, J.R.: Rapid multipoint linkage analysis via inheritance vectors in the Elston-Stewart algorithm. Hum Hered 51, 226–240 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Gudbjartsson, D., Hansen, J.A., Ingólfsdóttir, A., Johnsen, J., Knudsen, J. (2003). Single Point Algorithms in Genetic Linkage Analysis. In: Moreno-Díaz, R., Pichler, F. (eds) Computer Aided Systems Theory - EUROCAST 2003. EUROCAST 2003. Lecture Notes in Computer Science, vol 2809. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45210-2_34
Download citation
DOI: https://doi.org/10.1007/978-3-540-45210-2_34
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20221-9
Online ISBN: 978-3-540-45210-2
eBook Packages: Springer Book Archive