Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques

Constraints

Volumn 13, Issue 1-2, 2008, Pages 130-154

  Sanchez, Marti ^a   De Givry, Simon ^a   Schiex, Thomas ^a  

^a CEMAGREF   (France)

Author keywords

Complex pedigrees; Genetics; Mendelian genotyping error detection; Weighted constraint satisfaction

Indexed keywords

ERROR CORRECTION; ERROR DETECTION; LARGE SCALE SYSTEMS; OPTIMIZATION; PROBLEM SOLVING;

GENOTYPING ERRORS; WEIGHTED CONSTRAINT NETWORK (WCN);

CONSTRAINT THEORY;

EID: 42749097983     PISSN: 13837133     EISSN: 15729354     Source Type: Journal    
DOI: 10.1007/s10601-007-9029-5     Document Type: Article

References (30)

1. Aceto, L., Hansen, J. A., Ingólfsdóttir, A., Johnsen, J., & Knudsen, J. (2004). The complexity of checking consistency of pedigree information and related problems. Journal of Computer Science Technology, 19(1), 42-59.
2. Bennewitz, J., Reinsch, N., & Kalm, E. (2002). GENCHECK: A program for consistency checking and derivation of genotypes at co-dominant and dominant loci. Journal of Animal Breeding and Genetics, 119(5), 350-360.
3. Bistarelli, S., Fargier, H., Montanari, U., Rossi, F., Schiex, T., & Verfaillie, G. (1999). Semiring-based CSPs and valued CSPs: Frameworks, properties and comparison. Constraints, 4, 199-240.
4. Cooper, M. (2005). High-order consistency in valued constraint satisfaction. Constraints, 10(3), 283-305.
5. Cooper, M. (2003). Reduction operations in fuzzy or valued constraint satisfaction. Fuzzy Sets and Systems, 134(3), 311-342.
6. Cooper, M., de Givry, S., & Schiex, T. (2007). Optimal soft arc consistency. In Proc. of IJCAI-2007 (pp. 68-73). Hyderabad, India.
7. Dechter, R. (2003). Constraint processing. Morgan Kaufmann Publishers.
8. Eén, N., & Sörensson, N. (2006). Translating Pseudo-Boolean constraints into SAT. Journal on Satisfiability, Boolean Modeling and Computation, 2, 61-96.
9. Ehm, M. G., Cottingham Jr., R. W., & Kimmel, M. (1996). Error detection in genetic linkage data using likelihood based methods. American Journal of Human Genetics, 58(1), 225-234.
10. Fishelson, M., Dovgolevsky, N., & Geiger, D. (2005). Maximum likelihood haplotyping for general pedigrees. Human Heredity, 59, 41-60.
11. de Givry, S., Larrosa, J., Meseguer, P., & Schiex, T. (2003). Solving Max-SAT as weighted CSP. In Proc. of CP-2003 (pp. 363-376). Cork, Ireland.
12. de Givry, S., Schiex, T., & Verfaillie, G. (2006). Exploiting tree decomposition and soft local consistency in weighted CSP. In Proc. of AAAI-2006. Boston, MA.
13. Larrosa, J. (2002). On arc and node consistency in weighted CSP. In Proc. of AAAI-2002 (pp. 48-53). Edmondton.
14. Larrosa, J., & Dechter, R. (2000). On the dual representation of non-binary semiring-based CSPs. In CP'2000 workshop on soft constraints. Singapore.
15. Larrosa, J., de Givry, S., Heras, F., & Zytnicki, M. (2005). Existential arc consistency: Getting closer to full arc consistency in weighted CSPs. In Proc. of IJCAI-2005 (pp. 84-89). Edinburgh, Scotland.
16. Larrosa, J., Morancho, E., & Niso, D. (2005). On the practical applicability of Bucket elimination: Still-life as a case study. Journal of Artificial Intelligence Research, 23, 421-440.
17. Larrosa, J., & Schiex, T. (2003). In the quest of the best form of local consistency for weighted CSP. In Proc. of IJCAI-2003 (pp. 239-244). Acapulco, Mexico.
18. Lecoutre, C., Sais, L., Tabary, S., & Vidal, V. (2006). Last conflict based reasoning. In Proc. of ECAI-2006 (pp. 133-137). Trento, Italy.
19. Lynce, I., & Marques Silva, J. P. (2006). Efficient haplotype inference with Boolean satisfiability. In Proc. of AAAI-2006. Boston, MA.
20. Marinescu, R., & Dechter, R. (2006). Memory intensive branch-and-bound search for graphical models. In Proc. of AAAI-2006. Boston, MA.
21. Mengshoel, O., Roth, D., & Wilkins, D. (2006). Controlled generation of hard and easy Bayesian networks: Impact on maximal clique size in tree clustering. Artificial Intelligence, 170(16-17), 1137-1174.
22. O'Connell, J. R., & Weeks, D. E. (1998). PedCheck: A program for identification of genotype incompatibilities in linkage analysis. American Journal of Human Genetics, 63(1), 259-266.
23. O'Connell, J. R., & Weeks, D. E. (1999). An optimal algorithm for automatic genotype elimination. American Journal of Human Genetics, 65(6), 1733-1740.
24. Park, J. D., & Darwiche, A. (2004). Complexity results and approximation strategies for MAP explanations. Journal of Artificial Intelligence Research, 21, 101-133.
25. Saito, M., Saito, A., & Kamatani, N. (2002). Web-based detection of genotype errors in pedigree data. Journal of Human Genetics, 47(7), 377-379.
26. Schiex, T. (2000). Arc consistency for soft constraints. In Proc. of CP-2000 (pp. 411-424). Singapore.
27. Sheini, H., & Sakallah, K. (2006). Pueblo: A hybrid Pseudo-Boolean SAT solver. Journal on Satisfiability, Boolean Modeling and Computation, 2, 61-96.
28. Thomas, A. (2005). GMCheck: Bayesian error checking for pedigree genotypes and phenotypes. Bioinformatics, 21(14), 3187-3188.
29. Vitezica, Z., Elsen, J.-M., Rupp, R., & Díaz, C. (2005). Using genotype probabilities in survival analysis: A scrapie case. Genetics Selection Evolution, 37(4), 403-415.
30. Vitezica, Z., Mongeau, M., Manfredi, E., & Elsen, J.-M. (2004). Selecting loop breakers in general pedigrees. Human Heredity, 57, 1-9.