Avoiding Recomputation in Linkage Analysis

• Published in: Human heredity 1994-07, Vol.44 (4), p.225-237
• Main Authors: Schäffer, Alejandro A., Gupta, Sandeep K., Shriram, K., Cottingham, Robert W.
• Format: Article
• Language: English
• Subjects: Algorithms; Automatic Data Processing - instrumentation; Automatic Data Processing - statistics & numerical data; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Fundamental and applied biological sciences. Psychology; Genetic Linkage - genetics; Genetics of eukaryotes. Biological and molecular evolution; Genotype; Humans; Methods, theories and miscellaneous; Original Paper; Pedigree; Recombination, Genetic; Software
• ISSN: 0001-5652; 1423-0062
• DOI: 10.1159/000154222

We describe four improvements we have implemented in a version of the genetic linkage analysis programs in the LINKAGE package: subdivision of recombination classes, better handling of loops, better coordination between the optimization and output routines, and a checkpointing facility. The unifying theme for all the improvements is to store a small amount of data to avoid expensive recomputation of known results. The subdivision of recombination classes improves on a method of Lathrop and Lalouel [Am J Hum Genet 1988;42:498-505]. The new method of handling loops extends a proposal of Lange and Elston [Hum Hered 1975;25:95-105] for loopless pedigrees with multiple nuclear families at the earliest generation. From a practical point of view, the most important improvement may be the checkpointing facility which allows the user to carry out linkage computations that are much longer than the meantime-to-failure of the underlying computer.