EFFICIENT INFERENCE OF HAPLOTYPES FROM GENOTYPES ON A PEDIGREE

39108021 陳政儀

Author ： Jing Li, Tao Jiang

Source ： Journal of Bioinformatics and Computational Biology, Vol. 1, No. 1 (2003) 41-69 (PDF)

Abstract ：

The trend of genetic variation and haplotype map project are：1. discovery and typing of SNPs﹐
2. development of high-resolution maps of genetic variation and haplotypes for human. Using rule-based haplotype reconstruction methods on pedigree is faster than statistical methods. Based on the minimum recombination principle, we use an efficient iterative (heuristic) algorithm (called block-extension) for Minimum-Recombination Haplotype Configuration (MRHC) problem and also consider the special case of haplotype reconstruction where no recombinants are assumed. Our algorithm first identifies all necessary constraints and then solves the equations using a simple method based on Gaussian elimination. Test results of simulated data and real data show that rule-based haplotyping methods could be useful for large scale haplotyping projects on pedigree data.

Reference ：

1. D. Qian and L. Beckmann, Minimum-recombinant haplotyping in pedigrees Am. J. Hum. Genet. 70(6), 1434{1445 (2002).

2. M. J. Daly, J. D. Rioux, S. F. Schaner, T. J. Hudson and E. S. Lander, High - resolution haplotype structure in the human genome Nature Genetics 29(2), 229 - 232(2001).

3. S. B. Gabriel, S. F. Schaner, H. Nguyen, J. M. Moore, J. Roy, B. Blumenstiel, J. Higgins, M. DeFelice, A. Lochner, M. Faggart, S. N. Liu-Cordero, C. Rotimi, A. Adeyemo, R. Cooper, R. Ward, E. S. Lander, M. J. Daly and D. Altshuler The structure of haplotype blocks in the human genome Science 296(5576), 2225 – 2229 (2002).

Author homepage ：

Jing Li http://www.cs.ucr.edu/~jili/

Tao Jiang http://www.cs.ucr.edu/~jiang/