Algorithms for Haplotype Block Partitioning By Michael Waterman, Ph.D. Professor of Biological Sciences, Computer Science and Mathematics University of Southern California Abstract A reference human genome sequence is known with good accuracy, and variation among individuals is now of great interest. In this lecture we develop dynamic programming algorithms for haplotype block partitioning to minimize the number of representative single nucleotide polymorphisms (SNPs) required to account for most of the haplotype quality in each block. The block quality is a function of the haplotypes defined by the SNPs in the block. Any measure of haplotype quality can be used in the algorithm and of course the measure should depend on the specific application. The dynamic programming algorithm is applied to analyze the haplotype data on chromosome 21 of Patil et al (Science, 294:1719-1723, 2001). Using the same criteria as in Patil et al., we are able to reduce the resources required to perform genome studies. PSCI, Room 208 Friday, February 6, 2004 4:00 PM OPEN TO THE PUBLIC Michael S. Waterman Page 1 of 2 Michael S. Waterman University Professor Professor of Mathematics Professor of Biological Sciences Professor of Computer Science University of Southern California MAIL: 1042W 36th Place, DRB 155, Los Angeles, California 90089-1113 PHONE: (213) 740-2408 FAX: (213) 740-2437 OFFICE: DRB 284 EMAIL: [email protected] Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after positions at Los Alamos National Laboratory and Idaho State University. His bachelors in Mathematics is from Oregon State University, and his PhD in Statistics and Probability is from Michigan State University. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Art and Sciences (1995), and was elected to the National Academy of Sciences (2001). Also he is a Fellow of the American Association for the Advancement of Science and Fellow of the Institute of Mathematical Statistics. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at University of Montreal. He is Professor-at-large at the Keck Graduate Institute of Life Sciences and in fall 2000 he became the first Fellow of Celera Genomics. In 2002 he received a Gairdner Foundation International Award Professor Waterman works in the area of Computational Biology, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA, and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a founding editor of Journal of Computational Biology, is on the editorial board of seven journals, and is author of the text Introduction to Computational Biology: Maps, Sequences and Genomes. http://www-hto.usc.edu/people/Waterman.html 1/23/2004 Michael S. Waterman Page 2 of 2 Books Research Reports & Papers Selected New CEG Selected Papers Conference Online Pictures Mexico Photograhphs Proceedings Essays USC Computational Biology Home Page http://www-hto.usc.edu/people/Waterman.html, [email protected], 4th December 2000 http://www-hto.usc.edu/people/Waterman.html 1/23/2004.