PPT-What Have We Learned? Using all associated or even all genotyped SNPs explains much more

Rare variants have larger effects but collectively contribute small amount h2 Few examples of dominance variance 13 Much genetic variance captured by arrays Few interactions currently seen are with very large effect loci like MHC. Gil . McVean. The real heroes. PanMap. – Genome sequencing of 10 Western Chimpanzees. Patterns of small insertion and deletion . are quite . different and reveal details of DNA repair pathways. Patterns of recombination in humans and chimpanzees are highly diverged at the fine-scale, but largely conserved at broad scales. Copy Number Variations. and SNP Array. Xiaole Shirley Liu. and . Jun Liu. 2. Outline. Definition and motivation. SNP distribution and characteristics. Allele frequency, LD, population stratification. Gil McVean. Department of Statistics, Oxford. What is the 1000 Genomes Project?. A catalogue of . all. types of genetic . variation, including . rare. variants (c. 1% frequency) obtained by sequencing . Arthur M. . Lesk. Bologna Winter School 2011. 1. What are SNPs and why are they important?. SNP = Single nucleotide polymorphism, an . isolated. change in a single nucleotide. SNPs are one type of mutation . Kun Huang. Department of Biomedical Informatics. OSUCCC Biomedical Informatics Shared Resource. The Ohio State University. 2011. Outline . Introduction. Genetic variations. Technologies. Array-based technology. :. Using Genetic Clues to Personalize Nutrition. . . Janet Zarowitz, MS, RD, CDN. NYSAND Annual Meeting & Expo. May 21. , . 2016. Nutrigenomics!. The study of the effects of foods and food constituents on gene expression. Comm. 301. Reasons for changes in SNP set. History. Single list created across breeds. Poor performing SNPs removed. SNP selection criteria changed. Updated assembly changed SNP locations. Additional QTLs as . March 2012 AIPL Update Topics Genomics overview April 2012 changes Accounting for bias Selection index adjustments Cow adjustments Calving traits update Whole-genome selection Use many markers to track inheritance of chromosomal segments George Wiggans, CDCB Technical Advisor. Highlights of U.S. system. Over half a million animals genotyped in 2016. 67% of AI breedings to genomic bulls. Genomic relationship between genotyped cows and marketed bulls available. Fatchiyah.lecture.ub.ac.id. Why do we care about genetic variations?. 3.. Genetic variations reveal clues of ancestral human migration history. . 2.. Genetic variations determine our predisposition to complex diseases and responses to drugs and environmental factors. A molecule consisting of two strands that wrap around each other to form a “twisted ladder” shape, with the sides made of sugar and phosphate, with rungs made of nitrogen-containing chemicals called bases. Linkage disequilibrium (LD). Definition of linkage disequilibrium. Importance of disequilibrium . Measures of disequilibrium. SNP selection. Public resources. Tag SNP selection programs. Imputation. Definitions. McDonald-. Kreitman. Test. Changes in Protein Coding Sequence. 11-14-2017. Review of Tajima’s D. Skews in the Allele Frequency Spectrum. Solutions to Last Week’s Exercises. McDonald-. Kreitman. Test. . Dan Schaid. Curtis L. Carlson Professor of Genomics Research. Mayo Clinic. Email: schaid@mayo.edu. Polygenic Risk Score (PRS). PRS = Many Gene Score. Weighted. sum of genotypes across . genetic markers (SNPs) .