Visualization of Results from Genomic Predictions
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This document discusses the visualization of results from genomic predictions. It notes that genomic evaluation produces large amounts of numerical data that can be difficult to compare and interpret. The author advocates using graphical methods like small multiples, sparklines, and pseudocolor plots to complement numerical techniques and provide greater insight into genomic data. Several examples of different visualization techniques applied to genomic prediction results are presented. Acknowledgments are provided for organizations that contributed genotyping data and computing resources.
Visualization of Results from Genomic Predictions
- 1. John B. ColeJohn B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 john.cole@ars.usda.gov Visualization of Results from Genomic Predictions
- 2. ADSA, July 2009 (2) Cole Introduction • Genomic evaluation produces lots of numbers • Holsteins: 38K SNP × 31 traits • Data are difficult to compare • Levels of detail are obscured • Results cannot easily be tabulated
- 3. ADSA, July 2009 (3) Cole Visualization • “Graphical methods can retain the information in the data.” ― Deming • Complements numerical techniques • Tukey (1977), Tufte (1983, 1990, 1997, 2006) , Cleveland (1985, 1993) • Some work by animal breeders • Huang and Shanks (1995), Kachman (2004), VanRaden and Tooker (2007), Schlesser et al. (2009)
- 4. ADSA, July 2009 (4) Cole Marker Effects ― Small Multiples
- 5. ADSA, July 2009 (5) Cole Marker Effects ― Detail
- 6. ADSA, July 2009 (6) Cole Marker Effects ― NCBI Mashup
- 7. ADSA, July 2009 (7) Cole Net Merit by Chromosome Freddie (1HO08784)Freddie (1HO08784) - highest Net Merit bull- highest Net Merit bull
- 8. ADSA, July 2009 (8) Cole Chromosomal EBV Sparklines
- 9. ADSA, July 2009 (9) Cole Text with Chromosomal EBV Sparklines “For example, cows with positive CEBV for chromosomes 13, 14, 16, 17, 19, or 20 might be selected for breeding to the bull O-Bee Manfred Justice-ET (7HO6417; Figure 5).” (Cole et al. 2009. J. Dairy Sci. 92(6):2931―2946.)
- 10. ADSA, July 2009 (10) Cole Text with Genetic Trend Figure “The incidence of SB increased from 11.2% in 1980 to 12.0% in 2004 for heifers, and decreased from 5.8% in 1980 to 5.6% in 2005 for multiparous cows.” (Cole et al. 2007. J. Dairy Sci. 90(5):2480―2488.)
- 11. ADSA, July 2009 (11) Cole Text with Genetic Trend Sparklines “The incidence of SB increased from 11.16% in 1980 to 11.08% in 2005 for heifers, and decreased from 5.29% in 1980 to 4.83% in 2005 for multiparous cows.” (Cole et al. 2007. J. Dairy Sci. 90(5):2480―2488.)
- 12. ADSA, July 2009 (12) Cole Location of Autosomal Recessives
- 13. ADSA, July 2009 (13) Cole Genotype Parents and Grandparents Manfred O-Man Jezebel O-Style Teamster Deva Dima
- 14. ADSA, July 2009 (14) Cole Expected Relationship Matrix1 PGS PGD MGS MGD Sire Dam Bull Manfred 1.0 .0 .0 .0 .5 .0 .25 Jezebel .0 1.0 .0 .0 .5 .0 .25 Teamster .0 .0 1.0 . 0 .0 .5 .25 Dima .0 .0 .0 1.0 .0 .5 .25 O-Man .5 .5 .0 .0 1.0 .0 .5 Deva .0 .0 .5 .5 .0 1.0 .5 O-Style .25 .25 .25 .25 .5 .5 1.0 1 Calculated assuming that all grandparents are unrelated 1HO9167 O-Style1HO9167 O-Style
- 15. ADSA, July 2009 (15) Cole Pedigree Relationship Matrix PGS PGD MGS MGD Sire Dam Bull Manfred 1.053 .090 .090 .105 .571 .098 .334 Jezebel .090 1.037 .051 .099 .563 .075 .319 Teamster .090 .051 1.035 .120 .071 .578 .324 Dima .105 .099 .120 1.042 .102 .581 .342 O-Man .571 .563 .071 .102 1.04 5 .086 .566 Deva .098 .075 .578 .581 .086 1.060 .573 O-Style .334 .319 .324 .342 .566 .573 1.043 1HO9167 O-Style1HO9167 O-Style
- 16. ADSA, July 2009 (16) Cole Genomic Relationship Matrix PGS PGD MGS MGD Sire Dam Bull Manfred 1.201 .058 .050 .093 .609 .054 .344 Jezebel .058 1.131 .008 .135 .618 .079 .357 Teamster .050 .008 1.110 .100 .014 .613 .292 Dima .093 .135 .100 1.139 .131 .610 .401 O-Man .609 .618 .014 .131 1.16 6 .080 .626 Deva .054 .079 .613 .610 .080 1.148 .613 O-Style .344 .357 .292 .401 .626 .613 1.157 1HO9167 O-Style1HO9167 O-Style
- 17. ADSA, July 2009 (17) Cole Difference (Genomic – Pedigree) PGS PGD MGS MGD Sire Dam Bull Manfred .149 -.032 -.040 -.012 .038 -.043 .010 Jezebel -.032 .095 -.043 .036 .055 .004 .038 Teamster -.040 -.043 .075 -.021 -.057 .035 -.032 Dima -.012 .036 -.021 .097 .029 .029 .059 O-Man .038 .055 -.057 .029 .121 -.006 .060 Deva -.043 .004 .035 .029 -.006 .087 .040 O-Style .010 .038 -.032 .059 .060 .040 .114 1HO9167 O-Style1HO9167 O-Style
- 18. ADSA, July 2009 (18) Cole Pseudocolor Plots ― O-Style
- 19. ADSA, July 2009 (19) Cole Pseudocolor Plot ― Simulated Pedigree
- 20. ADSA, July 2009 (20) Cole Pseudocolor Plot ― Interbreed Relationships
- 21. ADSA, July 2009 (21) Cole Closing Thoughts • Substance over style • The goal is greater insight • Better tools are needed • Scripting is essential • Color is still difficult • Print versus electronic publication • We need to share ideas • Not all ideas will be good ones
- 22. ADSA, July 2009 (22) Cole Acknowledgments • Genotyping and DNA extraction: • BFGL, U. Missouri, U. Alberta, GeneSeek, Genetics & IVF Institute, Genetic Visions, and Illumina • Computing: • AIPL staff (Leigh Walton, Jay Megonigal) • Funding: • NRI grants 2006-35205-16888 and 2006- 35205-16701 • Agriculture Research Service • Holstein, Jersey and Brown Swiss breed associations • Cooperative Dairy DNA Repository (CDDR)
- 23. ADSA, July 2009 (23) Cole CDDR Contributors • National Association of Animal Breeders (Columbia, MO) • ABS Global (DeForest, WI) • Accelerated Genetics (Baraboo, WI) • Alta (Balzac, AB, Canada) • Genex (Shawano, WI) • New Generation Genetics (Fort Atkinson, WI) • Select Sires (Plain City, OH) • Semex Alliance (Guelph, ON, Canada) • Taurus-Service (Mehoopany, PA)
Editor's Notes
- #14: We are all familiar with a traditional pedigree chart. Animal is expected to be an average of his parents.