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Visualization of Results from Genomic Predictions

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Presentation on theme: "Visualization of Results from Genomic Predictions"— Presentation transcript:

1 Visualization of Results from Genomic Predictions

2 Genomic evaluation produces lots of numbers
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 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 Marker Effects ― Small Multiples

5 Marker Effects ― Detail

6 Marker Effects ― NCBI Mashup

7 Net Merit by Chromosome
Freddie (1HO08784) - highest Net Merit bull

8 Chromosomal EBV Sparklines

9 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 J. Dairy Sci. 92(6):2931―2946.)

10 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 J. Dairy Sci. 90(5):2480―2488.)

11 Text with Genetic Trend Sparklines
“The incidence of SB increased from 11.16% in to 11.08% in 2005 for heifers, and decreased from 5.29% in to 4.83% in 2005 for multiparous cows.” (Cole et al J. Dairy Sci. 90(5):2480―2488.)

12 Location of Autosomal Recessives

13 Genotype Parents and Grandparents
Manfred O-Man Jezebel O-Style Teamster Deva Dima We are all familiar with a traditional pedigree chart. Animal is expected to be an average of his parents.

14 Expected Relationship Matrix1
1HO9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1.0 .0 .5 .25 Jezebel Teamster . 0 Dima O-Man Deva O-Style 1Calculated assuming that all grandparents are unrelated

15 Pedigree Relationship Matrix
1HO9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1.053 .090 .105 .571 .098 .334 Jezebel 1.037 .051 .099 .563 .075 .319 Teamster 1.035 .120 .071 .578 .324 Dima 1.042 .102 .581 .342 O-Man 1.045 .086 .566 Deva 1.060 .573 O-Style 1.043

16 Genomic Relationship Matrix
1HO9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred 1.201 .058 .050 .093 .609 .054 .344 Jezebel 1.131 .008 .135 .618 .079 .357 Teamster 1.110 .100 .014 .613 .292 Dima 1.139 .131 .610 .401 O-Man 1.166 .080 .626 Deva 1.148 O-Style 1.157

17 Difference (Genomic – Pedigree)
1HO9167 O-Style PGS PGD MGS MGD Sire Dam Bull Manfred .149 -.032 -.040 -.012 .038 -.043 .010 Jezebel .095 .036 .055 .004 Teamster .075 -.021 -.057 .035 Dima .097 .029 .059 O-Man .121 -.006 .060 Deva .087 .040 O-Style .114

18 Pseudocolor Plots ― O-Style

19 Pseudocolor Plot ― Simulated Pedigree

20 Pseudocolor Plot ― Interbreed Relationships

21 Closing Thoughts Substance over style Better tools are needed
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 Acknowledgments Genotyping and DNA extraction: Computing: Funding:
BFGL, U. Missouri, U. Alberta, GeneSeek, Genetics & IVF Institute, Genetic Visions, and Illumina Computing: AIPL staff (Leigh Walton, Jay Megonigal) Funding: NRI grants and Agriculture Research Service Holstein, Jersey and Brown Swiss breed associations Cooperative Dairy DNA Repository (CDDR)

23 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)

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