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Commercial Genetic Test Validation

IGENITY Carcass Composition and Average Daily Gain:

Summary:

The IGENITY profile was found to be significantly associated with marbling score, back fat thickness, quality grade, ribeye area, and yield grade carcass traits and average daily gain in a commercial predominately Bos taurus sample population of 1364 animals.  This test was not evaluated on a Bos indicus-influenced or purebred Bos indicus population.

Significance* of the Igenity Molecular Breeding Values for Carcass Traits and Average Daily Gain

Breed	TRAIT	Panel	b**	F	p	N
Commercial Validation population	USDA Marbling Score	MBS	0.76	28.6	0.0000001	1354
	Backfat Thickness	BFAT	0.81	12.46	0.0002	1354
	Quality Grade[1] (% ≥ Choice)	% ≥ CHOICE	0.73	14.06	0.00009	1364
	Ribeye Area	REA	1.01	10.99	0.0005	1354
	Yield Grade	YG	1.16	21.98	0.000002	1354
	Average Daily Gain	ADG	0.61	14.69	0.00007	1364

* Molecular breeding values (MBVs) for each trait were provided by Igenity based on the various SNP panels for each trait.

**The column labeled ‘b’ is the regression of phenotypes in the test population on the MBVs reported for the DNA test. It is a measure of how well the MBV scales with the phenotype. There are many reasons that this value would differ from its nominally expected value of 1. Traits scale differently in different environments, management scenarios and methods of measurement. Therefore, we would not practically expect this value to be exactly 1. However, values substantially less than 1 suggest that differences in phenotypes observed in other cattle managed under conditions representative of U.S. beef production are likely to be less than those predicted by the MBV. This would not affect how animals would be ranked by the MBV, but would impact the weighting given to differences in MBVs relative to differences in EPDs based on phenotypic data.

1 Quality Grade was analyzed as an “all or none” trait (each animal was either USDA Choice or better, or it was not). Such traits have the property that the size of the effect is quite dependent on the population mean. This does not reduce the ability of the test to rank animals correctly, but it does complicate the interpretation of the effect sizes. The size of effect is greatest in populations that grade approximately 50% Choice or better, but can be much lower in populations with either a high or low proportion of animals that grade Choice or better.

Test Claims:

The IGENITY® profile includes panels of DNA markers significantly associated with marbling score, quality grade (% grading USDA Choice or higher), yield grade, back fat thickness, ribeye area, and average daily gain.

Test Details:

IGENITY reports an MBV (Molecular Breeding Value) which is converted to a score (1-10) for each trait derived from analysis of an undisclosed number of SNP markers per trait.

Sample Populations:

1,364 records of purebred and crossbred offspring of 285 sires from 7 states fed in 7 different Midwestern feed yards and harvested at a single Midwestern packing plant. The sires included the following breeds: 202 Angus, 7 Red Angus, 6 Charolais, 7 Gelbveh , 4 Horned Hereford , 11 Polled Hereford, 4 Limousin , 7 Simmental, 1 Braford, 3 Shorthorn, 12 were of mixed breed, and 21 were of unknown breed. Cows were: 360 Angus, 6 Red Angus, 11 Charolais, 2 Horned Hereford , 5 Polled Hereford, 2 Limousin, 9 Simmental, 15 Shorthorn, 598 were crossbred cows, and 356 were of unknown breed composition.

Quantiles for Molecular Breeding Values*:

Breed	TRAIT	Panel	Mean	Max	Min	Median  (Q2)	25% (Q1)	75% (Q3)
Commercial Validation Population	USDA Marbling Score	MBS	44.201	88.977	-12.91	44.37	34.224	54.292
	Backfat Thickness	BFAT	-0.011	0.035	-0.062	-0.011	-0.021	-0.001
	Quality Grade (% ≥ Choice)	% CHOICE	0.038	0.241	-0.213	0.041	-0.009	0.087
	Ribeye Area	REA	-0.413	0.052	-0.74	-0.416	-0.485	-0.344
	Yield Grade	YG	0.131	0.299	-0.118	0.131	0.090	0.174
	Average Daily Gain	ADG	0.440	0.669	0.066	0.450	0.377	0.515

*Molecular breeding values (MBVs) were provided by Igenity based on the various SNP panels for each trait. These were the MBV distibutions in the data analyzed and are not necessarily reflective of those of any other population.

Significance* of the Igenity Molecular Breeding Values for Carcass Traits and Average Daily Gain:

Breed	TRAIT	Panel	b**	F	p	N
Commercial Validation population	USDA Marbling Score	MBS	0.76	28.6	0.0000001	1354
	Back Fat Thickness	BFAT	0.81	12.46	0.0002	1354
	Quality Grade[1]      (% ≥ Choice)	% ≥ CHOICE	0.73	14.06	0.00009	1364
	Ribeye Area	REA	1.01	10.99	0.0005	1354
	Yield Grade	YG	1.16	21.98	0.000002	1354
	Average Daily Gain	ADG	0.61	14.69	0.00007	1364

* Molecular breeding values (MBVs) for each trait were provided by Igenity based on the various SNP panels for each trait. The F test was based on a model including fixed contemporary group and breed of sire, random sire, and regressions of days on feed and of the Igenity score for the trait in question (December 2008).

**The column labeled ‘b’ is the regression of phenotypes in the test population on the MBVs reported for the DNA test. It is a measure of how well the MBV scales with the phenotype. There are many reasons that this value would differ from its nominally expected value of 1. Traits scale differently in different environments, management scenarios and methods of measurement. Therefore, we would not practically expect this value to be exactly 1. However, values substantially less than 1 suggest that differences in phenotypes observed in other cattle managed under conditions representative of U.S. beef production are likely to be less than those predicted by the MBV. This would not affect how animals would be ranked by the MBV, but would impact the weighting given to differences in MBVs relative to differences in EPDs based on phenotypic data.

1 Quality Grade was analyzed as an “all or none” trait (each animal was either USDA Choice or better, or it was not). Such traits have the property that the size of the effect is quite dependent on the population mean. This does not reduce the ability of the test to rank animals correctly, but it does complicate the interpretation of the effect sizes. The size of effect is greatest in populations that grade approximately 50% Choice or better, but can be much lower in populations with either a high or low proportion of animals that grade Choice or better. As an example, consider a test scaled such that its effects are relevant to a population grading 50% Choice: then an animal with an MBV 25% above the population average would have a probability of grading at least Choice of 75%. However, if the population average was 80% Choice or better, an animal could still have an MBV 25% above average, but it obviously could not have a probability of 105% of grading at least Choice; the probability would have to be less than 100%. Therefore, the same DNA test result that is interpreted to be 25% above an average of 50% Choice or better should be interpreted to have a substantially smaller numerical effect in a pen that grades 80% Choice or better. The same would also be true in a pen that graded 20% Choice.

• Commercial Tests
• All Tests:
• – Pfizer
• – IGENITY
• – MMI
• – Ancillary Results
• Sample Populations