CDCB Quick Turnaround genomic predictions service¶

• Table of contents
• CDCB Quick Turnaround genomic predictions service
  • Introduction
    • Key Characteristics
  • Policy document
  • End User Agreement
  • Application process
  • Technical information
    • SNP array requirement
    • Input file
    • Output file
    • Limitations
    • Available traits

Introduction¶

The Council on Dairy Cattle Breeding offers a Quick Turnaround (QTurn) genomic predictions service to Approved CDCB Genomic Nominators. QTurn provides a rapid snapshot of an animal’s genetic merit using genomic information. QTurn predictions may include up to 15 traits, selected by the genomic nominator offering the service. Certified nominators may develop customized quick turnaround predictions based on the specific SNP arrays they choose to support. The subsequent results are one-time estimates and are not updated after they are generated. Results are typically returned almost immediately, but always within 48 hours. QTurn is designed as a rapid prediction tool, not as a substitute for official genomic evaluations.

QTurn genotypes and resulting predictions do not enter the National Cooperator Database. Results are delivered only to the genomic nominator requesting the service.

For the most accurate and complete genomic evaluations, CDCB recommends using the genomic nomination service marked with the Powered by CDCB logo, which follows the full CDCB evaluation pipeline.

Key Characteristics¶

• One-time estimates that are not updated
• Fast turnaround (typically within the hour, certainly less than 48 hours)
• No pedigree information used (parentage verification is a separate service (CDCB Quick Discovery of close relatives service)
• No genotype imputation or haplotype construction
• Breed code provided with the genotype is used to select the appropriate SNP set and express DGV on the corresponding breed scale
• Minimum input quality control, including only gender checks (males are excluded).
• No breed verification checks

Policy document¶

Quick Turnaround Genomic Predictions Policy

End User Agreement¶

Quick Turn Around End User Agreement

Application process¶

Please open a Redmine ticket to initiate the process. Customer service will guide you through the process.

Technical information¶

SNP array requirement¶

For best performance, CDCB strongly recommends using SNP arrays containing at least 30,000 SNPs.

Input file¶

Genotypes are required in FinalReport.zip format, and must be placed in the designated QTurn in folder for the requesting genomic nominator.
Placing files in this folder constitutes an implicit request for the service and acceptance of the associated fees.

Output file¶

The output file [prefix]_QTurn.zip will be placed in the designated QTurn out folder for the requesting genomic nominator.

Limitations¶

QTurn is a simplified and rapid prediction service and therefore does not include many components of the full CDCB genomic evaluation process.

Important limitations include:

• Only female genotypes are processed
• No parentage verification or parentage discovery
• No recessive haplotype detection
• No Breed Base Representation (BBR) estimates
• No genotype imputation
• No pedigree-based information incorporated into the evaluation

Because of these limitations, QTurn results should be interpreted as preliminary genomic predictions and not as official CDCB genomic evaluations.

Available traits¶

Deliverables may include no more than 15 traits, selected from the following:

Group	Trait number	Trait
Production	1	Milk yield
	2	Fat Yield
	3	Protein Yield
	4	Fat Percentage
	5	Protein Percentage
Longevity	6	Productive Life
	7	Livability
Health	8	Somatic Cell Score
Fertility	9	Heifer Conception Rate
	10	Cow Conception Rate
	11	Daughter Pregnancy Rate
	12	Early First Calving
Calving	13	Daughter Calving Ease
	14	Daughter Stillbirth
Conformation	15	Final Score
	16	Dairy Form
	17	Udder Composite
	18	Feet/Legs Composite
	19	Body Size Composite
Selection Indices	20	Net Merit (NM$)
	21	Fluid Merit (FM$)
	22	Cheese Merit (CM$)