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QC Metrics for submitted genotypes

The performance metrics is CDCB quality control standard that CDCB expects nominators to satisfy. Certification status can be promoted/demoted from current status based on performance review that is done periodically. In order for genotyping labs to check their performance, a lab report card that includes statistics of the lab performance is generated for labs every month.
Following list shows thresholds to determine if your submission succeed/failed for each metric.

  • Submissions with fewer than 10 animal genotypes
    • Metric classification class: Critical
    • Threshold: 10%
    • Expression: Percentage over total number of SUBMISSIONS
    • Explanation: Submissions of a low number of animals require the same processing setup time, therefore increase the inefficiency of the system. Although allowed because of specific conditions and corrections required, submissions of batches with a low number of animals is strongly discouraged.
  • Submissions failing on SNP call rate.
    • Metric classification class: Critical
    • Threshold: 50%
    • Expression: Percentage over total number of SUBMISSIONS
    • Explanation: Such submissions fail when at least 10% of the SNPs have call rates lower than 90%. Although a number of submissions having these low-call SNPs are accepted, we discourage these files being sent routinely without filtering for a large number of SNPs with low call rate.
  • Submissions failing on SNP parent-progeny conflicts
    • Metric classification class: Critical
    • Threshold: 25%
    • Expression: Percentage over total number of SUBMISSIONS
    • Explanation: This metric denotes problems in the "direction" of SNPs. SNPs with more than 2% parent-progeny conflicts are discarded, therefore special attention should be taken on these cases.
  • Submissions failing on HWE
    • Metric classification class: Critical
    • Threshold: 50%
    • Expression: Percentage over total number of SUBMISSIONS
    • Explanation: A large number of submissions with SNPs out of HWE (Hardy-Weinberg Equilibrium; heterozygote frequencies departing from the expected range), can be determined by low genotyping quality.
  • Percentage of animal genotypes with No Nomination
    • Metric classification class: Major
    • Threshold: 5%
    • Expression: Integer number of percentage over total number of GENOTYPES
    • Explanation: Although the genotyping laboratory is not formally responsible for this (as the CDCB approved genomic nominators do the nomination), the genotyping laboratory is required to alert nominators when nominations are missing and should postpone submission until nomination is completed.
  • Submissions failing on excessive conflicts per chip
    • Metric classification class: Major
    • Threshold: 10%
    • Expression: Percentage over total number of SUBMISSIONS
    • Explanation: Submissions with more than 80% of animals conflicting by chip are flagged. Typically, this problem arises when there is a misidentification of genotypes. This can be at the source (nominator) or at the lab level. Therefore, although a certain flexibility is allowed, the time-consuming nature of these corrections make a large number of such submissions undesirable.
  • Percentage of animal genotype reassigned
    • Metric classification class: Minor
    • Threshold: N/A at the moment (for monitoring purposes)
    • Expression: Integer number of percentage over total number of GENOTYPES
    • Explanation: Currently monitoring this metric, although no threshold is set.

Extra information

For 50 or fewer genotypes in submission
  • FAIL not specified for Low call rate, parent-progeny conflicts, or HWE
For more than 50 genotypes
  • FAIL if low call rate for more than 0.5% (.005) of usable SNP
  • FAIL if parent-progeny conflicts for more than 0.05% (.0005) of usable SNP
  • If > 250 genotypes FAIL if HWE out of range for more than 0.05% of usable SNP
  • Else FAIL if HWE out of range for more than ½% of usable SNP