QC Metrics for Genotyping Laboratories¶
The performance metrics is CDCB quality control standard that CDCB expects laboratories 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.
The following list shows the thresholds for determining whether or not your submission was successful 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 with a low number of animals require the same processing setup time, which increases the inefficiency of the system. Although it is allowed, due to certain specific conditions and corrections required, submissions of batches with a low number of animals is strongly discouraged.
Submissions failing on SNP call rate (across animal)¶
- Metric classification class: Critical
- Threshold: 50% on submissions with 50 or more genotypes.
- Expression: Percentage over total number of SUBMISSIONS
- Explanation: Such submissions fail when at least 0.5% (5/1000 for Illumina) or 2% (2/100 for Affymetrix) of the SNPs across animal have call rates lower than 90%. This statistic is produced on submissions with 50 or more genotypes. 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% on submissions with 50 or more genotypes.
- Expression: Percentage over total number of SUBMISSIONS
- Explanation: This metric denotes problems in the "reliability" of SNPs, and is based on submissions with more than 50 genotypes. SNPs with more than 2% parent-progeny conflicts are counted; therefore special attention should be taken on these cases. The threshold for a "single submission" to fail in parent-progeny conflicts is 0.05% (5/10,000).
Submissions failing on Hardy-Weinberg equilibrium (HWE)¶
- Metric classification class: Critical
- Threshold: 50% on submissions with 50 or more genotypes.
- 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. This statistic is calculated on submissions with 50 or more genotypes.
Percentage of animal genotypes with No Nomination¶
- Metric classification class: Info
- Threshold: NA
- 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 flagged on excessive conflicts per chip¶
- Metric classification class: Info
- Threshold: NA
- 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 makes a large number of such submissions undesirable.
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