What are the QC metrics for the CytoScan HT-CMA assay and what does each metric indicate?
Copy Number QC Metrics:
a. SNPQC ≥ 10 - SNPQC is a measure of how well genotype alleles are resolved in the microarray data.
b. MAPD ≤ 0.28 - A global measure of the variation of all microarray probes across the genome. It represents the median of the distribution of changes in Log2 Ratio between adjacent probes. Since it measures differences between adjacent probes, it is a measure of short range noise in the microarray data.
c. Waviness SD ≤ 0.07 - A global measure of variation of microarray probes that is insensitive to short-range variation and focuses on long-range variation.
Genotyping QC Metrics:
a. DQC ≥ 0.88 - DQC is a single-sample measure of "interference" between foreground and background signal distributions. It is independent of other samples in the analysis run. Values range from 0 to 1, with higher values being better. Water is ~0.05 and 'bad' sample or assay problems center around 0.5.
b. QC Call Rate ≥ 98.5% - A metric computed over a representative set of well-behaved probe sets. Low QC call rate over well-behaved probe sets suggest problems with sample quality. Samples with low QC call rate but high DQC values are consistent with sample contamination. Monitor DQC values by plate and time to detect problem trends and problem plates.
SMN metrics:
a. MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.
b.MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
a. SNPQC ≥ 10 - SNPQC is a measure of how well genotype alleles are resolved in the microarray data.
b. MAPD ≤ 0.28 - A global measure of the variation of all microarray probes across the genome. It represents the median of the distribution of changes in Log2 Ratio between adjacent probes. Since it measures differences between adjacent probes, it is a measure of short range noise in the microarray data.
c. Waviness SD ≤ 0.07 - A global measure of variation of microarray probes that is insensitive to short-range variation and focuses on long-range variation.
Genotyping QC Metrics:
a. DQC ≥ 0.88 - DQC is a single-sample measure of "interference" between foreground and background signal distributions. It is independent of other samples in the analysis run. Values range from 0 to 1, with higher values being better. Water is ~0.05 and 'bad' sample or assay problems center around 0.5.
b. QC Call Rate ≥ 98.5% - A metric computed over a representative set of well-behaved probe sets. Low QC call rate over well-behaved probe sets suggest problems with sample quality. Samples with low QC call rate but high DQC values are consistent with sample contamination. Monitor DQC values by plate and time to detect problem trends and problem plates.
SMN metrics:
a. MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.
b.MAPD (SMN) ≤ 0.35 - A global measure of the variation of all microarray probes across the genome calculated during SMN copy number analysis.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.