IQ/OV/PQ for Genetitan and Bekmen
Training
Final Report generation:
Sensitivity-gender determination, LOD for sample contamination
Accuracy-concordance with reference data
Precision-concordance within plate and between plates
Proficiency testing Z score or Acceptable difference as per CLSI PG 29
Level of analysis
DQC, Genotyping Step 1,Genotyping Step 2, Plate performance
NOT included :
SNP metricss and SNP QC
Plate design:
2x 2 plates-96 reference HapMap samples
2x 2 plates-48 HapMap samples and 48 QBB samples incuding PC,NC and sample contamination
Qchip
Qchip Clinical content validation
Plan for clinical validation
Samples and variants, positives and negatives, number of samples and plates
Analysis level 1 and level 2
Data exported for linking for screening or diagnosis
Report generation
Qchip research content validation
Sample selection criteria and number of samples
SNP selection criteria and list with all SNPs with breakdown
Library generation with threshold setting from Affymetrix based on (3.5.10 plates?) or dr Andrew
DQC, Genotype calls 1 and 2
SNPolisher;
SNP metrics and SNP QC
PLINK PDE
PLINK TPDE
VCF
TXT
Bioinformatics
QBB Lab performance verification
Proficiency testing with Rutgers
To be decided plate type and sample distribution
Automation workflow verification
Manual workflow verification
4 plates
