Qchip

QBB Lab performance verification

Manual workflow verification

4 plates

Automation workflow verification

4 plates

Proficiency testing with Rutgers

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

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

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

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

IQ/OV/PQ for Genetitan and Bekmen

Training