Qchip

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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