Molecular Genetics

PTEN

This is a sample exchange program where participating laboratories provide specimens to RCPAQAP, which will be de-identified, re-labelled and distributed. This program assesses laboratory performance in the detection of variants in the phosphatase and tensin homolog (PTEN) gene.

Frequency / Number of samples

1 survey / 3 samples per survey (DNA in TE buffer)

Tests

Molecular genetic analysis; variant screening of the PTEN gene

Quality Assessment of DNA Extracts

This module assesses laboratory perfomance in the extraction of total genomic DNA from various tissue types (except FFPE tissue). Participants will be required to extract and return up to five DNA samples of their choice to the RCPAQAP for external quality assessment.

Frequency / Number of samples

1 survey / 5 samples per survey (DNA samples to be submitted by participating laboratories to the RCPAQAP)

Tests

Total genomic DNA extraction

Quality Assessment of FFPE DNA Extracts (Pilot)

This module assesses laboratory perfomance in the extraction of total genomic DNA from FFPE tissue. Participants will be required to extract and return up to five DNA samples of their choice to the RCPAQAP for external quality assessment.

Frequency / Number of samples

1 survey / 5 samples per survey (DNA samples to be submitted by participating laboratories to the RCPAQAP)

Tests

Total genomic DNA extraction

Quantitative Analysis of Circulating Free DNA (cfDNA) (Pilot)

This module quantitatively assesses laboratory performance in the detection and reporting of gene variants and the allele fraction in cfDNA samples.

Frequency / Number of samples

1 survey / 8 samples (cfDNA in TE buffer)

Tests

cfDNA

Sanger DNA Sequencing

This is a technical module to assess laboratory performance in Sanger sequencing. There are two components in this module, technical and diagnostic. For the technical component, participants are required to submit their raw sequencing data files for for analysis. For the diagnostic component, participants are required to report and interpret on the genetic DNA variants detected.

Frequency / Number of samples

1 survey / 2 samples (Non-purified PCR product)

Tests

PCR product clean-up; Post-sequencing clean-up; Sanger sequencing

Thalassaemia (alpha, beta)

This module qualitatively assesses laboratory performance in the detection of α-thalassemia (HBA1/HBA2) and/or β-thalassemia (HBB) gene variants.

Frequency / Number of samples

2 surveys / 3 samples per survey (DNA in TE buffer)

Tests

Molecular genetic analysis; Mutation screening of the HBA1/HBA2 and HBB genes

Thrombosis (F5, F2, MTHFR)

This module qualitatively assesses laboratory performance in the detection of Factor V Leiden, Methylenetetrahydrofolate reductase and Prothrombin variants.

Frequency / Number of samples

1 survey / 8 samples per survey (DNA in TE buffer)

Tests

Molecular genetic analysis; variant screening of the F2, F5 and MTHFR genes

TP53 Deletions at 17p13.1 in CLL (FISH)

This module qualitatively assesses laboratory performance in the detection of TP53 deletions at 17p13.1 in CLL using fluorescence in-situ hybridisation (FISH).

Frequency / Number of samples

1 survey / 3 samples per survey (Interphase nuclei -Fixed cells on slides)

Tests

Molecular/cytogenetic analysis of TP53 deletion in 17p13.1

UKNEQAS LI BCR-ABL1 Major Quantification

In this programme participants are provided with lyophilised cell-lines for quantitative BCR-ABL1 analysis. Participants are asked to submit quantitative results, either as %BCR-ABL1/control gene or %BCR-ABL1/control gene on the international scale (IS) together with details of the methodology.

Frequency / Number of samples

3 surveys / 2 samples per survey (Lyophilised cell lines)

Tests

Molecular genetic analysis; Quantitative PCR testing