Molecular Genetics

Genetics is an integral part of pathology with implications in disease pathogenesis and progression, identification of diagnostic and prognostic biomarkers, as well as targeted treatments. The RCPAQAP Molecular Genetics discipline offers diagnostic and technical proficiency testing programs for inherited diseases, oncology, molecular haematology and rare genetic disorders (as sample exchanges).

In addition, the RCPAQAP Molecular Genetics discipline partners with major external quality assurance providers to provide customers with as many options for molecular genetics testing as is currently available, this includes the:

  • European Molecular Genetics Quality Network (EMQN) – View catalogue
  • Cystic Fibrosis European Network (CF Network) – View catalogue
  • UK National External Quality Assessment Scheme for Leucocyte Immunophenotyping (UK NEQAS LI) – View catalogue
  • Quality Control for Molecular Diagnostics (QCMD) – View Catalogue
  • Australasian Society of Diagnostic Genomics (ASDG)

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BCR-ABL Qualitative

This module qualitatively assesses laboratory performance in the detection and identification of BCR-ABL fusion transcripts in chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL).

Catalogue Number

23140102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

RNA

Sample volume

Up to 2µg of lyophilised, purified RNA provided in each case

Schedule

April, September

Measurand/Test

Molecular genetic testing for BCR-ABL1 fusion transcripts (p190, p210, e1a2, e1a3, e13a2, e13a3, e14a2, e14a3).

Storage and Handling

Upon receipt, store samples at -70°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Chimerism Analysis

This module quantitatively assesses laboratory performance in the evaluation and reporting of donor versus recipient cells in post-transplant peripheral blood or bone marrow specimens.

Catalogue Number

23150102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

Up to 1.5µg of purified DNA in TE pH 8.0 provided in each case

Schedule

February, July

Measurand/Test

Chimerism analysis of donor and recipient DNA.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Coeliac Disease HLA Genotyping

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of the HLA-DQ haplotypes and associated HLA-DQA1 and HLA-DQB1 alleles.

Catalogue Number

23010102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

January, June

Measurand/Test

Molecular genetic testing for HLA-DQA1 and HLA-DQB1 alleles.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

FLT3 ITD and TKD

This module qualitatively and quantitatively assesses laboratory performance in the detection of internal tandem duplication (ITD) and tyrosine kinase domain (TKD) variants of the fms related receptor tyrosine kinase 3 (FLT3) gene.

Catalogue Number

23160102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

March, August

Measurand/Test

Molecular genetic testing for FLT3 ITD and TKD gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Hereditary Haemochromatosis (HFE)

This module qualitatively assesses laboratory performance in the detection of hereditary hemochromatosis gene variants (C282Y, H63D).

Catalogue Number

23170102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

February, July

Measurand/Test

Molecular genetic testing for HFE gene variants, C282Y and H63D.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Human Leukocyte Antigen B*57

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of the HLA-B*5701 allele.

Catalogue Number

23020102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

January, June

Measurand/Test

Molecular genetic testing for HLA-B*57:01.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

IDH Mutation Analysis in AML (IDH1, IDH2)

This module qualitatively assesses laboratory performance in the detection of isocitrate dehydrogenase (IDH) 1 and 2 gene variants in acute myeloid leukaemia (AML).

Catalogue Number

23180102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

January, June

Measurand/Test

Molecular genetic testing for IDH1 and IDH2 gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Immunogenotyping (IgH,TCR)

This module qualitatively assesses laboratory performance in the detection of immunoglobulin heavy chain (IgH) and T-cell receptor (TCR) gene rearrangements.

Catalogue Number

23190102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

Up to 2µg of purified DNA in TE pH 8.0 provided in each case

Schedule

May, October

Measurand/Test

Molecular genetic testing for IgH and TCR gene rearrangement.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Kennedy’s Disease

This module qualitatively assesses laboratory performance in the detection of androgen receptor (AR) gene variants.

Catalogue Number

23070102

Frequency (No of surveys/year)

1

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

April

Measurand/Test

Molecular genetic testing for CAG trinucleotide repeat expansion in the AR gene.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

This program is not covered under the scope of accreditation by NATA. This is a sample exchange program where participating laboratories provide samples to RCPAQAP. All samples will be de-identified, re-labelled and distributed.

Product details last updated on August 21, 2024

Lymphoid NGS Panel Testing

This module qualitatively assesses laboratory performance in the detection and reporting of various genes associated with lymphoid haematological malignancy using next generation sequencing (NGS).

Catalogue Number

23260102

Frequency (No of surveys/year)

1

Cases/samples per survey

1

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

June

Measurand/Test

Next generation sequencing; Molecular genetic testing for ALK, ARID1A, ATM, BCL2, BCL6, BIRC3, B2M, BRAF, BTK, CARD11, CD274, CD79B, CDKN2A, CREBBP, CXCR4, DNMT3A, EP300, ETV6, EZH2, FOXO1, HAVCR2, ID3, IDH1, IDH2, IKZF1, JAK1, JAK2, JAK3, KLF2, KMT2A, KRAS, MEF2B, MYC, MYD88, NFKBIE, NOTCH1, NRAS, PDCD1LG2, PIM1, PTPRD, RHOA, RUNX1, SF3B1, SOCS1, STAT3, STAT5B, STAT6, TCF3, TET2, TNFAIP3, TP53, XPO1 gene variants

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Maternal Cell Contamination

This module qualitatively and quantitatively assesses laboratory performance in the detection, determination and interpretation of maternal cell contamination levels in mock prenatal samples.

Catalogue Number

23090102

Frequency (No of surveys/year)

2

Cases/samples per survey

2 family trios

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

February, July

Measurand/Test

Maternal cell contamination studies.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Molecular Testing in Glioma (IDH1/2, MGMT)

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of isocitrate dehydrogenase (IDH) 1 and 2 gene variants, and methylguanine-DNA Methyltransferase (MGMT) promoter methylation in glioma.

What's new

This program is previously called IDH Mutation Analysis in Glioma. MGMT promoter methylation is now included in this module.

Catalogue Number

23030102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

FFPE tissue sections (patient derived)

Sample volume

Virtual H&E and five unstained 6µM sections (mounted) provided in each case

Schedule

May, October

Measurand/Test

FFPE DNA extraction; Molecular genetic testing for IDH1 and IDH2 gene variants, MGMT gene methylation and variant allele frequency

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Mutation Detection in Colorectal Cancer

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of KRAS proto-oncogene, GTPase (KRAS), NRAS proto-oncogene, GTPase (NRAS) and/or B-Raf proto-oncogene, serine/threonine kinase (BRAF) gene variants in colorectal cancer.

Catalogue Number

23040102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

FFPE tissue sections (patient derived)

Sample volume

Virtual H&E and five unstained 6µM sections (mounted) provided in each case.

Schedule

April, September

Measurand/Test

FFPE DNA extraction; Molecular genetic testing for KRAS, NRAS and/or BRAF gene variants and variant allele frequency

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Mutation Detection in Lung Cancer (NSCLC)

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of epidermal growth factor receptor (EGFR) and/or KRAS proto-oncogene, GTPase (KRAS) gene variants in lung cancer.

Catalogue Number

23050102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

FFPE tissue sections (patient derived)

Sample volume

Virtual H&E and five unstained 6µM sections (mounted) provided in each case.

Schedule

May, October

Measurand/Test

FFPE DNA extraction; Molecular genetic testing for EGFR and/or KRAS gene variants and variant allele frequency

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Mutation Detection in Melanoma

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of B-Raf proto-oncogene, serine/threonine kinase (BRAF) and/or NRAS proto-oncogene, GTPase (NRAS) gene variants in melanoma.

Catalogue Number

23060102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

FFPE tissue sections (patient derived)

Sample volume

Virtual H&E and five unstained 6µM sections (mounted) provided in each case.

Schedule

April, September

Measurand/Test

FFPE DNA extraction; Molecular genetic testing for BRAF and NRAS gene variants and variant allele frequency

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Myeloid NGS Panel Testing

This module qualitatively assesses laboratory performance in the detection and reporting of various genes associated with acute myeloid leukaemia (AML) using next generation sequencing (NGS).

Catalogue Number

23130102

Frequency (No of surveys/year)

2

Cases/samples per survey

1

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

April, September

Measurand/Test

Next generation sequencing; Molecular genetic testing for ASXL1, BCOR, BRAF, CALR, CBL, CEBPA, CSF3R, DDX41, DNMT3A, ETV6, EZH2, FLT3, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NPM1, NRAS, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2 gene variants

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline.

Product details last updated on August 23, 2024

Myeloproliferative Neoplasms (JAK2, CALR, MPL)

This module qualitatively assesses laboratory performance in the detection of janus kinase 2 (JAK2), calreticulin (CALR) and MPL proto-oncogene, thrombopoietin receptor (MPL) gene variants associated with myeloproliferative neoplasms.

Catalogue Number

23200102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

Up to 1.5µg of purified DNA in TE pH 8.0 provided in each case

Schedule

February, July

Measurand/Test

Molecular genetic testing for JAK2, CALR and MPL gene variants and JAK2 variant allele frequency

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

NPM1

This module qualitatively assesses laboratory performance in the detection of nucleophosmin 1 (NPM1) gene variants.

Catalogue Number

23210102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

March, August

Measurand/Test

Molecular genetic testing for NPM1 gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

PML-RARA

This module qualitatively assesses laboratory performance in the detection of PML nuclear body scaffold/retinoic acid receptor alpha (PML-RARA) fusion gene.

Catalogue Number

23220102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

RNA

Sample volume

Up to 2µg of lyophilised, purified RNA provided in each case

Schedule

April, September

Measurand/Test

Molecular genetic testing for PML-RARA fusion transcripts (bcr1, bcr2, bcr3).

Storage and Handling

Upon receipt, store samples at -70°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

PTEN

This module qualitatively assesses laboratory performance for the detection of phosphatase and tensin homolog (PTEN) gene variants.

Catalogue Number

23080102

Frequency (No of surveys/year)

1

Cases/samples per survey

3

Sample Type

DNA

Sample volume

1µg of purified DNA provided in each case

Schedule

March

Measurand/Test

Molecular genetic testing for PTEN gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

This program is not covered under the scope of accreditation by NATA. This is a sample exchange program where participating laboratories provide samples to RCPAQAP. All samples will be de-identified, re-labelled and distributed.

Product details last updated on August 21, 2024

Quality Assessment of DNA Extracts

This module assesses and validates the quality of genomic DNA extracts from various tissue types (except FFPE tissue). Participants will be required to extract and return DNA samples of their choice to the RCPAQAP for quality assessment.
Purity ratio of DNA extracts submitted will be assessed.

Catalogue Number

23100102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

n/a

Schedule

May, October

Measurand/Test

Genomic DNA extraction from any tissue type except FFPE.

Product details last updated on August 21, 2024

Quality Assessment of FFPE DNA Extracts

This module assesses and validates the quality of DNA extracts from FFPE tissue. Participants will be required to extract DNA from the tissue provided and return the DNA samples of their choice to the RCPAQAP for quality assessment.
Purity ratio of FFPE DNA extracts submitted will be assessed.

Catalogue Number

23110102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

FFPE tissue curl (cell line or patient derived)

Sample volume

One 15µM to 20µM FFPE section (vial) provided for DNA extraction.

Schedule

March, August

Measurand/Test

Genomic DNA extraction from FFPE.

Product details last updated on August 21, 2024

RCPAQAP DPYD Genotyping

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of clinically relevant dihydropyrimidine dehydrogenase (DPYD)  variants for fluoropyrimidine toxicity.

What's new

New for 2025

Catalogue Number

23290102

Frequency (No of surveys/year)

1

Cases/samples per survey

2

Sample Type

Purified DNA

Schedule

August

Measurand/Test

Molecular testing of clinically relevant DPYD variants

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure.

Product details last updated on January 3, 2025

RCPAQAP Non-Small Cell Lung Carcinoma Panel Testing

This module qualitatively assesses laboratory performance in the detection, reporting and interpretation of nucleic acid-based multi-gene panel test of non-small cell lung carcinoma for variants in EGFR, BRAF, KRAS, MET and fusion status of ALK, ROS1, RET and NTRK1/2/3.

What's new

New for 2025

Catalogue Number

23280102

Frequency (No of surveys/year)

1

Cases/samples per survey

2

Sample Type

Virtual H&E and five unstained 6µM sections (mounted) provided in each case

Schedule

May

Measurand/Test

Molecular genetic testing for EGFR, BRAF, KRAS and MET exon 14, and fusion status of ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 genes

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Reproductive Carrier Screening

What's new

New for 2025

Catalogue Number

23270102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH8.0 provided in each case

Schedule

March, August

Measurand/Test

Genotyping and clinical interpretation of the CFTR, FMR1 and SMN1 genes

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on January 3, 2025

Sanger DNA Sequencing

This is a technical module to assess laboratory performance in Sanger sequencing. There are two components in this module; (i) Technical component – participants are required to submit raw sequencing data files for analysis, (ii) Diagnostic component – participants are required to report gene variants detected.

Variant nomenclature and zygosity status of variant detected will be assessed under the Diagnostic component.

Catalogue Number

23120102

Frequency (No of surveys/year)

2

Cases/samples per survey

1

Sample Type

PCR products and sequencing primers

Sample volume

20µL of PCR products provided in each case
Lyophilised forward and reverse primers at 10µM

Schedule

March, August

Measurand/Test

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

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Product details last updated on August 21, 2024

Thalassaemia (alpha, beta)

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

Catalogue Number

23230102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

Up to 1.5µg of purified DNA in TE pH 8.0 provided in each case

Schedule

May, October

Measurand/Test

Molecular genetic testing for HBA1/HBA2 and/or HBB gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

Thrombosis (F5, F2)

This module qualitatively assesses laboratory performance in the detection of coagulation factor V (F5) and coagulation factor II, thrombin (F2) gene variants.

Catalogue Number

23240102

Frequency (No of surveys/year)

2

Cases/samples per survey

2

Sample Type

DNA

Sample volume

1µg of purified DNA in TE pH 8.0 provided in each case

Schedule

February, July

Measurand/Test

Molecular genetic testing for F5 and F2 gene variants.

Storage and Handling

Upon receipt, store samples at 2-8°C or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

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

In collaboration with Australasian Society of Diagnostic Genomics (ASDG), this module qualitatively assesses laboratory performance in the detection of TP53 deletions at 17p13.1 in chronic lymphocytic leukaemia (CLL) using fluorescence in-situ hybridisation (FISH).

Catalogue Number

23250102

Frequency (No of surveys/year)

1

Cases/samples per survey

2

Sample Type

Interphase nuclei (bone marrow)

Sample volume

Two slides provided in each case

Schedule

July

Measurand/Test

Fluorescence in situ hybrisation testing for TP53 deletion in 17p13.1

Storage and Handling

Upon receipt, store samples at room temperature or according to your standard operating procedure

Additional Comments

Available to order in myQAP under the Haematology Discipline

Product details last updated on August 21, 2024

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