AWMGS - Which genetic test do you require?

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Service	R or M Code	Speciality	Method	Target Gene
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Li Fraumeni syndrome (TP53)	R216	Cancer Genetics	DNA NGS Panel	TP53
LIPIDS - Familial Hypercholesterolaemia (FH)	R134	Specialist Rare Disease	Small panel	Familial hypercholesterolaemia – targeted panel (772)
Lymphoma Service	M95.3, M96, M97.1, M98.1, M99.1-M99.7, M101.1, M102.1, M102.2, M103.1-M103.3, M107.4, M107.5, M111.2, M182.2, 225.1,225.3	Haematology	FISH, complex targeted mutation testing	MYC, BCL2, BCL6, 11q MYC-IGH, MYC-IGK MYC-IGL, IGH-BCL2, IGH-CCND1, P53-CEN17 ALK, IRF4, TP63, DUSP22, TCRB, TCRG, MALT
Lynch syndrome/Hereditary Non-Polyposis Colorectal Cancer (HNPCC)	M1.4, M1.5	Oncology	Microsatellite instability or IHC	MSI or MMR (MLH1, MSH2, MSH6, PMS2) deficiency
Lynch syndrome/Hereditary Non-Polyposis Colorectal Cancer (HNPCC) follow-up	M1.5	Pathology	Pyrosequencing	BRAF hotspot, MLH1 Promoter hypermethylation
Lynch syndrome/Hereditary Non-Polyposis Colorectal Cancer (HNPCC) gene screen	R210	Oncology	DNA NGS panel	MLH1, MSH2, MSH6
Melanoma (DNA)	M7.1, M7.2	Oncology	DNA panel, simple targeted mutation testing	BRAF, KIT, NRAS
Myelodysplasia	M82	Haematological Malignancy
Myeloma Service	M92.2, M92.4, M92.5, M92.8, M92.10, M92.11, M92.12	Haematology	FISH	TP53, IGH, MAF, CCND1, FGFR3, CDKN2C, CKS1B
Myotonic dystrophy type 1	R72.1	Neurology	STR testing	DMPK STR
Myotonic dystrophy type 2 (DM2)	R410	Neurology	STR testing	CNBP (ZNF9) STR
Neurofibromatosis type 1 (NF1)	R222	Cancer Genetics	DNA NGS panel	NF1
Next Generation Sequencing for Myeloid Malignancies	M80.2, M82.1, M85.1, M89.4	Haematology		ASXL1, BCOR, CALR, CEBPA, CBL, DNMT3A, EZH2, ETV6, FLT3, GATA2, IDH1, IDH2, JAK2, KRAS, KIT, MPL, NRAS, NPM1, NOTCH1, PDGFRA, RUNX1, SF3B1, SRSF2, SETBP1, TET2, TP53, U2AF1
Non Small Cell Lung Cancer, NSCLC (Circulating Tumour DNA, ctDNA)	M4.5	Oncology	Simple targeted mutation testing	EGFR
Non Small Cell Lung Cancer, NSCLC (DNA)	M4.1	Oncology	DNA Panel	EGFR, ALK, BRAF, KRAS ROS1, RET, ELM4-ALK, NTRK1, NTRK2, NTRK3
Non Small Cell Lung Cancer, NSCLC (FISH)	M4.6, M4.10	Oncology	FISH	ALK, ROS1 (Confirmation of IHC results by prior arrangement)
Non small cell lung cancer, NSCLC (RNA)	M4.2	Oncology	Panel Simple targeted mutation testing FISH/Simple targeted mutation testing	ALK, ROS1, RET, MET, EGFR, NTRK 1, NTRK 2, NTRK 3
Non-Invasive Prenatal Testing (NIPT)	NA	Prenatal	Massively Parallel Shotgun Sequencing	Chromosomes 13, 18 and 21
NTRK (RNA)	M1.6, M2.3, M215. M3.5, M4.2, M231.2, M5.2, M6.2, M7.3, M187.4, M8.2. M9.2, M9.4, M10.2, M11.4, M12.2 . M13.2, M14.4, M15.2, M15.6, M16.2, M17.2, M18.6, M217.3, M218.2, M219.2, M220.1, M221.1, M222.2, M226.1, M227.1, M20.5, M21.21, M22.9, M23.11, M24.6, M25.9, M26.4, M27.15, M28.8, M29.8, M30.4, M31.6, M32.5, M34.7, M35.8, M36.14, M37.4, M38.5, M39.4, M183.9, M184.8, M185.5, M186.8, M213.2, M189.2, M190.2, M191.21, M192.21, M193.21, M194.24, M42.5, M43.3, M45.4, M46.3, M47.3, M48.3, M49.1, M50.3, M52.3, M53.5, M55.1, M56.3, M57.1, M58.3, M60.3, M61.1, M62.3, M63.3, M64.3, M65.3, M66.3, M67.3, M68.4, M70.3, M71.3, M72.1, M73.3, M74.3, M75.3, M75.1, M76.3, M77.3, M78.1, M79.3, M196.4, M198.5, M199.2, M200.1, M201.4, M202.7, M203.6, M204.6, M205.8, M206.8, M207.7, M208.1, M209.5, M210.1, M211.4, M85.3, M119.2, M120.6, M124.10, M126.3, M127.4, M195.4, M130.5, M131.5, M132.2, M133.4, M136.3, M137.2, M138.3, M139.2, M143.5, M145.14, M146.7, M147.8, M148.9, M149.3, M150.8, M151.6, M152.16, M153.5, M155.4, M156.9, M157.3, M158.6, M159.6, M160.2, M161.5, M162.9, M165.7, M212.15, M166.3, M167.5, M168.6, M169.5, M170.7, M171.8, M172.7, M173.3, M174.4, M178.4, M179.10, M180.7	Oncology	RNA	NTRK1, NTRK2, NTRK3
Opthamology - Leber Hereditary Optic Neuropathy (LHON)	R42.1	Specialist Rare Disease	Targeted mutation testing	Three common LHON variants
Ovarian Cancer (blood testing)	M2.1	Oncology	DNA NGS Panel	BRCA1, BRCA2
Ovarian Cancer (tumour testing)	M2.1, M2.5	Oncology	DNA NGS panel or Myriad HRD testing	BRCA1/2 and/or Genomic Instability
Peutz-Jegher Syndrome	R212	Cancer Genetics	DNA NGS panel	STK11
Pilot study – Non-Invasive-Prenatal Testing (NIPT) in pregnancies with fetal anomalies		Prenatal	Massively Parallel Shotgun Sequencing	Chromosomes 13, 18 and 21
Polyposis, including Familial Adenomatous Polyposis (FAP, AFAP) and MUTYH-associated Polyposis (MAP)	R211	Cancer Genetics	DNA NGS panel	APC, MUTYH, BMPR1A, SMAD4, POLD1, POLE
Postnatal Cytogenetic Analysis	R297, R265, R314, R146	Developmental Delay	Karyotype Common aneuploidy testing Microarray	As determined by indication Genomewide Sex chromosomes
Pregnancy Related Rapid Sequencing (R14)	R14	Core Rare Disease	Whole Genome Sequencing, Whole Exome Sequencing	Paediatric Disorders
Prenatal Cytogenetic Analysis	R401, R22	Prenatal	Common aneuploidy testing Microarray	Genomewide
Prenatal Service: Abnormal Scan Single Nucleotide Polymorphism Array (SNP Array)	R22	Prenatal
Prostate BRCA test (PARP inhibitor eligibility) - Blood	R444.2	Oncology	DNA NGS panel	BRCA1, BRCA2
Prostate BRCA test (PARP inhibitor eligibility) - Tumour (NTRK can also be requested on this form)	M218.1	Oncology	DNA NGS panel	BRCA1, BRCA2
PTEN hamartoma syndrome (PTEN), Cowden Syndrome	R213	Cancer Genetics	DNA NGS Panel	PTEN
QF-PCR Aneuploidy Screening	R401.1, R26, R314.1	Prenatal	Common aneuploidy testing	Genomewide Sex chromosomes
Rapid BRAF testing for anaplastic thyroid carcinoma (FFPE DNA)	n/a	Oncology	FFPE Pyrosequencing (BRAF only)	BRAF
Rapid BRAF testing for metastatic melanoma (ctDNA)	n/a	Oncology	ctDNA Pyrosequencing (BRAF only)	BRAF
Rapid BRAF testing for metastatic melanoma (FFPE)	n/a	Oncology	FFPE Pyrosequencing (BRAF only)	BRAF
Respiratory - Cystic Fibrosis (CF)	R184.1	Specialist Rare Disease	Targeted Testing	CFTR 8 common Welsh variants, CFTR 50 common European variants *Please note CF50 tests are currently being referred to an external lab until 30/11/23
Sarcoma	M42.1, M42.2, M43.1, M45.1, M45.2, M48.1, M50.1, M56.1, M58.1, M62.1, M63.1, M63.2, M66.1, M67.1, M68.3, M74.1, M76.1, M77.1, M79.1, M196.1, M197.2, M197.3, M197.4, M197.8, M198.1, M199.3, M199.4, M199.5, M199.6, M199.7, M199.8, M199.9, M199.10, M200.2	Pathology	FISH	PAX3-FOXO1,TFE3, EWSR1, COL1A1-PDGFB, NR4A3, ETV6-NTRK3, TPM4-ALK, TPM3-ALK, EWSR1, DDIT3, MDM2, MYC, FUS, SS18. FOXO1, USP6
Single nucleotide polymorphism (SNP) array Service for Developmental Disorders	R337.1	Developmental Delay	SNP Array	Whole genome CNV
Solid Tissue Cytogenetic Analysis	R318, R322	Prenatal	Common aneuploidy testing Microarray	Genomewide
Spinal Muscular Atrophy (SMA) Type I / II / III / IV	R70	Neurology	MLPA or equivalent	SMN1
Spinocerebellar Ataxia Type 1 / 2 / 3 / 6 / 7 / 17 (SCA1 / 2 / 3 / 6 / 7 / 17)		Neurology	STR Testing	ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP
Systemic Mastocytosis	M86.2	Haematology	Simple targeted mutation testing	cKIT
Thyroid (DNA)	M9.1, M10.1, M11.1, M12.1	Oncology	DNA Panel, Pyrosequencing	BRAF, KRAS, NRAS, HRAS RET TP53
Thyroid (RNA)	M9.2, M10.2, M11.4, M12.2	Oncology	RNA Panel	NTRK1, NTRK2, NTRK3, RET, EGFR
Tuberous Sclerosis Complex	R228	Cancer Genetics	DNA NGS panel	TSC1, TSC2
Validation of copy number variants using real-time quantitative PCR (qPCR)	R240.1, R244.1	Developmental Delay	Targeted Mutation Testing	Specific Target
Waldenstrom Macroglobulinemia (WM) service / lymphoplasmacytic lymphoma	M104.2	Haematology	Simple targeted mutation testing	MYD88
Whole Exome Sequencing for Rare Diseases (WES)	R27, R29	Rare Disease	Whole Exome Sequencing
Whole Genome Sequencing for Rare Diseases (WGS)	R27, R29, WINGS/R14	Rare Disease	Whole Genome Sequencing