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Updates to the National Genomic Test Directory: October 2022

Update

Updates to the National Genomic Test Directory: October 2022

An updated version of the National Genomic Test Directory, which specifies which genomic tests are commissioned by the NHS in England, was published on the 31st October 2022. A number of changes have been made which impact the genomic tests for Cancer and Rare and Inherited Diseases. Please find a list of the core changes here.

October 31, 2022

To view the full updated National Test Directories, including patient eligibility criteria and information about the clinical specialities who would be expected to request tests, please visit the NHS website: https://www.england.nhs.uk/publication/national-genomic-test-directories/

The North Thames GLH delivers these tests for patients across North London and much of Essex and Hertfordshire. Please visit the section for healthcare professionals if you need further information about ordering a genetic test and ordering whole genome sequencing for your patients.

Updates to the National Genomic Test Directory for Cancer

New Clinical Indications

Group	Test and Indication	Changes made
Haematological Tumours and Solid tumours	M242 Patient receiving solid organ transplantation	CITT M242.1 and M242.2 available for any patient receiving solid organ transplantation (only in cases where passenger lymphocyte syndrome is suspected)
Solid Tumours	M243 Thymic Carcinoma	CITT M243.1 available for patients with Thymic Carcinoma with KIT as target gene
	M244 All solid tumours for NTRK1/2/3 testing	CITT M244.1 available for All solid tumours for NTRK1/2/3 testing by FISH

New indications for Cancer WGS

Group	Test and indication
Solid Tumour	M226 Cancer of Unknown Primary by WGS. In both adult and paediatric population. Can be performed at any stage of presentation (e.g., diagnosis, progression, relapse).

Changes to directory

Group	Test and Indication	Change made
Haematological	M80 Acute Myeloid Leukaemia	BCR-ABL1 TKD sequencing test method changed from Sanger to NGS panel
	M84 Chronic Myeloid Leukaemia	BCR-ABL1 TKD sequencing test method changed from Sanger to NGS panel
	M89 Acute Leukaemia Other	BCR-ABL1 TKD sequencing test method changed from Sanger to NGS panel
	M91 Acute Lymphoblastic Leukaemia	BCR-ABL1 TKD sequencing test method changed from Sanger to NGS panel Added IKZF1 SNV testing Added TMPT & NUDT15 genotyping
	M85 Myeloproliferative Neoplasm	CHEK2 gene target removed
	M224 MDS/MPN	CHEK2 gene target removed
	M88 Juvenile Myelomonocytic Leukaemia	CHEK2 gene target removed
	M94 Chronic Lymphocytic Leukaemia	SNP Array added as an alternative technology for CNV detection
Neurological	M26 Ependymomas- paediatric	Clinical indication name changed from ‘Ependymomas Paediatric’ to ‘Ependymomas Adult’ Methylation profiling permissive to support testing where anatomical position of the ependymoma indicates posterior fossa ependymoma
	M25 Ependymomas supratentorial- adult	Methylation profiling permissive to support testing where anatomical position of the ependymoma indicates posterior fossa ependymoma
Paediatric	M152 Neuroblastoma	Added TERT promoter rearrangements by FISH technology
Sarcoma	M67 Myxoid/Round Cell Liposarcoma	Added MDM2 amplification in patients with suspected myxoid pleomorphic liposarcoma
	M79 Well Differentiated/Dedifferentiated Liposarcoma	Typological error corrected which supports MDM2 amplification testing by FISH
Solid Tumours	M4 Non-Small Cell Lung Cancer	Eligibility criteria updated

Updates to the National Genomic Test Directory for Rare and Inherited conditions

New Clinical Indications

Speciality	Test and Indication	Tests available
Respiratory	R426 Pulmonary alveolar microlithiasis	For target gene SLC34A2, single gene sequencing >=10 amplicons or exon level CNV detection by MLPA or equivalent
Organ transplantation	R428 Patient receiving solid organ transplantation (only in cases where passenger lymphocyte syndrome is suspected)	STR testing for relevant gene(s) or loci FISH testing for sex chromosome testing

Changes to directory

Speciality	Test and Indication	Change made
Skin	R110 Segmental overgrowth disorders	Moved to deep sequencing; Amended eligibility criteria; Opened sample pathways to facilitate tissue sample testing; Added requesting specialities: clinical genetics and plastic surgery.
	R227 Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome	Added new test targets: GTF2E2; RNF113A; CARS1
Neurology	R222 Neurofibromatosis Type 1	Added new gene target SPRED1; Added paediatrics as requesting speciality
	R82 Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies	Changed eligibility criteria to: “Clinical features that indicate a likely limb girdle muscular dystrophy or a genetic condition with overlapping phenotype such as distal myopathy or myofibrillar myopathy”
Renal	R257 Unexplained young onset end-stage renal disease	Increased age of eligible patient from 18 to 36
Mitochondrial	R42 Leber hereditary optic neuropathy	Removed R42.4. DNAJC30 added to R41 optic neuropathy panel
Ophthalmology	R41 Optic neuropathy	Included test type R41.3 three common LHON variants targeted mutation testing.
Haematology Core	R96 Iron metabolism disorders – NOT common HFE mutations	Amended eligibility criteria to “Iron overload (with raised transferrin saturation and/or raised serum ferritin) or features of other disorders of iron metabolism in which common HFE mutations have been excluded or are unlikely”
	Iron overload – hereditary haemochromatosis testing	Amended eligibility criteria to: “Unexplained iron overload (with raised transferrin saturation and/or raised serum ferritin) suggestive of hereditary haemochromatosis”
Inherited cancer	R208 Inherited breast cancer and ovarian cancer	Added new gene targets: RAD51C and RAD51D; Amended eligibility criteria: Criteria 1f. Amend to using either a combined pathology adjusted Manchester score of ≥15, or single gene pathology adjusted score of ≥ 10 or BOADICEA/CanRisk score of ≥ 10. Criteria 4 Living unaffected relative change criteria 4b to combined pathology adjusted Manchester score of ≥20, or BOADICEA/CanRisk score of ≥20% for affected relative or BOADICEA/CanRisk score of ≥10% for unaffected relative. Criteria 4 add a phrase following criteria a-d stating that “where more than one family member may be eligible for unaffected testing, consideration of the residual probability of a causative pathogenic variant in the family taking into account prior normal unaffected tests should be undertaken”
	Inherited MMR deficiency (Lynch syndrome)	Added prostate, gastric and pancreas cancers as types of lynch cancers
Paediatrics	Acutely unwell children with a likely monogenic disorder	Moved from exome to WGS testing