The Leeds Teaching Hospitals NHS Trust

Rare Disease Tests

Rare Disease Tests - By Specialism

Genetic testing is performed in accordance with the National Genomic Test Directory.

 For detailed information about testing criteria and who can request core and specialist - tests please consult the National Genomic Test Directory - eligibility criteria.

 Patients must meet NHS clinical eligibility criteria in order to be accepted for testing.

Panel content is defined according to Genomics England PanelApp. Our reports will always include the ‘green’ genes in the panelapp panel – please contact us if you need to ask about analysis of amber genes. According to National consensus red genes are not reported.

The Leeds Genomics Laboratory will continue to receive samples, perform genomic tests and dispatch DNA samples for specialist testing to the appropriate laboratory, as part of the NEYGLH.

When requesting a genetic test, please include the appropriate clinical interpretation code (R number) and as much phenotypic information on as possible on the referral from to assist us in the analysis and interpretation of the results.

Complex results may require further clinical input prior report issue and will be considered on a case by case basis. Referring clinicians may be invited to a virtual MDT (Genomic Rare Disease Advisory Board (GRDAB)) to discuss the case and results in more detail.

Important: For NHS England patients, only tests listed on the National Genomic Test Directory are available. Some historic tests have been removed and are no longer provided. We strongly recommend that you check for test availability on the Directory before sending a sample. In particular please note that a number of targeted tests previously available have been replaced by multipanel tests. It is important to understand the nature of these new tests in order that informed consent can be obtained from your pateint.

Specialist service groups and tests

The services listed below are reported by the Leeds Genomics Laboratory

Where the service name is followed by “WGS”, this indicates that the testing is delivered centrally by Whole Genome Sequencing and reported by the Leeds Genomics Laboratory. Please refer to North East and Yorkshire Genomics website for links to WGS supporting documentation including eligibility criteria, the test order process etc.

Multi-purpose tests

  • R240 Diagnostic testing for known familial variants
  • R242 Predictive testing for known familial variants
  • R242 Prenatal testing for known familial variants
  • R244 Carrier testing for known familial variants

Core

  • R134 Familial hypercholesterolaemia
  • R184 Cystic fibrosis diagnostic testing
  • R185 Cystic fibrosis carrier testing
  • R253 Cystic fibrosis Newborn Screening Programme
  • R411 Y-chromosome microdeletions

Musculoskeletal

  • R104 Skeletal dysplasias (WGS)
  • R340 Amelogenesis Imperfecta (National service)
  • R371 Malignant hyperthermia (National service)

Neurology

  • R62 Adult-onset leukodystrophy
  • R83 Arthrogryposis (WGS)
  • R84 Cerebellar anomalies (WGS)
  • R85 Holoprosencephaly (WGS)
  • R86 Hydrocephalus (WGS)
  • R87 Cerebral malformation disorders (WGS)
  • R88 Severe microcephaly (WGS)
  • R109 Childhood-onset leukodystrophy (WGS)
  • R222 Neurofibromatosis type 1 (NF1)
  • R221 Neurofibromatosis type 2 (NF2)
  • R228 Tuberous sclerosis
  • R336 Cerebral vascular malformations, including cerebral cavernomas (National service)

Haematology

  • R229 Fanconi anaemia (following confirmation by breakage testing)
  • R313 Neutropenia consistent with ELANE mutations

Inherited cancer

To assist the laboratory in the interpretation of any genomic findings please include as much clinical information as possible including results from tumour studies e.g. LOH, MSI, IHC data where available.R208 Breast/Ovarian cancer

  • R207 Inherited ovarian cancer (without breast cancer)
  • R208 Inherited breast/ovarian cancer
  • R209 Inherited colorectal cancer (with or without polyposis)
  • R210 Inherited mismatch repair deficiency (Lynch syndrome)
  • R211 Inherited polyposis
  • R213 PTEN hamartoma Tumour Syndrome
  • R216 Li Fraumeni Syndrome
  • R220 Wilms tumour with features suggestive of predisposition
  • R224 Inherited Renal Cancer
  • R225 Von Hippel Lindau syndrome
  • R254 Familial Melanoma
  • R363 Inherited predisposition to GIST
  • R365 Fumarate hydratase-related tumour syndromes
  • R414 APC associated polyposis
  • RXX BAP1 associated tumour predisposition 
  • R404 Testing of unaffected individuals for inherited cancer predisposition syndromes*

*Testing of unaffected relatives can also be accessed if appropriate. Referrals should only be made in consultation with/through clinical genetics.

Where a germline blood sample from an affected individual is unavailable and the patient/ family history meets the clinical eligibility criteria, testing of tumour material (gDNA from FFPE material [tumour or normal]) in deceased individuals is available for identification of germline genomic changes. Analysis may not yield a diagnostic result in all cases and CNV/ dosage changes are not reliably detected. Test sensitivity for analysis of FFPE gDNA may therefore be reduced.