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Requesting genetic testing

Ideally genetic testing should be requested via Encompass, however it is still possible use our paper form, which can be downloaded here.

Genetic tests typically requested by non-genetic specialists (see also Patients who are UNLIKELY to benefit from a referral to Clinical Genetics):

  • Alpha-1-antitrypsin deficiency (R191). AATD is typically diagnosed via a serum biochemical test, as opposed to a genetic test.
  • Cystic fibrosis (R184), including carrier testing (R185).
  • Haemochromatosis (R95).
  • Non-genetic specialists can request additional genetic tests if they are listed as a Requesting Specialty in the National Genomic Test Directory (see ‘Step By Step Guide’ below).
    • In NI, there is some deviance from the Test Directory, in testing criteria and requesting specialties (see ‘Examples of Differences’ below).

 

Genetic tests typically requested by a Clinical Genetics specialist only:

  • Exome and genome sequencing.
  • Predictive tests for a known variant in the family (e.g. testing a healthy individual for a known familial variant in BRCA1/2).
  • Neuro-predictive tests (e.g. where there is a family history of Huntington’s disease or CADASIL).
  • For these tests, please refer the patient to Clinical Genetics.

 

Lab user bulletins

Please see here for recent bulletins regarding genetic testing, from the RMDS.

  • A Step By Step Guide to Requesting Genetic Tests on Encompass:
    1. The National Genomic Test Directory provides guidance on what genetic tests are available, which specialists can request them, and the testing criteria.
      1. The test directory can be accessed here (choose the PDF document):
        1. Please note, the Test Directory is curated by Genomics England. There are some differences in access to genetic testing in NI (see ‘Examples of Differences’ below).
      2. Navigate to the test which you feel may be appropriate for your patient.
        1. The contents page lists conditions by specialty, or you can search the document for relevant text (Ctrl+F).
        2. See below for examples of the most commonly used R numbers.
        3. GeNotes is a helpful educational resource which can also help guide you.
          1. Clinical presentations are listed by specialty.
        4. If you feel your patient meets the criteria for more than one test, please refer the patient to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
      3. Check whether or not your patient meets the ‘Testing Criteria’.
        1. If your patient does not meet testing criteria, but you still feel they may need genetic testing, please refer the patient to Clinical Genetics.
      4. Check whether your speciality is listed under Requesting Specialty.
        1. If your speciality is not listed here, please refer the patient to Clinical Genetics.
        2. Please note, the list of requesting specialities may differ in NI (see ‘Examples of Differences’ below).
      5. If your patient meets the testing criteria AND you are listed as a Requesting Specialty, note the R number (e.g. R377 – Intellectual disability – microarray only) and the criteria which your patient fulfils.
      6. On Encompass Orders, search for the genetic test using the R number.
        1. See below for examples of the most commonly used R numbers.
      7. Select Diagnostic test (R240).
        1. Predictive tests (R242) (i.e. testing a healthy individual for a known familial variant, are typically requested by Clinical Genetics only).
      8. “What criteria does this patient meet?”
        1. Select ‘Criteria 1’.
        2. A free text box will appear. In here, enter the criteria which the patient fulfils according to the National Genomic Test Directory.
        3. If the appropriate criteria is not included, the test request will be rejected by the lab, and a ‘DNA storage report’ will be issued.
      9. “Family history details available?”
        1. Yes – if the patient’s family is known to Clinical Genetics, insert the PED number.
        2. No – if the patient’s family is not known to us.
          1. It is still helpful to include family history information in the ‘Clinical Information’ free text box.
        3. “Clinical information”
          1. Include any additional, relevant clinical or family history information. Include the suspected diagnosis.
        4. Consent
          1. Typically patients will provide full consent. For a reminder of what this consent includes, hover over the circular i symbol.
            1. You may also wish to use the smart phrase in your encounter notes .GeneticsConsentRMDS
          2. If the patient provides only partial consent, clearly outline the limits of the consent in the Comments box.
  • General / multispecialty , most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R346 DNA to be stored If you are unsure which test is the most appropriate, you can take an EDTA (purple top) sample for DNA storage and then contact the lab (GeneticsLabs@belfasttrust.hscni.net) or refer to clinical genetics.

     

    DNA storage can be particularly valuable for patients who are receiving end of life care.  See patient information leaflet.
    R240 Diagnostic testing for known variant(s) “Diagnostic” refers to patients who are at risk of inheriting a familial variant and DO show relevant clinical features.

     

    These patients may benefit from a referral to Clinical Genetics.
    R242 Predictive testing for known familial variants (s) “Predictive” refers to patients who are at risk of inheriting a familial variant and do NOT show any features of the condition yet.

     

    This type of testing should only be undertaken by Clinical Genetics.
    R244 Carrier testing for known familial variants(s) Carrier testing for familial variants in cystic fibrosis, haemochromatosis and alpha-1 antitrypsin deficiency can be requested by non-genetic specialists.  For more information see Patients who are UNLIKELY to benefit from a referral to clinical genetics.

     

    For carrier testing in other conditions, please refer the patient to Clinical Genetics.

     

    Please state the details of related individuals on the request (e.g. the name and D.O.B of an affected relative or a relative who is a known carrier).
    R377 Intellectual disability – microarray only Intellectual disability (ID) is the most common indication for a microarray, however a microarray may be appropriate for other presentations (e.g. suspected sex aneuploidy, a fetus with multiple anomalies, suspected Di George syndrome, etc.).  See also R28.

     

    For individuals with ID, additional features and a normal microarray, consider referral to Clinical Genetics for further testing (e.g. exome sequencing).
    R29 Intellectual disability (gene panel) In NI, patients felt to be appropriate for this panel should be referred to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).  These patients should have a microarray sent prior to referral (see R377).
    R26 Likely common aneuploidy For pre-natal common aneuploidy testing see R401.

    The karyotype requires a lithium heparin sample.

    A microarray (which required EDTA sample) can detect aneuploidies, but it would also detect microdeletions and microduplications.

    A karyotype can detect balanced translocations, while a microarray would miss these.

     

  • Cancer, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R207 Inherited ovarian cancer See also Cancer Genetics.
    R208 Inherited breast and ovarian cancer See also Cancer Genetics.
    R210 Inherited MMR deficiency (Lynch syndrome) See also Cancer Genetics.
    R217 Endocrine neoplasia

    (incorporates MEN1, MEN2 and Familial isolated pituitary adenoma (AIP).
    R223 Inherited phaeochromocytoma and paraganglioma excluding NF1 Typically, this panel will not include NF1 (see R222).  See also R363, Inherited predisposition to GIST.
  • Cardiology , most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R131 Hypertrophic cardiomyopathy In NI, cardiac gene panels can only be requested after discussion with the Inherited Cardiac Conditions (ICC) service.

     

    Please note, the R131 panel does not include the Noonan Syndrome genes, see R135 Paediatric or syndromic cardiomyopathy.
    R132 Dilated and arrhythmogenic cardiomyopathy In NI, cardiac gene panels can only be requested after discussion with the inherited cardiac conditions (ICC) service.
    R125 Thoracic aortic aneurysm or dissection

    (incorporates Marfan Syndrome and other aortopathies)

    		 In NI, aortopathy panels should only be requested by Clinical Genetics or the Inherited Cardiac Condition (ICC) service.

     
    R127 Long QT syndrome In NI, cardiac gene panels can only be requested after discussion with the inherited cardiac conditions (ICC) service.
    R134 Familial hypercholesterolaemia In NI, referrals are accepted from FH nurses, an appropriate chemical pathologist, clinical consultant or via one of the established pathways for Cardiac Rehabilitation, Primary Care, or Community Outreach.
  • Dermatology, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R136 Ectodermal dysplasia
    R165 Ichthyosis and erythrokeratoderma
    R236 Pigmentary skin disorders
  • Endocrinology, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R151 Familial hyperparathyroidism or Hypocalciuric hypercalcaemia Typically, this panel includes the cancer predisposition genes MEN1 and RET.
    R149 Severe early-onset obesity In NI, patients felt to be appropriate for this panel should be referred to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
    R218 Multiple endocrine neoplasia type 2 (RET) A wider panel incorporating RET may be more appropriate (e.g. R217, R223)
  • ENT, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R67 Monogenic hearing loss If the patient has syndromic features (e.g. Waardenburg /

    CHARGE syndrome), this should be clearly stated in the comments.
  • Gastrohepatology, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R172 Wilson disease
    R173 Polycystic liver disease
    R175 Pancreatitis
    R176 Gilbert syndrome In NI, testing for Gilbert syndrome is not routinely indicated. It may be appropriate if molecular confirmation will influence management.
    R95 Iron overload – hereditary haemochromatosis testing (HFE) In NI, the HFE testing criteria in the RMDS lab user manual.
  • Haematology, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R361 Sickle cell, thalassaemia and other haemoglobinopathies trait or

    carrier testing

    		 Typically, protein testing or red cell indices should be undertaken first.  For diagnostic testing for patients with these conditions, see R93.

     

    Inherited haematological conditions are usually managed by local Haematology departments, and/or the tertiary Haematology service at RBHSC or BCH.
    R93 Sickle cell, thalassaemia and other haemoglobinopathies Typically, protein testing or red cell indices should be undertaken first.  For carrier/trait testing see R361.
  • Immunology , most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R15 Primary immunodeficiency or monogenic Inflammatory Bowel Disease
  • Metabolic disorders , most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R98 Likely inborn error of metabolism A broad genetic test. Targeted tests may be more appropriate.
    R335 Fabry disease A wider panel incorporating GLA may be more appropriate (e.g. R62, R131, R98)
    R300 Possible mitochondrial disorder – whole mitochondrial genome sequencing Other disease specific mitochondrial tests are available.
  • Mitochondrial disorders, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R300 Possible mitochondrial disorder – whole mitochondrial genome sequencing Other disease specific mitochondrial tests are available.

     

    Please note, some mitochondrial disorders are caused by variants in the mitochondrial genome, and others are caused by variants in the nuclear genome. These require different testing modalities.
  • Musculoskeletal, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R101 Ehlers Danlos syndrome (EDS) with a likely monogenic cause If you suspect an aortopathy, the R125 Thoracic aortic aneurysm or dissection panel may be more appropriate.

     

    Please note, there is no genetic test to confirm or refute a diagnosis of Hypermobility Spectrum Disorder (a.k.a EDS type 3).
    R99 Common craniosynostosis syndromes Typically does not include SMAD6 and rarer causes of craniosynostosis. See also R100 and R416.
    R104 Skeletal dysplasia In NI, patients felt to be appropriate for this panel should be referred to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
  • Neurology, dementia & neuromuscular, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R58 Adult onset neurodegenerative disorder

    (incorporates Frontotemporal Dementia / Amyotrophic Later Sclerosis (ALS) testing, Parkinsonism, Cerebral amyloid angiopathy)

    		 Typically, this test is undertaken in two stages (gene panel +/- C9orf72 short tandem repeat (STR) testing.  See the patient’s report for guidance on follow-up testing.
    R54 Hereditary ataxia with onset in adulthood If you suspect a short tandem repeat (STR) disorder, state this clearly on the form (e.g. most Spinocerebellar Ataxias, Friedreich’s Ataxia, CANVAS, Fragile X-associated Tremor Ataxia Syndrome).
    R55 Hereditary ataxia with onset in childhood
    R60 Adult onset hereditary spastic paraplegia
    R61 Childhood onset hereditary spastic paraplegia
    R56 Adult onset dystonia, chorea or related movement disorder Typically, this panel does not include Huntington’s disease (R68).

    See also ataxia and spastic paraplegia panels.
    R57 Childhood onset dystonia, chorea or related movement disorder See also ataxia and spastic paraplegia panels.
    R77 Hereditary neuropathy – PMP22 copy number

    (incorporates Charcot Marie tooth (CMT) disease type 1/ Hereditary Motor and Sensory Neuropathy (HMSN) and Hereditary Neuropathy with liability to Pressure Palsies (HNPP)).

    		 CMT1 is caused by a deletion incorporating the PMP22 gene.  HNPP is caused by a duplication incorporating the PMP22 gene.  These conditions would also be detected on microarray (see R377 & R28).
    R73 Duchenne or Becker muscular dystrophy Initially, patients will have MLPA only (to look for intragenic deletions and duplications). If there is a strong index of suspicion for dystrophinopathy (See Testing Criteria), DMD sequencing can be requested as a follow-up test. See the patient’s report for guidance on follow-up testing.
    R78 Hereditary neuropathy or pain disorder If patients have features suggestive of CMT1 or HNPP, PMP22 copy number testing should be undertaken first (see R77).
    R222 Neurofibromatosis type 1 (NF1) NF1 is common.  Molecular confirmation should only be undertaken if it is required to influence management, or reproductive planning.
    R221 Familial tumours of the nervous system

    (incorporates schwannomas)

    		 Typically, this panel does not include NF1.  See also NF1 testing (R222) and Pigmentary skin disorders (R236)
    R72 Myotonic dystrophy type 1 See also R69 Hypotonic Infant.
    R74 Facioscapulohumeral muscular dystrophy (FSHD) If there is a strong index of suspicion for FSHD, the patient may require further testing (R345). See patient’s report for guidance.
    R79/R80/R81/

    R82/R83/R381

    		 Congenital muscular dystrophy

    Congenital myaesthenic syndrome

    Congenital myopathy

    LGMD/MFMs/distal myopathies

    Arthrogryposis

    Other rare neuromuscular disorders

    		 Consider referral to Clinical Genetics as these patients may benefit from a more extensive genetic test (e.g. exome sequencing).
    R68 Huntington disease Please note, testing a healthy individual for a known familial variant which causes CADASIL, or another neurodegenerative disorder, can only be undertaken by Clinical Genetics.
    R337 CADASIL
  • Ophthalmology, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R42 Leber hereditary optic neuropathy Multiple eye disorder panels are available.  See Testing Criteria.
    R32 Retinal disorders Typically includes the most common genes associated with retinitis pigmentosa.

     

    If the patient has additional features (e.g. developmental delay), consider referral to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
    R39 Albinism or congenital nystagmus In NI, molecular confirmation of oculocutaneous albinism is not routinely recommended. However, it may be appropriate for reproductive planning.
  • Paediatrics, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R28 Congenital malformation and dysmorphism syndromes – microarray only See also R377.

     

    For individuals with a normal microarray, congenital anomalies and dysmorphic features, consider referral to Clinical Genetics for further testing (e.g. exome sequencing).
    R27 Paediatric disorders In NI, patients felt to be appropriate for this panel should be referred to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
    R69 Hypotonic infant

    (can be used for ‘floppy baby’)

    		 In NI, hypotonic infant is interpreted as a request for spinal muscular atrophy (SMA), myotonic dystrophy (DM1) and Prader-Willi syndrome (PWS) testing. These can also be requested separately on Encompass (R70, R72, R48), but typically only one sample is needed for all three tests.  A hypotonic infant may also be appropriate for a trio exome (R14).
    R14 Acutely unwell children with a likely monogenic disorder The gene-agnostic trio exome is a very extensive genetic test which incorporates all the coding genes.  The R14 is typically undertaken as a trio (DNA from the child and both parents analysed together). In NI, rapid exomes must be requested by a clinical geneticist. Please refer to Clinical Genetics.
    R48 Prader-Willi syndrome (PWS) See also R69, hypotonic infant.  This test requires a specific methylation assay. Most cases of PWS will not be detected on other testing modalities. Read the report for guidance on follow-up testing.
    R47 Angelman Syndrome (AS) This test requires a specific methylation assay. Most cases of AS will not be detected on other testing modalities. Read the report for guidance on follow-up testing.
    R59 Early onset or syndromic epilepsy Consider referral to Clinical Genetics as these patients may benefit from a more extensive genetic test (e.g. exome sequencing).
    R452 Silver Russell Syndrome (SRS) and Temple Syndrome This test requires a specific methylation assay. Most cases of SRS will not be detected on other testing modalities (e.g. Monogenic short stature panel, R453). Read the report for guidance on follow-up testing.
    R149 Severe early-onset obesity In NI, patients felt to be appropriate for this panel should be referred to Clinical Genetics for consideration of a more extensive test (e.g. exome sequencing).
  • Prenatal, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R318 Recurrent miscarriage with products of conception available for testing
    R401 Common aneuploidy testing – prenatal
    R22 Fetus with a likely chromosomal abnormality
    R21 Fetal anomalies with a likely genetic cause These patients must be discussed with the testing laboratory in advance.  Please refer to Clinical Genetics.
    R251 Non-invasive prenatal sexing This blood test is used to identify male pregnancies who are at risk of inherited an X-linked recessive disorder. Please refer to Clinical Genetics.
  • Renal, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R193 Cystic renal disease Autosomal dominant polycystic kidney disease is common.  Molecular confirmation should only be undertaken if it is required to influence management, or reproductive planning.
    R194 Haematuria
    R197 Membranoproliferative glomerulonephritis including C3 glomerulopathy
    R198 Renal tubulopathies
    R202 Tubulointerstitial kidney disease
    R257 Unexplained young onset end-stage renal disease
  • Respiratory, most common R numbers
    R no. Genetic test name

    Comments

    See test directory (pdf) for criteria & requesting specialities
    R184 Cystic fibrosis diagnostic test This testing may be undertaken in 2 stages (common and rare mutation testing).  See the patient’s report for guidance on follow-up testing.
    R185 Cystic fibrosis carrier testing Please state the details of related individuals on the request (e.g. the name and D.O.B of an affected relative, or the name and D.O.B of their partner who is a known carrier).
    R191 Alpha-1-antitrypsin deficiency (A1ATD) We do not see patients with suspected or confirmed A1ATD in the Genetics clinic, unless there are additional issues.  Non-genetic specialists can request testing for A1ATD.  See patients who are UNLIKELY to benefit from a referral to clinical genetics.

     

    These patients are typically managed by Respiratory +/- Hepatology.
    R188 Pulmonary arterial hypertension
    R421 Pulmonary Fibrosis Familial
  • Examples of Differences, National Genomic Test Directory v. testing in NI

    In Northern Ireland,

    • We do not have routine access to whole genome sequencing as a testing methodology.
    • We do not have routine access to Non-Invasive Prenatal Diagnosis (NIPD) or Non-Invasive Prenatal Testing (NIPT).
    • Cardiac gene panels can only be requested after discussion with the inherited cardiac condition (ICC) service, or Clinical Genetics.
    • We do have access to routine gene-agnostic trio exomes. This is the preferred testing methodology for paediatric patients who are suitable for large panels (e.g. R27 Paediatric disorders, R29 Intellectual disability, R59 Early onset or syndromic epilepsy, R149 Severe early-onset obesity).
    • Some of our testing is undertaken through an accredited laboratory in Europe (e.g. Centogene). Our laboratory admin team may contact you to complete a lab-specific test request forms.
    • The R69 hypotonic infant corresponds to testing for SMA, myotonic dystrophy and Prader-Willi Syndrome, as opposed to a gene panel. These tests can also be requested individually. If the infant requires additional testing (e.g. R14 rapid exome sequencing) please refer the patient to Clinical Genetics.
  • Frequently Asked Questions (FAQs)
    1. Which sample types do I need for genetic testing?

    Most genetic tests are undertaken on EDTA (purple top) samples.  A minority of tests require a lithium heparin (green top) sample (e.g. karyotype, FISH) or a sample from an affected tissue (e.g. a skin biopsy for R110 segmental overgrowth disorders).  There is also emerging access to DNA extraction from saliva samples and buccal swabs (please contact Clinical Genetics if you need to explore these options).

     

    1. How do I know which genes are covered by the test I have requested?

    PanelApp can give you a general guide as to what genes would typically be on the gene panel.  However, the gene content of panels can vary between labs.  Therefore, it is important to state on the test request if there are any specific genes of interest.  Lab reports should also include the list of genes which were analysed.  Sometimes the lab report will mention specific diagnostic limitations of the test, and suggest further testing options.

     

    1. My patient seems to meet the criteria for more than one gene panel, which should I send?

    If the patient has a multisystem disorder, which meets the criteria for multiple tests, it is preferable to undertake a more extensive genetic test in the first instance (e.g. exome sequencing).  Please refer these patients to Clinical Genetics.

     

    1. I am not sure which test to request, or I need more information before I can decide?

    In these scenarios you can take an EDTA (purple top) sample of blood and request R346 DNA to be stored.  You can then contact the lab team at a later stage to activate testing (GeneticsLabs@belfasttrust.hscni.net), or refer to Clinical Genetics.  This is particularly valuable in for patients who are receiving end of life care (patient information leaflet of DNA storage).

     

    1. Why have the lab admin team contacted me to complete an additional test request form?

    In NI, some of our testing is undertaken through an accredited laboratory in Europe (e.g. Centogene).  These labs require a separate, and specific request form.  These tests cannot proceed until the form is complete. If you need any support completing the form please contact genetics.away@belfasttrust.hscni.net .

     

    1. Are genetic test results available on Encompass?

    Since January 2025, most genetic test results are available on Encompass (under Media).  Sensitive genetic results (e.g. Huntington predictive testing) are not uploaded to Encompass. Typically, historical genetic results are not available on Encompass.  A copy can be obtained by contacting GeneticsLabs@belfasttrust.hscni.net.

     

    1. I have requested genetic testing and I have not received any results, what should I do?

    Typically, genetic tests take several months and turnaround time can vary according to the test, and the laboratory.  If a reasonable period of time has passed, please feel free to contact GeneticsLabs@belfasttrust.hscni.net .

     

    1. How do I record consent for a genetic test on Encompass?

    When requesting any genetic test you will automatically be asked if the patients gives full or partial consent.  For a reminder of what this consent includes, hover over the circular i symbol.  You may also wish to use the smart phrase in your encounter notes .geneticsconsent.

     

    If you want a paper copy of the consent for the patient to sign, you can use the genetics test request form, or the NHS England Record of Discussion Regarding Genomic Testing.  This paper can be forwarded to the genetics lab with the samples, or you can upload a copy to the patient’s Media folder.

     

    If the patient provides only partial consent, clearly outline the limits of the consent in the Comments box.

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