Presentation: Infant with congenital malformation and dysmorphism syndrome

A four-week-old infant has been an inpatient since birth for management of choanal atresia and omphalocele diagnosed postnatally. Further evaluation has revealed small ears, a coloboma, a large ventricular septal defect and right-sided hydronephrosis.

• Genomic testing should be considered in the presence of facial dysmorphism, either alone or in combination with any congenital malformation (such as limb defects or organ abnormalities).
• The following clinical features may be the result of teratogenic exposure or may be of multifactorial inheritance, with interactions between genetic and environmental factors. However, combinations of these congenital anomalies with or without dysmorphic features should prompt potential genomic evaluation:
  • neural tube defects;
  • anencephaly or microcephaly;
  • cleft lip or palate;
  • gastroschisis;
  • gastrointestinal anomalies (such as oesophageal or intestinal atresia or stenosis, anorectal anomalies or a tracheoesophageal fistula);
  • diaphragmatic hernia, particularly if associated with cleft lip or palate or cardiac, central nervous system, renal or bone anomalies; and/or
  • urogenital anomalies.
• Genomic testing should be considered if there is a family history of congenital anomalies as an isolated trait.

Terminology: A malformation is defined as any structural defect arising from an intrinsically abnormal developmental process (for example, a cleft lip).  Malformations should be differentiated from both deformations and disruptions, both of which have a lower chance of being associated with an underlying genetic condition. Deformations are physical anomalies arising from mechanical force (for example, a club foot), and disruptions represent physical interruption or destruction of tissue that was normal during fetal life (for example, duodenal atresia secondary to vascular insufficiency).

• Consult the National Genomic Test Directory. From here you can access the rare and inherited disease eligibility criteria, which provides information about individual tests and their associated eligibility criteria. You can also access a spreadsheet containing details of all available tests.
  • For those working within NHS Wales, please consult the All Wales Medical Genomics Service website for information on how to arrange testing.
• To find out which genes are included on different gene panels, see the NHS Genomic Medicine Service (GMS) Signed Off Panels Resource.
• Decide which of the panels best suits the needs of your patient or family. For congenital malformations and/or dysmorphism, there are a number of available panels, including:
  • R26 Likely common aneuploidy testing. This should be performed first where aneuploidy (trisomy 13, trisomy 18 or trisomy 21) is considered to be the most likely diagnosis (send lithium heparin samples (alongside EDTA) in case a karyotype is required);
  • R28 Congenital malformation and dysmorphism syndromes (microarray only): This should be considered if there are clinical features suggestive of a chromosomal cause (where the clinical scenario permits, it is appropriate to start with a microarray before whole genome sequencing (WGS));
  • R14 Acutely unwell children with a likely monogenic disorder: This should be considered if the patient fulfil criteria for rapid WGS (the patient is acutely unwell, there is a likely monogenic disorder, and molecular diagnosis is likely to imminently alter management);
  • R27 Paediatric disorders: This should be considered if there are congenital malformations and/or dysmorphism. Testing of adults with congenital malformation and dysmorphism syndromes would also be appropriate under this clinical indication. If a microarray has already been performed, the WGS ‘super panel’ alone can be requested as R27.3. Additional panels relevant to the patient phenotype can also be added.
    • R27 is a large WGS super panel (a panel comprised of several different constituent panels forming one large panel), and requesting it currently requires authorisation from clinical genetics.
  • R29 Intellectual disability: In this test, a WGS panel can be added where there is also unexplained intellectual disability or global developmental delay.
  • Investigation for disorders of methylation may be appropriate in the following clinical presentations:
    • R47 Angelman syndrome (methylation testing and multiplex ligation-dependent probe amplification (MLPA));
    • R48 Prader-Willi syndrome (methylation testing and MLPA); and
    • R49 Beckwith-Wiedemann syndrome (methylation testing, MLPA and single gene sequencing).
  • For tests that are undertaken using WGS, including R27 and R29, you will need to:
    • complete an NHS GMS test order form with details of the affected child (proband) and their parents, including details of the phenotype (using human phenotype ontology (HPO) terms) and the appropriate panel name(s) with associated R number (see How to complete a test order form for WGS for support in completing WGS-specific forms):
    • complete an NHS GMS record of discussion (RoD) form for each person being tested – for example, if you are undertaking trio testing of an affected child and their parents, you will need three RoD forms (see How to complete a record of discussion form for support); and
    • submit parental samples alongside the child’s sample (this is trio testing) to aid interpretation, especially for the larger WGS panels (where this is not possible, for example because the child is in care or the parents are unavailable for testing, the child may be submitted as a singleton).
  • For tests that do not include WGS, including R26, R28, R47, R48 and R49:
    • you can use your local Genomic Laboratory Hub test order and consent (RoD) forms; and
    • parental samples may be needed for interpretation of the child’s result. Parental samples can be taken alongside that of the child, and their DNA stored, or can be requested at a later date if needed.
  • R14 is a WGS test that looks agnostically across the entire genome. Requesting it currently requires authorisation from clinical genetics. There is a special test order form and RoD form for this test, both of which are available from the Exeter Genetics Laboratory.
  • The majority of tests are DNA-based, and an EDTA sample (purple-topped tube) is required. Exceptions include karyotype testing and DNA repair defect testing (for chromosome breakage), which require lithium heparin (green-topped tube).
• Information about patient eligibility and test indications was correct at the time of writing. When requesting a test, please refer to the National Genomic Test Directory to confirm the right test for your patient.

For clinicians

• NHS England: National Genomic Test Directory
• Genomics England: NHS Genomic Medicine Service (GMS) Signed Off Panels Resource

For patients

• Unique (support for families of children with rare chromosome and gene disorders)