Menu Search Donate
NICU guideline identifier

Cytogenic and Molecular Genetic Studies in the Neonatal Period

This document is only valid for the day on which it is accessed. Please read our disclaimer.

Note: Given the increasing concerns around genetic testing without informed consent, only tests for diagnostic or management reasons should be carried out in the neonatal period.

Consultation with the Northern Regional Genetic Service is recommended when further advice is needed (Ext. 25870 AKH) 

Cord blood

  • Confirmation of suspected chromosomal disorder following abnormal antenatal ultrasound undertaken late in pregnancy or where further investigation declined during in the pregnancy. 
  • Chromosome mosaicism found at CVS, amniocentesis or cordocentesis (where indicated) 
  • DNA studies. Cord blood confirmation of single gene disorder suspected on ultrasound findings eg achondroplasia
  • Testing for late onset disorders should not be undertaken 
  • Confirmation of biochemistry where prenatal diagnosis of a known condition undertaken (requested by testing lab) 

Neonatal testing


  1. Clinical features consistent with known chromosomal abnormality.
  2. Multiple congenital anomalies consistent with possible chromosomal abnormality
  3. Ambiguous genitalia.

Which test to request

When the phenotype indicates a common aneuploidy (trisomy 21, 18, 13, or X aneuploidy) request a standard karyotype. If an urgent result is required, specify "Rapid FISH Analysis" on laboratory request form and identify the particular chromosome in question (trisomy 21, 18, 13, X monosomy). Click here for link to LabPlus test guide, for turnaround times.

In a baby with dysmorphism/abnormal neonatal adaptation/organ anomalies where a specific diagnosis is not apparent: request a standard karyotype (see test guide).

If a specific diagnosis is unlikely to alter management, consider an alternative request for a molecular karyotype (see test guide). If in doubt, please liaise with the clinical geneticist on call.

Where the phenotype suggests a specific microdeletion syndrome, particularly the 22q microdeletion syndrome, request the specific FISH test (rapid test also available for urgent 22q microdeletion requests, see test guide).

N.B: If Prader-Willi syndrome is suspected, request the methylation test for the 15q11.2-13 locus. For details on turnaround times, please click here. If clinical suspicion is high and a quicker result is desired, consider requesting the specific FISH test, keeping in mind that deletions account for 65-75% of patients with PWS.

Solid Tissues

Products of conception.
Post mortem - (1) - (3) as above.

Guidelines for DNA studies in the neonatal period

  • Features of a single gene disorder/syndrome (for diagnostic purposes) e.g. hypotonia
  • Mitochondrial myopathy syndrome.
  • Features of possible single gene disorder where infant may die and genetic testing may later become available (DNA storage)

Blood Collection Tubes

  • Chromosomes (conventional karyotype) and/or FISH (Lithium Heparin)
  • Molecular Karyotype/Microarray (EDTA) (see test guide).
  • Molecular Genetic/DNA studies (EDTA)

Information for families

See Lab Plus Information for Patients on Microarray Testing

Did you find this information helpful?

Document Control

  • Date last published: 19 September 2018
  • Document type: Clinical Guideline
  • Services responsible: Neonatology
  • Owner: Newborn Services Clinical Practice Committee
  • Editor: Sarah Bellhouse
  • Review frequency: 2 years