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Cytogenetic investigations in rare disease referrals

Karyotyping (G-banded analysis)

Karyotyping, or G-banded analysis, involves the microscopic examination of the chromosomes. This test can detect loss or gain of material from any region of any chromosome. In addition, karyotyping can detect both balanced and unbalanced structural rearrangements such as translocations and inversions.

Living cells are required for cell culture to produce the chromosome preparations, hence frozen or fixed material cannot be processed.

As this test examines the chromosomes microscopically, the level of detail is limited by the resolution of the microscope and imbalances of ~5Mb or greater can be detected.

Karyotyping is a front line test to detect balanced structural chromosome rearrangements such as translocations and inversions, to investigate sex chromosome abnormalities or mosaicism.

NHS England National Genomic Test Directory codes

  • R297 Possible structural chromosomal rearrangement requiring karyotype
  • R265 Individuals with possible mosaic chromosome abnormality requiring extended count karyotype
  • R314 Ambiguous genitalia presenting neonatally should be used to establish karyotypic sex in urgent neonatal situations

Array Comparative Genomic Hybridisation (Array CGH)

Array CGH involves:

  • labelling the patient's DNA with a fluorescent dye
  • hybridising against 'normal' control DNA labelled with a different dye
  • using a laser scanner to measure the ratio of the two dyes across sequential segments of the genome and, hence, detect loss or gain of chromosomal material in the patient.

This technique allows examination of the whole genome in greater detail than is possible by karyotyping and can detect imbalances of 100 - 200kb or greater. The software allows cross referencing to international databases to allow identification of the genes in the region of imbalance.

This test is primarily undertaken on blood, tissue and prenatal samples (please discuss with the laboratory for other sample types).

This test detects chromosomal imbalance and can also be used to further define the breakpoints and gene content of known chromosome abnormalities. This test does not detect balanced rearrangements.

Array CGH is a front line test for developmental delay / congenital malformation, fetal loss referrals and prenatal testing of pregnancies where abnormalities consistent with a chromosome imbalance have been identified on ultrasound scan.

NHS England National Genomic Test Directory codes

Common referrals

  • R22 Fetus with a likely chromosomal abnormality
  • R28 Congenital malformation and dysmorphism syndromes
  • R343 Chromosomal mosaicism - microarray should be used where a microarray is indicated
  • R318 Recurrent miscarriage with products of conception available for testing
  • R377 Intellectual disability

Other referrals

  • R14 Acutely unwell children with a likely monogenic disorder
  • R15 Primary immunodeficiency
  • R31 Bilateral congenital or childhood onset cataracts
  • R55 Hereditary ataxia with onset in childhood
  • R57 Childhood onset dystonia, chorea or related movement disorder
  • R59 Early onset or syndromic epilepsy
  • R61 Childhood onset hereditary spastic paraplegia
  • R83 Arthrogryposis
  • R84 Cerebellar anomalies
  • R86 Hydrocephalus
  • R87 Cerebral malformation
  • R88 Severe microcephaly
  • R100 Rare syndromic craniosynostosis or isolated multisuture synostosis
  • R104 Skeletal dysplasia
  • R109 Childhood onset leukodystrophy
  • R137 Congenital heart disease
  • R146 Disorders of sex development
  • R147 Growth failure in early childhood
  • R199 Congenital anomalies of the kidney and urinary tract (familial)

Fluorescence In Situ Hybridisation (FISH)

FISH is the microscopic examination of either interphase cells or chromosomes for the presence or absence of a fluorescently tagged probe. The probe can specifically target a region of a chromosome containing the genes for a particular genetic syndrome or condition (e.g. examination of 22q11 for DiGeorge syndrome or outflow cardiac abnormalities).

Each FISH probe is specific to a region of DNA (and associated syndrome) and, therefore, the syndrome or region for investigation must be specified on the referral card.

FISH investigations are available for most microdeletion syndromes and conditions.

FISH can be undertaken on preparations from cultured or uncultured cells (e.g. prenatal and postnatal investigations) or from paraffin embedded fixed material (e.g. tumour sections).

FISH is a front line test for developmental delay / congenital malformation referrals. It is also commonly used in family follow-up studies and to investigate possible mosaicism.

NHS England National Genomic Test Directory codes

  • R22 Fetus with a likely chromosomal abnormality
  • R26 Likely common aneuploidy
  • R298 Possible structural or mosaic chromosomal abnormality requiring FISH
  • R318 Recurrent miscarriage with products of conception available for testing
  • R401 Common aneuploidy testing - prenatal

Quantitative Fluorescence PCR (QFPCR)

QF-PCR measures the number of alleles for specific regions of DNA and, by examining a series of alleles along a specific chromosome, the copy number for that chromosome can be established.

This test is used as a rapid test to screen for trisomy of chromosome 13, 18 or 21, primarily in prenatal diagnosis or newborns and also fetal losses.

NHS England National Genomic Test Directory codes

  • R22 Fetus with a likely chromosomal abnormality
  • R26 Likely common aneuploidy
  • R314 Ambiguous genitalia presenting neonatally
  • R318 R318 - Recurrent miscarriage with products of conception available for testing
  • R401 Common aneuploidy testing - prenatal