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Paediatric Laboratory Medicine

X Inactivation Analysis

Clinical Significance

In females one of the two X-chromosomes becomes randomly inactivated early in embryogenesis to allow for dosage compensation of X-linked genes. In any one female somatic cell the inactive X may be either the paternal or maternal X chromosome. If the paternal X chromosome is inactivated more frequently than the maternal X chromosome or vice versa, the X inactivation pattern is skewed. If a woman carries a disease-causing mutation on just one of her X chromosomes, she normally would not show signs of the disease. However, skewed X inactivation may result in symptoms of an X-linked disease if the chromosome carrying the mutation is preferentially active. X inactivation is considered skewed if the ratio of the active to inactive X chromosome is less than 10 per cent or greater than 90 per cent.

The highly polymorphic androgen receptor (CAG)n repeat region, located on the X chromosome (Xq11-q12), is used to detect X inactivation. Methylation sensitive enzymes are used to cut the androgen receptor repeat region on the DNA strand. These enzymes digest DNA on the active X but do not cut sites on the inactive X. The quantitative PCR of androgen receptor repeats is compared with and without digestion to determine X inactivation ratio.

Test Name

X Inactivation Analysis

Test Code



Molecular Genetics


AR exon 1 trinucleotide repeat and methylation analysis

External Proficiency Testing


Turn Around Time

2 weeks (Prenatal samples), 2-3 weeks (Pregnancy/Urgent samples), 4-6 weeks (Routine)


X Inactivation Analysis

Specimen Type

Blood; gDNA. 

For details about specimen requirements, please refer to: Specimen Type & Requirements (PDF).

Minimum Specimen Requirements

5-10 mL EDTA or ACD 0.5 mL EDTA (neonate); minimum 10 ug in 100 uL low TE (pH8.0)


Room Temperature

Special Requirements

Special Instructions for Genome Diagnostics Samples

If sample shipment >48 hours, ship on ice.

Approval is not required

CPT Codes


Shipping and Contact Information

The Hospital for Sick Children
Rapid Response Laboratory
170 Elizabeth Street, Room 3642
Toronto, ON
M5G 2G3
Phone: 416-813-7200
Phone: 1-855-381-3212


Interpretation is provided in report

Information Sheet: X Chromosome Inactivation