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Fragile X Syndrome via FMR1 CGG Repeat Expansion

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Repeat Expansion

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
558 FMR1$390 81243 Add to Order
Pricing Comments

At this time, we do not accept saliva, buccal, or prenatal specimens for Fragile X testing. For price of the methylation test in CGG repeat expansion, please contact us for details.

If sequencing with CNV detection is desired, please see this link for Test Code, pricing, and turnaround time information.

Targeted Testing

For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity

FMR1 CGG repeat expansions of >200 are found in 1-2% of patients with developmental delay (Strom et al. 2007). FMR1 CGG repeat expansions are estimated to explain ~99% of FXS cases, with point mutations or deletions in the FMR1 locus accounting for the remaining 1%. However, careful studies which analyze both CGG repeat size and FMR1 gene sequence in FXS patients are lacking (Peprah 2012; Myrick et al. 2014; Monaghan et al. 2013). FMR premutation alleles were found in 2-4% of men with cerebellar ataxia who tested negative for SCA expansions (Brussino et al. 2005; Van Esch et al. 2005). FMR1 premutation alleles were found in 2-8% of idiopathic POI cases (Ferrarini et al. 2013; Bachelot et al. 2009).

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Clinical Features

Fragile X syndrome is the most common genetic cause of intellectual disability in males and the second most common cause in females, with a prevalence of 1:4000 males and 1:6000 females. Fragile X syndrome is characterized by developmental delay, moderate to severe intellectual disability and autistic behaviors. Fragile X syndrome is typically diagnosed at around three years of age when developmental delay becomes pronounced. Physical features of Fragile X syndrome include an elongated face, prominent jaw, broad forehead, prominent ears, macroorchidism in males, flat feet and hyperextensible finger joints (Gallagher and Hallahan 2012). Common behaviors associated with Fragile X syndrome include attention deficit hyperactivity disorder (ADHD), trouble sleeping, anxiety, mood disorders and aggression. Autistic-like behaviors seen in Fragile X syndrome patients include perseveration of speech, motor stereotypies such as hand flapping, restricted interests and poor eye contact. Approximately 30-50% of Fragile X syndrome patients meet the diagnostic criteria for autism, although symptoms tend to be less severe than in patients with idiopathic autism (McCary and Roberts 2013; McDuffie et al. 2015).

Premature Ovarian Failure (POF type 1) or Primary Ovarian Insufficiency (POI) refers to ovarian dysfunction that results in infertility or menopause before the age of 40 in women. Other indications of POF are increased serum FSH and low estradiol levels, indicative of hypoestrogenism. POF can result from follicular depletion or follicular dysfunction (Rafique et al. 2012). Approximately 20% of women who have an FMR1-premutation develop premature ovarian failure (Sullivan et al. 2005; Mailick et al 2014).

Fragile X Tremor/Ataxia Syndrome (FXTAS) is a progressive neurodegenerative disorder. It presents between 60 and 65 years with intention tremor and gait ataxia. MRI studies reveal a white matter hyperintensity of the middle cerebellar peduncle (MCP) in patients with fragile X tremor/ataxia syndrome and this MCP sign is associated with more severe disease progression (Hagerman and Hagerman 2013). Another key finding is the presence of ubiquitin positive intranuclear inclusions in neurons and astrocytes throughout the brain (Hagerman 2013). Both males and females can develop fragile X tremor/ataxia syndrome, but penetrance is higher and disease progression is more severe in males.

Genetics

Fragile X syndrome is inherited in an X-linked recessive manner and is caused by a repeat expansion in the 5'UTR of the FMR1 gene. FMR1 CGG expansions fall into four classes: normal (~5-44 repeats), intermediate (~45-54 repeats), premutation (~55-200 repeats) and full mutation (>200 repeats) (Monaghan et al. 2013). Only individuals with >200 CGG repeats in the FMR1 gene have Fragile X syndrome. More than 99% of Fragile X syndrome cases result from expansion of the CGG repeat located in the 5'-UTR of the FMR1 gene (Monaghan et al. 2013). Large CGG repeats (>200) are generally hypermethylated which leads to transcriptional silencing of the FMR1 gene. Penetrance in males with a full mutation is nearly 100%. Females heterozygous for a full mutation can have phenotypes ranging from mild to severe Fragile X Syndrome depending upon patterns of X-inactivation (Monaghan et al. 2013). Premutation alleles do not result in a Fragile X syndrome phenotype, but they have the ability to expand to a full mutation in a single generation. Females with a premutation allele are at risk for having a child with Fragile X syndrome.

Premature Ovarian Failure (POF1) or Primary Ovarian Insufficiency (POI): The premutation allele is found in roughly 1:200 females (Hagerman and Hagerman 2013). Females with a premutation allele are at risk for developing premature ovarian failure. Approximately 20% of females that carry an FMR1 premutation allele will experience menopause before 40 years of age. Females with a premutation allele of ~80-99 CGG repeats have the highest risk for developing premature ovarian failure (Sullivan 2005).

Fragile X Tremor/Ataxia Syndrome: The premutation allele is found in roughly 1:200 females and 1:400 males worldwide (Hagerman and Hagerman 2013). Both male and female carriers of an FMR1 pre-mutation allele are at risk for Fragile X tremor/ataxia syndrome. The age of onset and severity of this syndrome is correlated with the number of CGG repeats; carriers with >100 repeats are more likely to develop symptoms of Fragile X tremor/ataxia syndrome (Hunter et al. 2012).

FMR1 encodes the fragile-X mental retardation protein (FMRP) which is an RNA binding protein highly expressed in the brain. FMRP binds RNAs and transports them to synapses for local translation (Liu-Yesucevitz et al. 2011). FMRP is predicted to bind to as much as 4% of all mRNA in the brain and acts as a translational repressor. Fragile X syndrome is caused by loss of FMRP and improper translation of neuronal mRNAs (Bagni et al. 2012). FMRP mRNA targets are enriched for genes implicated in intellectual disability and autism spectrum disorders, suggesting a common molecular mechanism (Ascano et al. 2012). Loss of FMRP results in long, thin dendritic spines in the cortex which reduces neuronal contacts and impairs synaptic plasticity. The molecular cause of Fragile X related premature ovarian failure and Fragile X tremor/ataxia syndrome is proposed to be the elevated levels of FMR1 mRNA seen in individuals with premutation alleles. It is hypothesized that either repeat associated non-ATG (RAN) translation of FMR1 mRNA or sequestering of RNA binding proteins by excess FMR1 mRNA underlies disease pathogenesis (Todd et al. 2010; Sellier et al. 2013).

Testing Strategy

Repeat-primed PCR is used as a screening method for the presence or absence of a pathogenic CGG trinucleotide repeat expansion located in the 5' UTR of the FMR1 gene. Of note, this test is not designed to determine the precise number of CGG repeats in pathogenic expansions (CGG repeats >200). A methylation-sensitive PCR assay will be performed on all full mutation alleles (>200 CGG repeats) to determine methylation status.

Indications for Test

Candidates for FMR1 testing include males with intellectual disability and males or females with family history of Fragile X syndrome or intellectual disability of unknown cause. FMR1 testing should also be considered for males with symptoms of Fragile X tremor/ataxia syndrome in which pathogenic variations in the SCA genes have been ruled out, and females with symptoms of Premature Ovarian Failure. Carrier testing is available. At this time, we do not accept prenatal specimens for Fragile X testing.

Gene

Official Gene Symbol OMIM ID
FMR1 309550
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Autism Spectrum Disorders Sequencing Panel with CNV Detection
X-Linked Intellectual Disability Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Ascano M Jr. et al. 2012. Nature. 492: 382-6. PubMed ID: 23235829
  • Bachelot A. et al. 2009. European Journal of Endocrinology / European Federation of Endocrine Societies. 161: 179-87. PubMed ID: 19411303
  • Bagni C. et al. 2012. The Journal of Clinical Investigation. 122: 4314-22. PubMed ID: 23202739
  • Brussino A. et al. 2005. Neurology. 64: 145-7. PubMed ID: 15642922
  • Ferrarini E. et al. 2013. Maturitas. 74: 61-7. PubMed ID: 23107817
  • Gallagher A., Hallahan B. 2012. Journal of Neurology. 259: 401-13. PubMed ID: 21748281
  • Hagerman P. 2013. Acta Neuropathologica. 126: 1-19. PubMed ID: 23793382
  • Hagerman R., Hagerman P. 2013. The Lancet. Neurology. 12: 786-98. PubMed ID: 23867198
  • Hunter JE. et al. 2012. Neuropsychology. 26: 156-64. PubMed ID: 22251309
  • Liu-Yesucevitz L. et al. 2011. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 31: 16086-93. PubMed ID: 22072660
  • Mailick MR. et al. 2014. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics. 165B: 705-11. PubMed ID: 25346430
  • McCary LM., Roberts JE. 2013. Journal of Intellectual Disability Research : Jidr. 57: 803-14. PubMed ID: 22974167
  • McDuffie A. et al. 2015. Journal of Autism and Developmental Disorders. 45: 1925-37. PubMed ID: 24414079
  • Monaghan KG. et al. 2013. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 15: 575-86. PubMed ID: 23765048
  • Myrick LK. et al. 2014. European Journal of Human Genetics : Ejhg. 22: 1185-9. PubMed ID: 24448548
  • Peprah E. 2012. Annals of Human Genetics. 76: 178-91. PubMed ID: 22188182
  • Rafique S. et al. 2012. Obstetrics and Gynecology Clinics of North America. 39: 567-86. PubMed ID: 23182561
  • Sellier C. et al. 2013. Cell Reports. 3: 869-80. PubMed ID: 23478018
  • Strom CM. et al. 2007. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 9: 46-51. PubMed ID: 17224689
  • Sullivan AK. et al. 2005. Human Reproduction. 20: 402-12. PubMed ID: 15608041
  • Todd PK. et al. 2010. Plos Genetics. 6: e1001240. PubMed ID: 21170301
  • Van Esch H. et al. 2005. European Journal of Human Genetics : Ejhg. 13: 121-3. PubMed ID: 15483640
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TEST METHODS

Repeat-Primed PCR and Methylation Specific PCR

Test Procedure

As required, DNA is extracted from the patient specimen.

Repeat-primed PCR

The size of the CGG repeat in the FMR1 gene is determined using an AmplideX  FMR1 PCR kit from Asuragen (Filipovic-Sadic et al. 2010). This kit uses repeat-primed PCR to detect both normal and expanded CGG repeat alleles in the FMR1 gene. The PCR is performed with the following three types of primers:

- Two FMR1 specific primers that flank the CGG repeat region. The reverse primer is fluorescently labeled.

- A forward PCR primer that is complimentary to the CGG repeat. This primer can anneal at multiple sites along the repeat, resulting in a mixture of PCR products of increasing size. These PCR products are called CGG repeat primed peaks.

The two gene specific primers amplify full-length PCR products from each allele. The addition of the third repeat primer allows for detection of CGG repeat primed peaks, spanning from the smallest allele to the largest allele. The presence of repeat primed peaks allow for the detection of a very large CGG expansion, even if a gene specific peak is not detected to PCR dropout.

All PCR products are run on an ABI3730xl sequencer.

Methylation specific PCR

Methylation status of expanded alleles is assessed using an AmplideX  FMR1 mPCR kit from Asuragen (Filipovic-Sadic et al. 2010).  This kit pairs methylation sensitive DNA digestion with  FMR1 specific PCR amplification of the CGG repeat region to determine the methylation status of full mutation alleles.

Analytical Validity

A total of twenty-two samples were used for test validation. These include:

- Two DNA samples from Asuragen
- Ten DNA samples from Coriell Cell Respositories:
- 13 DNA samples previously tested at other laboratories

Control DNA samples from Coriell Cell Respositories:

- NA07538, NA07862, NA06896, NA07543, NA06891, NA06852 , NA06968, NA20234, NA20239, NA18310

Analytical Limitations

The repeat-primed PCR assay is not designed to determine the exact number of repeats in alleles containing over 200 repeats (full mutations). This test has been validated to detect up to 10% mosaicism. Only the methylation status of Full Mutations (>200 CGG repeats) is determined.

Interpretation of the test results is limited by the information that is currently available. Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics. However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Genetic counseling to help to explain test results to the patients and to discuss reproductive or medical options is recommended.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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