Isolated Craniosynostosis; Non-Syndromic Craniosynostosis; Coronal Craniosynostosis

The phenotype of Muenke syndrome varies considerably. Clinical features may include cranial suture synostosis, ocular hypertelorism, ptosis or proptosis, midface hypoplasia, temporal bossing, high-arched palate, strabismus, hearing loss, developmental delay, intellectual disability; carpal bone and/or tarsal bone fusions brachydactyly, broad toes, broad thumbs, and clinodactyly.

Muenke syndrome is inherited in an autosomal dominant manner, but shows reduced penetrance. All individuals are heterozygous for the FGFR3 mutation c.749C>G (p.Pro250Arg).

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of Muenke syndrome (non-syndromic craniosynostosis).
2. Carrier testing:
   1. Although this is an autosomal dominant condition, carrier testing may be relevant to identify non-penetrant mutation carriers.
3. Prenatal testing (technically feasible but not routinely performed – contact MGL to discuss):
   1. In pregnancies of a couple in which one parent has Muenke syndrome.

Bidirectional Sanger sequencing across the c.749C>G (p.Pro250Arg) FGFR3 mutation.

NM_000142.4 The ‘A’ within the initiation codon, ATG, is designated as nucleotide number 1.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays).  

Prenatal Specimens
Prenatal testing REQUIRES LABORATORY CONSULTATION PRIOR TO THE PROCEDURE and can only be ordered by a Medical Geneticist. Contact the laboratory at 604-875-2852 and choose the appropriate option for the Molecular Geneticist on service.
Chorionic Villi: 20 mg.
Direct Amniotic fluid: 25 mL collected in two separate tubes of equal volume.
Cultured Amniocytes: Two (2) 100% confluent T-25 flasks.
DNA extracted from prenatal specimens: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth. Ship samples by overnight courier with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays) as follows:

• Villi – on wet ice or in media at room temperature
• Amniocytes, Amniotic fluid, DNA – at room temperature

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Hereditary Motor and Sensory Neuropathy 1A

Charcot-Marie-Tooth disease is a chronic motor and/or sensory neuropathy typically characterized by distal muscle weakness, sensory loss, and pes cavus deformity. Charcot-Marie-Tooth Type 1A (CMT1A) accounts for ~75% of Charcot-Marie-Tooth type 1 (CMT1), and CMT1 accounts for nearly half of all Charcot-Marie-Tooth disease.

CMT1A is caused by an 1.5 Mb duplication in 17p11.2, which results in the inheritance of three copies of the PMP22 gene. Inheritance is autosomal dominant; 20 – 33% of cases are due to de novo duplications. Rare cases of homozygous duplications (resulting in a total of four copies of PMP22) have been described and, in general, manifest a more severe phenotype than the typical three-copy cases.

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of CMT1.
2. Prenatal testing (technically feasible but not routinely performed – contact MGL to discuss):
   1. Pregnancies to couples in which one person has confirmed CMT1A .
3. Presymptomatic testing
   1. Adults at risk of inheriting CMT1A from a parent may be referred for presymptomatic testing for CMT1A.
   2. Requests to test asymptomatic children who are at risk of developing CMT1A are only accepted following genetic counselling by a recognized genetic service.

Multiplex ligation-dependent probe amplification (MLPA) analysis is carried out with the P033-B2 probe mix (MRC-Holland) to determine the gene dosage (i.e. number of copies) of the PMP22 gene. Note: This assay will detect both CMT1A and HNPP.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: NOT ACCEPTED

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region, promoter mutations, and regulatory element mutations). In rare cases, a point mutation could be detected.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

Rare single nucleotide variants or polymorphisms could lead to false-negative results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Tay-Sachs disease: A progressive neurodegenerative disorder caused by intralysosomal storage of the specific glycosphingolipid GM2 ganglioside. Affected individuals generally die before the age of 4 years. The carrier frequency of this disorder in the Ashkenazi Jewish population is 1/30.

Fanconi anemia type C: A condition characterized by congenital anomalies, aplastic anemia and an increased risk of malignancies. The carrier frequency of this disorder in the Ashkenazi Jewish population is 1/90.

Canavan disease: Characterized by macrocephaly, lack of head control, developmental delays by the age of three to five months, severe hypotonia, and failure to achieve independent sitting, ambulation, or speech. Affected individuals generally live into their teens. The carrier frequency of this disorder in the Ashkenazi Jewish population is 1/40.

Familial dysautonomia: Characterized by gastrointestinal dysfunction, vomiting crises, recurrent pneumonia, altered sensitivity to pain and temperature perception, and cardiovascular instability. The carrier frequency of this disorder in the Ashkenazi Jewish population is 1/30.

All of these conditions have an autosomal recessive inheritance pattern. These conditions have an increased incidence in the Ashkenazi Jewish population, relative to other populations, due to founder mutations. 

In patients of Ashkenazi Jewish ancestry, these mutations account for 98% of Canavan disease alleles; over 99% of Familial dysautonomia alleles; greater than 90% of Fanconi anemia alleles; and 95% of Tay-Sachs disease alleles.

A completed AJ Carrier & Tay Sachs Enzyme Screening Supplemental Info Form must be received before testing will proceed.

1. Carrier testing:
   1. BOTH members of the couple MUST BE or MAY BE of Ashkenazi Jewish ancestry.  If the couple is NOT pregnant, testing should be sequential (a negative result in one member sufficiently reduces the risk such that additional testing is unnecessary).

NOTE: All four conditions are tested and reported; individual tests cannot be requested.  If a couple wishes Tay-Sachs screening only, see AJ Carrier & Tay Sach Enzyme Screening Algorithm.  

1. This test is not indicated for:
   1. Individuals of Ashkenazi Jewish ancestry whose partner is non-Ashkenazi (non-Jewish or Sephardi) (i.e. mixed couples). 
   2. Individuals of Sephardi Jewish or French Canadian ancestry seeking carrier screening for Tay-Sachs disease. 

See AJ Carrier & Tay Sachs Enzyme Screening Algorithm and the SOGC/CCMG Clinical Practice Guideline for further details.

     2. This test is not indicated for children who have not yet reached reproductive age.

     3. This test cannot distinguish homozygotes from heterozygotes and so is not generally useful for diagnostic testing or prenatal diagnosis; consult the on-service Molecular Geneticist. 

The Elucigene Ashplex 1 Assay (Gen-Probe, Inc) is used to assess the c.1274_1277dup, c.805G>A and c.1421+1G>C mutations in the HEXA gene; the c.693C>A and c.854A>C mutations in the ASPA gene; the c.2087G>C and the c.2204+6T>C mutations in the IKBKAP gene; and the c.456+4A>T mutation in the FANCC gene. The normal sequence is not assessed; detection of a mutation in the context of carrier screening is interpreted as heterozygosity for the mutation. Individual mutations/conditions can not be independently tested.

Pregnancy-related/Prenatal

If pregnancy management will be altered, 3 weeks; otherwise, routine TAT.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

A completed AJ Carrier & Tay Sachs Enzyme Screening Supplemental Info Form MUST accompany the requisition.

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., mutations outside the regions tested as described above, large genomic deletions, promoter mutations, regulatory element mutations).

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In rare cases, DNA alterations of undetermined or unclear clinical significance may be identified.

Rare single nucleotide variants or polymorphisms could lead to false-negative results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Thanatophoric Dwarfism; Platyspondylic Skeletal Dysplasia

Thanatophoric dysplasia (TD) is a severe skeletal dysplasia that is usually lethal in the perinatal period. There are 2 types of TD both of which are characterized by micromelia with bowed femurs. In TD type II, moderate to severe cloverleaf skull deformity is virtually always present, while in TD type I, cloverleaf skull deformities of varying severity are observed only occasionally. Other features common to both types of TD include short ribs, narrow thorax, macrocephaly, distinctive facial features, brachydactyly, hypotonia, and redundant skin folds along the limbs. Most infants with TD die of respiratory insufficiency shortly after birth, although rare long-term survivors have been reported.

TD is caused by mutations in the FGFR3 gene. Inheritance is autosomal dominant, although cases are invariably the result of de novo mutations in this lethal condition. Eleven mutations in FGFR3 (p.Arg248Cys; p.Ser249Cys; p.Gly370Cys; p.Ser371Cys; p.Tyr373Cys; p.Lys650Met; p.X807Leu; p. X807Gly; p.X807Arg; p.X807Cys; and p. X807Trp) have been found to account for greater than 99% of cases of TD type I. The missense substitution p.Lys650Glu accounts for all cases of TD type II.

1. Confirmation of diagnosis:
   1. In neonates with clinical features suggestive of TD.
2. Prenatal testing (prenatal diagnosis requests are not normally accepted from physicians other than Medical Geneticists):
   1. When ultrasound findings are suggestive of thanatophoric dysplasia. 
   2. When a couple has had a previous fetus with TD; due to the risk of gonadal mosaicism.

Bidirectional Sanger sequencing of four FGFR3 regions containing the 11 common TD type I mutations and the common TD type II mutation.

NM_000142.4 The ‘A’ within the initiation codon, ATG, is designated as nucleotide number 1.

Pregnancy-related/Prenatal

If pregnancy management will be altered, 3 weeks; otherwise, routine TAT.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays).  

Prenatal Specimens
Prenatal testing REQUIRES LABORATORY CONSULTATION PRIOR TO THE PROCEDURE and can only be ordered by a Medical Geneticist. Contact the laboratory at 604-875-2852 and choose the appropriate option for the Molecular Geneticist on service.
Chorionic Villi: 20 mg.
Direct Amniotic fluid: 25 mL collected in two separate tubes of equal volume.
Cultured Amniocytes: Two (2) 100% confluent T-25 flasks.
DNA extracted from prenatal specimens: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth. Ship samples by overnight courier with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays) as follows:

• Villi – on wet ice or in media at room temperature
• Amniocytes, Amniotic fluid, DNA – at room temperature

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Familial Recurrent Polyneuropathy; Tomaculous Neuropathy

Hereditary Neuropathy with Liability to Pressure Palsies (HNPP) is characterized by repeated focal pressure neuropathies such as carpal tunnel syndrome and peroneal palsy with foot drop, typically with a family history consistent with autosomal dominant inheritance. Prolonged distal nerve conduction latencies is found on electrophysiologic studies of all individuals, symptomatic or not.

In the majority of cases (80%), HNPP is caused a 1.5 Mb contiguous gene deletion at 17p11.2, which includes the PMP22 gene. In the remaining 20%, the condition is caused by a point mutation in the PMP22 gene. Inheritance is autosomal dominant, although 20% of cases arise due to de novo mutations.

1. Confirmation of diagnosis:
   1. In individuals wtih clinical features suggestive of HNPP.
2. Prenatal diagnosis (technically feasible but not routinely performed – contact MGL to discuss):
   1. Pregnancies to couples in which one person has HNPP
3. Presymptomatic testing:
   1. Adults at risk of inheriting HNPP from a parent and who are not yet symptomatic may be referred for predictive testing for HNPP.
   2. Requests to test asymptomatic children who are at risk of developing HNPP are only accepted following genetic counselling by a recognized genetic service.

Multiplex ligation-dependent probe amplification (MLPA) analysis is carried out with the P033-B2 probe mix (MRC-Holland) to determine the gene dosage (i.e. number of copies) of the PMP22 gene. Note: This assay will detect both CMT1A and HNPP.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: NOT ACCEPTED

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region, promoter mutations, and regulatory element mutations). In rare cases, a point mutation could be detected.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

Rare single nucleotide variants or polymorphisms could lead to false-negative results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Machado-Joseph Disease; Olivopontocerebellar Atrophy (OPCA); Cerebelloparenchymal Disease; Menzel type OPCA; Schut-Haymaker type OPCA; Holguin Ataxia; Wadia-Swami Syndrome; Azorean Ataxia; Spinopontine Atrophy; Nigrospinodentatal Degeneration

The spinocerebellar ataxias (SCA) are characterized by slowly progressive gait ataxia, and are often associated with poor coordination of hands, speech, and eye movement.

SCA type 1, 2, 3, 6, and 7 are autosomal dominant conditions caused by expansion of the CAG repeat in ATXN1, ATXN2, ATXN3, CACNA1A, and ATXN7 respectively. 

SCA alleles are classified based on size, and reported based on classification, as outlined below.  Exact repeat sizes are not reported:

SCA1 (ATXN1):

• Normal: ≤38 repeats or 39-44 interrupted repeats
• Full Penetrance (pathogenic): 39-44 uninterrupted repeats or ≥45 repeats

SCA2 (ATXN2)

• Normal: ≤31 repeats
• Uncertain: 32-34 repeats
• Full Penetrance (pathogenic): ≥35 repeats

SCA3 (ATXN3)

• Normal: ≤44 repeats
• Uncertain: 45-~59 repeats*
• Full Penetrance (pathogenic): ≥~60 repeats*

           *The repeat size of the smallest full penetrance pathogenic allele is not well-defined.

SCA6 (CACNA1A)

• Normal: ≤18 repeats
• Uncertain: 19 repeats
• Full Penetrance (pathogenic): ≥20 repeats

SCA7 (ATXN7)

• Normal: ≤33 repeats
• Uncertain: 34-36 repeats
• Full Penetrance (pathogenic): ≥37 repeats

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of SCA1, 2, 3, 6 or 7.
2. Prenatal testing (prenatal diagnosis requests are not normally accepted from physicians other than Medical Geneticists; technically feasible, but not routinely performed – contact MGL to discuss):
   1. Pregnancies at risk of being affected with one of these ataxias
3. Presymptomatic testing:
   1. Adults at risk to develop one of these ataxias due to a molecularly confirmed family history. Predictive testing will only be performed following genetic counselling by a recognized genetic service.

Sizing of the CAG repeats associated with each gene is carried out on an ABI genetic analyzer following fluorescence-based PCR amplification.  Digestion with SfaN1 is performed on SCA1 alleles between 39 – 44 repeats to differentiate between interrupted (normal) and uninterrupted (pathogenic) repeats.  Alleles ≤44 CAG repeats that are interrupted by CAT repeats are normal, whereas alleles with 39-44 uninterrupted CAG repeats are considered fully penetrant (pathogenic).  As required, triplet-primed (tp) PCR is performed for SCA2 and SCA7.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region of the gene, large genomic deletions, promoter mutations, regulatory element mutations). For some trinucleotide repeat disorders, repeat expansions have been described that cannot be amplified by PCR. Consideration should be given to this particularly in cases with severe clinical features or early onset; consult the on-service Molecular Geneticist to discuss specific repeat disorders.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

In certain scenarios of repeat size mosaicism, false negative results may occur. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Fragile X syndrome; Premature Ovarian Insufficiency; Fragile X Associated Tremor/Ataxia Syndrome; Martin Bell syndrome

FMR1-related disorders include fragile X syndrome, fragile X-associated tremor/ataxia syndrome (FXTAS), and FMR1-related premature ovarian insufficiency (POI). Fragile X syndrome is characterized by moderate intellectual disability in males and mild intellectual disability in affected females.  Males may also display a characteristic appearance, macroorchidism after puberty and behavioral abnormalities.  FXTAS may occur in males and, rarely, in females who have an FMR1 premutation, and is characterized by late-onset, progressive cerebellar ataxia and intention tremor.  FMR1-related POI occurs in approximately 20% of females who have an FRM1 premutation.

The FMR1-related disorders are caused by mutations in the FMR1 gene on the X-chromosome, the most common mutation being expansion of the CGG repeat in the 5′ untranslated region of exon 1. Repeat alleles in the FMR1 gene are classified in our lab as:

• Normal: ~5 to ~54 repeats
• Premutation: ~55 to ~200 repeats and unmethylated
• Full mutation: >200 repeats and methylated

More than 99% of individuals with fragile X syndrome have a loss-of-function mutation in the FMR1 gene caused by the expansion of CGG trinucleotide repeats into the full mutation range, which results in aberrant methylation of the FMR1 gene.

Other mutations in FMR1 that cause fragile X syndrome include deletions and point mutations that disrupt RNA splicing, and missense mutations. All individuals with FXTAS or FMR1-related POI have an FMR1 premutation.

1. Confirmation of diagnosis:
   1. Fragile X Syndrome: Individuals of either sex with global developmental delay (GDD) or intellectual disability (ID) of unknown etiology , or autism spectrum disorders (ASD).  Testing females with learning disabilites may also be considered.
   2. FXTAS: Patients over 50 years of age who have progressive cerebellar ataxia and intention tremor in whom other common causes of ataxia have been excluded.
   3. Premature Ovarian Insufficiency: Women with unexplained premature ovarian insufficiency or reproductive or fertility problems associated with an elevated follicle stimulating hormone (FSH) level in the postmenopausal range before the age of 40.
2. Carrier testing. 

   NB: Carriers have the potential for health problems (FXTAS or FMR1-related POI) in addition to the ability to transmit disease to offspring, therefore this testing in an asymptomatic individual is presymptomatic testing.

   1. Adults with a family history of fragile X syndrome, fragile X tremor/ataxia syndrome, or premature ovarian failure (in more than one family member) if the pedigree structure is consistent with X-linked inheritance and the individual is at risk of inheriting the mutated gene. Referral to a medical geneticist for counselling and assessment should be considered in these cases. 
   2. Adults who have at least one male relative with autism or mental retardation/developmental delay of an unknown etiology within a three-generation pedigree, if the pedigree structure is consistent with X-linked inheritance and the individual is at risk of inheriting the mutated gene. 
3. Prenatal testing (prenatal diagnosis requests are not normally accepted from physicians other than Medical Geneticists):
   1. Pregnancies of females known to have an FMR1 mutation.

Population-based carrier screening (i.e., screening in the absence of any other indication) is not covered by Health Insurance BC (BC MSP). Please contact MGL to discuss.

PCR amplification is performed across the CGG repeat region of the FMR1 gene to determine the repeat size.  In some cases, triplet-primed (tp) PCR (Amplidex PCR/CE FMR1 Reagents, Asuragen, Inc) is performed to assess for the presence of expanded alleles. This assay does not assess methylation status; however, in most cases the repeat is sized well into the full mutation range and, thus, hypermethylation can be assumed.  In rare cases, a repeat collection and testing by Southern blot analysis will be recommended.

 For more information, see FAQ

 Please note: MGL reports repeat sizes only when relevant for risk estimate counselling (i.e. premutation range from 55 – ~120 repeats); otherwise, repeats are categorized as normal, premutation, and full mutation only.

Pregnancy-related/Prenatal

If pregnancy management will be altered, 3 weeks; otherwise, routine TAT.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays).  

Prenatal Specimens
Prenatal testing REQUIRES LABORATORY CONSULTATION PRIOR TO THE PROCEDURE and can only be ordered by a Medical Geneticist. Contact the laboratory at 604-875-2852 and choose the appropriate option for the Molecular Geneticist on service.
Chorionic Villi: 20 mg.
Direct Amniotic fluid: 25 mL collected in two separate tubes of equal volume.
Cultured Amniocytes: Two (2) 100% confluent T-25 flasks.
DNA extracted from prenatal specimens: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth. Ship samples by overnight courier with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays) as follows:

• Villi – on wet ice or in media at room temperature
• Amniocytes, Amniotic fluid, DNA – at room temperature

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used.  This method will not detect all mutations (e.g., point mutations in the coding region of the gene, large genomic deletions, promoter mutations, regulatory element mutations). 

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member.  Ideally, this information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In certain scenarios of repeat size mosaicism, false negative results may occur.  If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

Rare single nucleotide variants or polymorphisms could lead to false-negative results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype.  Consult the on-service Molecular Geneticist for approach to testing in such individuals. 

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing.  However, if there is no clinical urgency, the cautious approach is to wait one week post-packed red cell transfusion before collecting a sample for genetic testing.  Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Machado-Joseph Disease; Olivopontocerebellar Atrophy (OPCA); Cerebelloparenchymal Disease; Menzel type OPCA; Schut-Haymaker type OPCA; Holguin Ataxia; Wadia-Swami Syndrome; Azorean Ataxia; Spinopontine Atrophy; Nigrospinodentatal Degeneration

The spinocerebellar ataxias (SCA) are characterized by slowly progressive gait ataxia, and are often associated with poor coordination of hands, speech, and eye movement.

SCA type 1, 2, 3, 6, and 7 are autosomal dominant conditions caused by expansion of the CAG repeat in ATXN1, ATXN2, ATXN3, CACNA1A, and ATXN7 respectively. 

SCA alleles are classified based on size, and reported based on classification, as outlined below.  Exact repeat sizes are not reported:

SCA1 (ATXN1):

• Normal: ≤38 repeats or 39-44 interrupted repeats
• Full Penetrance (pathogenic): 39-44 uninterrupted repeats or ≥45 repeats

SCA2 (ATXN2)

• Normal: ≤31 repeats
• Uncertain: 32-34 repeats
• Full Penetrance (pathogenic): ≥35 repeats

SCA3 (ATXN3)

• Normal: ≤44 repeats
• Uncertain: 45-~59 repeats*
• Full Penetrance (pathogenic): ≥~60 repeats*

           *The repeat size of the smallest full penetrance pathogenic allele is not well-defined.

SCA6 (CACNA1A)

• Normal: ≤18 repeats
• Uncertain: 19 repeats
• Full Penetrance (pathogenic): ≥20 repeats

SCA7 (ATXN7)

• Normal: ≤33 repeats
• Uncertain: 34-36 repeats
• Full Penetrance (pathogenic): ≥37 repeats

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of SCA1, 2, 3, 6 or 7.
2. Prenatal testing (prenatal diagnosis requests are not normally accepted from physicians other than Medical Geneticists; technically feasible, but not routinely performed – contact MGL to discuss):
   1. Pregnancies at risk of being affected with one of these ataxias
3. Presymptomatic testing:
   1. Adults at risk to develop one of these ataxias due to a molecularly confirmed family history. Predictive testing will only be performed following genetic counselling by a recognized genetic service.

Sizing of the CAG repeats associated with each gene is carried out on an ABI genetic analyzer following fluorescence-based PCR amplification.  Digestion with SfaN1 is performed on SCA1 alleles between 39 – 44 repeats to differentiate between interrupted (normal) and uninterrupted (pathogenic) repeats.  Alleles ≤44 CAG repeats that are interrupted by CAT repeats are normal, whereas alleles with 39-44 uninterrupted CAG repeats are considered fully penetrant (pathogenic).  As required, triplet-primed (tp) PCR is performed for SCA2 and SCA7.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region of the gene, large genomic deletions, promoter mutations, regulatory element mutations). For some trinucleotide repeat disorders, repeat expansions have been described that cannot be amplified by PCR. Consideration should be given to this particularly in cases with severe clinical features or early onset; consult the on-service Molecular Geneticist to discuss specific repeat disorders.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

In certain scenarios of repeat size mosaicism, false negative results may occur. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Friedreich ataxia (FRDA) is characterized by slowly progressive ataxia, typically arising in late childhood or early adolescence. Common features include dysarthria, muscle weakness, spasticity in the lower limbs, scoliosis, bladder dysfunction, absent lower limb reflexes, and loss of position and vibration sense. Cardiomyopathy and diabetes mellitus are relatively common.

FRDA is an autosomal recessive condition caused by biallelic pathogenic variants of the frataxin (FXN) gene on chromosome 9q13.  Approximately 95% of patients with Friedreich ataxia are homozygous for an FXN GAA-repeat expansion; the remaining patients are compound heterozygotes for an FXN GAA-repeat expansion and either an inactivating point mutation or deletion of FXN.  To date, no affected individuals with two non-GAA triplet repeat mutations have been reported.

GAA repeat lengths are classified according to their phenotypic expression:

• Normal alleles: 5 – 33 repeats
• Mutable normal allels: 34 – ~65 repeats

The exact boundary between normal and full penetrance alleles has not been determined; alleles at the boundary are assessed further.

• Full penetrance (expanded) alleles: ~66 repeats or greater

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of Friedreich Ataxia.
2. Carrier testing:
   1. Adults at risk to be carriers because of a family history of FRDA.
3. Prenatal testing: (technically feasible, but rarely performed – contact MGL to discuss):
   1. Pregnancies known to be at risk of FRDA and the mutations are known.
4. Presymptomatic testing:
   1. Requests to test asymptomatic children who are at risk of developing FRDA are only accepted following genetic counselling by a recognized genetic service.

PCR and triplet-primed (tp) PCR amplification is performed across the GAA repeat region of the FXN gene to assess for normal and expansion allelles.  

For more information, see FAQ

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region of the gene, large genomic deletions, promoter mutations, regulatory element mutations). For some trinucleotide repeat disorders, repeat expansions have been described that cannot be amplified by PCR. Consideration should be given to this particularly in cases with severe clinical features or early onset; consult the on-service Molecular Geneticist to discuss specific repeat disorders.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

In certain scenarios of repeat size mosaicism, false negative results may occur. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Machado-Joseph Disease; Olivopontocerebellar Atrophy (OPCA); Cerebelloparenchymal Disease; Menzel type OPCA; Schut-Haymaker type OPCA; Holguin Ataxia; Wadia-Swami Syndrome; Azorean Ataxia; Spinopontine Atrophy; Nigrospinodentatal Degeneration

The spinocerebellar ataxias (SCA) are characterized by slowly progressive gait ataxia, and are often associated with poor coordination of hands, speech, and eye movement.

SCA type 1, 2, 3, 6, and 7 are autosomal dominant conditions caused by expansion of the CAG repeat in ATXN1, ATXN2, ATXN3, CACNA1A, and ATXN7 respectively. 

SCA alleles are classified based on size, and reported based on classification, as outlined below.  Exact repeat sizes are not reported:

SCA1 (ATXN1):

• Normal: ≤38 repeats or 39-44 interrupted repeats
• Full Penetrance (pathogenic): 39-44 uninterrupted repeats or ≥45 repeats

SCA2 (ATXN2)

• Normal: ≤31 repeats
• Uncertain: 32-34 repeats
• Full Penetrance (pathogenic): ≥35 repeats

SCA3 (ATXN3)

• Normal: ≤44 repeats
• Uncertain: 45-~59 repeats*
• Full Penetrance (pathogenic): ≥~60 repeats*

           *The repeat size of the smallest full penetrance pathogenic allele is not well-defined.

SCA6 (CACNA1A)

• Normal: ≤18 repeats
• Uncertain: 19 repeats
• Full Penetrance (pathogenic): ≥20 repeats

SCA7 (ATXN7)

• Normal: ≤33 repeats
• Uncertain: 34-36 repeats
• Full Penetrance (pathogenic): ≥37 repeats

1. Confirmation of diagnosis:
   1. In individuals with clinical features suggestive of SCA1, 2, 3, 6 or 7.
2. Prenatal testing (prenatal diagnosis requests are not normally accepted from physicians other than Medical Geneticists; technically feasible, but not routinely performed – contact MGL to discuss):
   1. Pregnancies at risk of being affected with one of these ataxias
3. Presymptomatic testing:
   1. Adults at risk to develop one of these ataxias due to a molecularly confirmed family history. Predictive testing will only be performed following genetic counselling by a recognized genetic service.

Sizing of the CAG repeats associated with each gene is carried out on an ABI genetic analyzer following fluorescence-based PCR amplification.  Digestion with SfaN1 is performed on SCA1 alleles between 39 – 44 repeats to differentiate between interrupted (normal) and uninterrupted (pathogenic) repeats.  Alleles ≤44 CAG repeats that are interrupted by CAT repeats are normal, whereas alleles with 39-44 uninterrupted CAG repeats are considered fully penetrant (pathogenic).  As required, triplet-primed (tp) PCR is performed for SCA2 and SCA7.

Blood: 4 mL EDTA is optimal (Minimum: 1 mL EDTA)
DNA: 100 μL at 200 ng/μL is optimal (Minimum: 30 μL at 200 ng/μL)

Label each sample with three patient identifiers; preferably patient name, PHN, and date of birth and ship to the address below. Samples should be shipped at room temperature with a completed MGL Requisition to arrive Monday to Friday (not on Canadian statutory holidays). 

Testing is only available to residents of Canada, except in very specific circumstances where testing is urgent or emergent.  Payment is not required when requests are made for individuals who are insured by Health Insurance BC (administered through the BC Medical Services Plan (MSP)) AND eligible for testing according to the test utilization guidelines / policy. If the individual undergoing testing is not insured by these providers or does not meet utilization guidelines or policy, please complete a billing form; testing will only commence after receipt of billing informationTest prices can be found here.

Molecular genetic testing is limited by the current understanding of the genome and the genetics of a particular disease, as well as by the method of detection used. This method will not detect all mutations (e.g., point mutations in the coding region of the gene, large genomic deletions, promoter mutations, regulatory element mutations). For some trinucleotide repeat disorders, repeat expansions have been described that cannot be amplified by PCR. Consideration should be given to this particularly in cases with severe clinical features or early onset; consult the on-service Molecular Geneticist to discuss specific repeat disorders.

For carrier/predictive testing due to family history, it is generally important to first document the gene mutation in an affected or carrier family member. This information should be provided to the laboratory for assessment of whether the assay is appropriate for detection of the familial mutation, and to aid in the interpretation of data.

In some cases, DNA alterations of undetermined or unclear clinical significance may be identified.

In certain scenarios of repeat size mosaicism, false negative results may occur. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

Rare single nucleotide variants or polymorphisms could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, consult the on-service Molecular Geneticist.

A previous bone marrow transplant from an allogenic donor will result in molecular data that reflects the donor genotype rather than the recipient (patient) genotype. Consult the on-service Molecular Geneticist for approach to testing in such individuals.

Transfusions performed with packed red blood cells will generally not affect the outcome of molecular genetic testing. However, if there is no clinical urgency, the cautious approach is to wait one week post packed red cell transfusion before collecting a sample for genetic testing. Consult the on-service Molecular Geneticist as needed.

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.