Genetic Tests Available

Test available as expedited (including prenatal and newborn) as well as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20 mg

Cultured amniocytes or CVS: 2xT25 flasks

DNA: 200ng (minimum concentration: 50ng/ul)

Test details

A Methylation-specific MLPA assay (SALSA MLPA ME028 Prader Willi/Angelman probemix, MRC Holland) is used to assess the methylation pattern and the copy number changes in the PWCR. This assay can identify greater than 99% of PWS cases due to deletion, UPD, or ID; however, it is unable to distinguish between UPD and ID due to epimutations. Recurrent risk in a family is dependent on the underlying mechanism in the proband. Follow-up studies are usually required to determine the underlying mechanism, when an individual is positive by this assay.

Test limitations

A negative result does not rule out a diagnosis of Angelman Syndrome, since up to 25% of cases are due to mutations in the UBE3A gene that do not result in abnormal methylation at the AS locus.

Turnaround time

Expedited: 2 weeks

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 
(For Prenatal/cord blood: separate MCC requisition required)

Additional requirements

ONLY samples referred through Neonatology, Cardiology or Genetics Clinics are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. A maternal blood sample (5 mL in EDTA tube) is also required to rule out maternal cell contamination.

Gene content

Lists of variants analyzed outside of coding regions

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Sensitivity/specificity and test limitations

The test has >99.9% sensitivity for single nucleotide variants (SNVs) and small indels (<15bp), and >95% for deletions and duplications >1 exon. Larger indels (15bp to exon size) and single exon CNVs are detected with reduced sensitivity.

This assay detects genetic changes in the tested genes/loci based on current understanding of the disorder. A normal result does not rule out a genetic disorder, as some DNA abnormalities may be undetectable with this technology. Test results should be interpreted in the context of clinical findings, family history, and other relevant data. Inaccurate results may occur if DNA quality is suboptimal or extracted by other laboratories. The assay has limited ability to detect certain variants, such as low-level mosaicism of SNVs (<15% variant allele frequency) and CNVs, low heteroplasmy in mtDNA, and variants in high complexity genomic regions. It cannot detect structural variants, CNVs on chromosomes affected by aneuploidies or large deletions/duplications, variants affecting TTN exons 174-196, or CNVs in MT-TI.

Turnaround times

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations) 

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Cardiology or Genetics Clinic are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Genes included in the ATS Next-Generation Sequencing (NGS) panel

Gene: SLC2A10

Test details

DNA results are based on the analysis of the coding sequence and 10 base pairs immediately adjacent to each exon of SLC2A10 (NM_030777.3). In addition, several deep intronic regions are analyzed for the presence of likely pathogenic, pathogenic and/or other clinically relevant variants. This test is performed by oligonucleotide-based target capture (Illumina DNA Prep with Enrichment kit and Twist Custom Panel Probes, Twist Biosciences) followed by next generation sequencing using the NextSeq 2000 instrument (Illumina). Additional Sanger sequencing is performed for regions that have insufficient coverage, and to confirm clinically significant variants and variants of unknown significance when applicable.

Test limitations

This assay is based on the current state of knowledge of the genetic basis of this disorder and designed to identify constitutional genetic changes in the tested genes/loci (see Test Details).

Turnaround time

Routine: 10 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations)

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Neonatology, Cardiology or Genetics Clinics are accepted

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. A maternal blood sample (5 mL in EDTA tube) is also required to rule out maternal cell contamination.

Gene contents

SCN5A-including variants outside of coding regions: c.612-189C>T, c.612-229T>G, c.612-233G>C (NM_001267550.2)

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Sensitivity/specificity and test limitations

The test has >99.9% sensitivity for single nucleotide variants (SNVs) and small indels (<15bp), and >95% for deletions and duplications >1 exon. Larger indels (15bp to exon size) and single exon CNVs are detected with reduced sensitivity.

This assay detects genetic changes in the tested genes/loci based on current understanding of the disorder. A normal result does not rule out a genetic disorder, as some DNA abnormalities may be undetectable with this technology. Test results should be interpreted in the context of clinical findings, family history, and other relevant data. Inaccurate results may occur if DNA quality is suboptimal or extracted by other laboratories. The assay has limited ability to detect certain variants, such as low-level mosaicism of SNVs (<15% variant allele frequency) and CNVs, low heteroplasmy in mtDNA, and variants in high complexity genomic regions. It cannot detect structural variants, CNVs on chromosomes affected by aneuploidies or large deletions/duplications.

Turnaround time

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations)

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Cardiology or Genetics Clinics are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. A maternal blood sample (5 mL in EDTA tube) is also required to rule out maternal cell contamination.

Gene content

Lists of the variants analyzed outside of coding regions

Historial Panels

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Requisition form

Cardiomyopathy and Arrhythmia Requisition - available via the Requisitions and forms page.

Test available as expedited (including prenatal, newborns and new acute leukemias) as well as routine.

Sample requirements

Blood: Sodium Heparin (green top) tube 

Bone marrow: Sodium Heparin (green top) tube

Adults and children: 1 x 10 mL 

Newborns: 1 x 3 mL 

Prenatal Samples: click here for more details 

Amniotic Fluid: 1 x 20 mL 

Chorionic villi: 10-20 mg 

Oncology lymph nodes/tumour biopsies/skin biopsies: 3-4 mm fresh tissue biopsy (sterile container with culture medium). Click for more details on the Sample requirements and shipping page. 

Test details

Chromosome analysis or karyotyping, also known as conventional cytogenetic testing, is used to detect numerical and/or large structural chromosome abnormalities. It requires viable dividing cells from sterile samples, and is available on postnatal, prenatal and oncology samples.

Clinical indications

IMPORTANT: For individuals/newborns with intellectual/learning disability, autism spectrum disorder, developmental delays, and/or congenital abnormalities that are not suggestive of a common chromosome aneuploidy involving chromosomes 13/18/21/X/Y, chromosome analysis is not the appropriate test. Refer to Microarray analysis. 

IMPORTANT: For products of conceptions (POCs), intrauterine fetal deaths (IUFDs) and stillbirths, chromosome analysis is not available. Refer to Rapid Aneuploid Detection (RAD) and Microarray analysis. 

Congenital anomalies suggestive of common chromosome aneuploidy or large chromosome abnormality

Detection of acquired chromosome abnormalities in some neoplasias 

Disorders of sex development 

Infertility 

Molar pregnancy 

Prenatal diagnosis (maternal age >=40 for singletons or >=35 for multiples at delivery; positive prenatal screening; fetal ultrasound anomalies; family history) 

Recurrent pregnancy losses (minimum of three miscarriages); specimens from both partners required; or 3+ unsuccessful in-vitro fertilization (IVF) treatment cycles with unexplained infertility; or 1-2 miscarriages with history of infertility 

Screen for familial chromosome abnormalities (please provide a copy of the relevant cytogenetic report(s) whenever possible) 

Newborns with features suggestive of a common chromosome aneuploidy involving chromosomes 13/18/21/X/Y, in the absence of prenatal testing/screening 

Individuals/newborns with clinical features suggestive of chromosome mosaicism 

Sex chromosome abnormality features: primary amenorrhea; sperm abnormalities (azoospermia, oligospermia); primary ovarian insufficiency/premature ovarian failure; hypogonadism or cryptorchidism; ambiguous genitalia

Test limitations

Detection of structural chromosome anomalies depends on sample type, limited to approximately 10 Mb in postnatal samples. Cannot rule out molecular defects, point mutations, UPD, subtelomeric rearrangements. Detection of tissue-specific mosaicism is limited. Detection is performed by conventional banding methods on metaphase cell preparations visible by oil-immersion light microscopic methods (1000x total magnification). A normal karyotype does not exclude the possibility of a subtle structural rearrangement. Cannot detect imprinting defects or epigenetic modifications. Detection of alterations can also be limited by non-proliferation of an abnormal clone, low-level mosaicism, and alterations below the reporting threshold/resolution of cytogenomic testing.

Turnaround time

Prenatal

• Amniotic fluid: 2 weeks
• CVS: 3 weeks
• Cord blood: 1 week

Postnatal

• Newborn: 1 week
• Couple where partner is pregnant: 1-2 weeks 
• Routine: 4 weeks

Oncology

• Acute leukemia at diagnosis: 2 weeks
• Other indications: 3 weeks

Requisition form

Standard Cytogenetic Requisition - available via the Requisitions and forms page. 

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Neonatology, Cardiology or Genetics Clinics are accepted

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. A maternal blood sample (5 mL in EDTA tube) is also required to rule out maternal cell contamination.

Gene content

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Sensitivity/specificity and test limitations

The test has >99.9% sensitivity for single nucleotide variants (SNVs) and small indels (<15bp), and >95% for deletions and duplications >1 exon. Larger indels (15bp to exon size) and single exon CNVs are detected with reduced sensitivity.

This assay detects genetic changes in the tested genes/loci based on current understanding of the disorder. A normal result does not rule out a genetic disorder, as some DNA abnormalities may be undetectable with this technology. Test results should be interpreted in the context of clinical findings, family history, and other relevant data. Inaccurate results may occur if DNA quality is suboptimal or extracted by other laboratories. The assay has limited ability to detect certain variants, such as low-level mosaicism of SNVs (<15% variant allele frequency) and CNVs, low heteroplasmy in mtDNA, and variants in high complexity genomic regions. It cannot detect structural variants, CNVs on chromosomes affected by aneuploidies or large deletions/duplications.

Turnaround time

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations) 

Requisition form

You can find the requisition form for this test here.

Test available as routine only.

Sample requirements

Blood: EDTA (purple top) tube.

Adult: 2 x 6 mL

Child or infant: 2 x 3 mL

Prenatal samples are NOT accepted for FSHD testing.

Acceptance criteria:

1. Blood collected in EDTA received within 5 days of collection and stored/shipped at approximately 4 degrees celsius. 

Test details

Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is an autosomal dominant form of muscular dystrophy caused by a contraction of the D4Z4 repeat array in the subtelomeric region of chromosome 4q35 on a chromosome 4 permissive haplotype (4qA). Normal alleles are D4Z4 repeat arrays with ≥12 units or with any number of repeat units on a non-permissive haplotype (4qB). Reduced-penetrance alleles are D4Z4 repeat arrays with 10 or 11 units on 4qA. Full-penetrance alleles are D4Z4 repeat arrays with >1 and ≤9 units on 4qA. High molecular weight DNA is extracted and fluorescently labeled (SP Blood & Cell Culture DNA Isolation and DLS DNA Labeling, Bionano Genomics). Optical genome mapping of the labeled DNA is performed on the Bionano Saphyr system. Bionano EnFocus FSHD analysis pipeline is used to size the D4Z4 repeat arrays on chromosomes 4 and 10, as well as to assign the permissive and non-permissive haplotypes. The accuracy of sizing is approximately +/- 1 unit. Copy number variants in the proximity of the SMCHD1 gene on chromosome 18 may also be detected and reported.

Test limitations

The analytical sensitivity of this assay to size pathogenic D4Z4 repeat arrays and assign haplotypes is approximately 100%. However, for extremely large repeat arrays (typically >50 units) there may not be molecules long enough to span the full D4Z4 array and the distal haplotype region. As a result, these large repeats may not be detectable or an estimate on the lower bound of the repeat size is reported and the haplotype is reported as unknown. This assay can identify approximately 95% individuals affected with FSHD caused by a contraction of D4Z4 repeats at 4q35. A negative result does not rule out a diagnosis of FSHD due to the possibility of co-occurrence of a pathogenic SMCHD1 variant and a permissive 4qA haplotype. Rare events, when disease-causing sequence elements translocate from chromosome 4 to chromosome 10 (PMID 33436523, 20724583) can result in a false negative result.

Turnaround time

Routine: 8 weeks

Requisition form

You can find the requisition form for this test here.

Eligibility requirements for OHIP patients only: Patients must reside in Champlain and Southern/Western/Northern Ontario catchment areas. Samples are otherwise accepted across Canada and internationally, with the exception of the United States.

Test available as expedited (including prenatal and newborn) as well as routine

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2x 3ml

Infant (<1 yr of age): 1 x3 mL

Cultured amniocites only (CVS not accepted): 2xT25 flasks

DNA: 3000-5000ng(minimum concentration 200ng/ul)

Additional requirements

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Test details

PCR amplification of the CGG repeat using the FRAX kit from Asuragen and in some cases Southern blot analysis is used to determine the CGG repeat number.

Test limitations

It is estimated that >99% of Fragile X syndrome cases have an expansion of the CGG repeat in the 5' untranslated region of the FMR1 gene. The remaining cases have deletions or point mutations within the FMR1 gene. Therefore, a normal result does not rule out a diagnosis of Fragile X syndrome.

Turnaround time

Expedited: 2 weeks
Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Eligibility requirements for OHiP patients only: Patients must reside in Champlain and Southern/Western/Northern Ontario catchment areas. Samples are otherwise accepted across Canada and internationally, with the exception of the United States.

Test available as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult only: 2x 6 mL

DNA: 100ng (minimum concentration 50ng/ul)

Test details

PCR amplification of the CGG repeat using the FRAX kit from Asuragen and in some cases Southern blot analysis is used to determine the CGG repeat number.

Test limitations

Testing is recommended for individuals with symptoms and/or family history of FMR1-related disorders. Penetrance is not complete, and not all individuals with FMR1 premutations will develop symptoms of FXTAS.

Turnaround time

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Eligibility requirements for OHIP patients only: Patients must reside in Champlain and Southern/Western/Northern Ontario catchment areas. Samples are otherwise accepted across Canada and internationally, with the exception of the United States.

Test available as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult only: 2x 6 mL

DNA: 100ng (minimum concentration: 50ng/ul)

Test details

PCR amplification of the CGG repeat using the FRAX kit from Asuragen and in some cases Southern blot analysis is used to determine the CGG repeat number.

Test limitations

Testing is recommended for individuals with symptoms and/or family history of FMR1-related disorders. Penetrance is not complete, and not all individuals with FMR1 premutations will develop symptoms of FXTAS.

Turnaround time

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Eligibility requirements for OHIP patients only: Patients must reside in Champlain or Northern Ontario catchment areas. Samples are otherwise accepted across Canada and internationally, with the exception of the United States.

Test available as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult only: 2 x 6mL

200 ng (minimum concentration: 50ng/ul)

Test details

HFE sequences are amplified using the polymerase chain reaction and digested with appropriate restriction enzymes to detect both the p.Cys282Tyr and p.His63Asp mutations.

Test limitations

Approximately 88% of hemochromatosis cases are caused by two mutations in the HFE gene. As ~ 7% of patients do not have the mutations listed, a negative result does not rule out a diagnosis of hemochromatosis.

Turnaround time

Routine: 6 weeks

Referral and more information

You can find the requisition form for this test here

Find more information on Hereditary Hemochromatosis here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements:

ONLY samples referred through Neonatology, Cardiology or Genetics Clinic are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Gene contents

Lists of variants outside of coding regions

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Sensitivity/specificity and test limitations

The test has >99.9% sensitivity for single nucleotide variants (SNVs) and small indels (<15bp), and >95% for deletions and duplications >1 exon. Larger indels (15bp to exon size) and single exon CNVs are detected with reduced sensitivity.

This assay detects genetic changes in the tested genes/loci based on current understanding of the disorder. A normal result does not rule out a genetic disorder, as some DNA abnormalities may be undetectable with this technology. Test results should be interpreted in the context of clinical findings, family history, and other relevant data. Inaccurate results may occur if DNA quality is suboptimal or extracted by other laboratories. The assay has limited ability to detect certain variants, such as low-level mosaicism of SNVs (<15% variant allele frequency) and CNVs, low heteroplasmy in mtDNA, and variants in high complexity genomic regions. It cannot detect structural variants, CNVs on chromosomes affected by aneuploidies or large deletions/duplications.

Turnaround time

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations)

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Cardiology or Genetics Clinic are accepted

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Gene contents

Genes: SLC2A10, SMAD2, SMAD3, TGFB2, TGFB3, TGFBR1, and TGFBR2

Including MLPA of: TGFBR1 and TGFBR2

Test details

DNA results are based on the analysis of the coding sequence and 10 base pairs immediately adjacent to each exon of the relevant genes known to be associated with LDS (see Genes included in LDS). In addition, several deep intronic regions are analyzed for the presence of likely pathogenic, pathogenic and/or other clinically relevant variants. This test is performed by oligonucleotide-based target capture (Illumina DNA Prep with Enrichment kit and Twist Custom Panel Probes, Twist Biosciences) followed by next generation sequencing using the NextSeq 2000 instrument (Illumina). Additional Sanger sequencing is performed for relevant regions that have insufficient coverage, and to confirm clinically significant variants and variants of unknown significance when applicable. To detect large genomic deletions and duplications, multiplex ligation-dependent probe amplification (MLPA) using the MRC Holland MLPA kit for analysis of TGFBR1 and TGFBR2 (P148) is performed.

Test limitations

This array is based on the current state of knowledge of the genetic basis of this disorder and designed to identify constitutional genetic changes in the tested genes/loci (see Test Details). This analysis detects >99% of variants within the tested genes.

Turnaround time

Routine: 10 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations)

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Neonatology, Cardiology or Genetics Clinics are accepted

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. A maternal blood sample (5 mL in EDTA tube) is also required to rule out maternal cell contamination.

Gene content

Genes: Genes: CACNA1C, CALM1, CALM2, CALM3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNQ1, SCN5A, TECRL, TRDN

List of variants analyzed outside of coding regions

Test details

DNA results are obtained using targeted probe-based capture (Twist Biosciences) and sequencing on a NextSeq 1000/2000. Primary and secondary analysis is performed using Illumina’s DRAGEN Bio-IT Platform. Sanger sequencing is performed for regions of interest that are not captured or have insufficient coverage (<20X). Emedgene software (Illumina) is used for tertiary analysis, focusing on protein-coding exons, exon-intron boundaries, and specific deep intronic variants. Variants that do not meet internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, qPCR, or MLPA). Sequence variants are reported according to the Human Genome Variation Society (HGVS) guidelines. Copy number variants (CNVs) are reported based on approximate chromosome coordinates, with precise breakpoints potentially differing. SNVs and CNVs are classified based on ACMG/AMP (PMIDs 25741868, 29300372), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group, and/or CHEO-specific guidelines. For questions regarding specific gene coverage, methodology, or interpretation, please contact the laboratory directly.

Sensitivity/specificity and test limitations

The test has >99.9% sensitivity for single nucleotide variants (SNVs) and small indels (<15bp), and >95% for deletions and duplications >1 exon. Larger indels (15bp to exon size) and single exon CNVs are detected with reduced sensitivity.

This assay detects genetic changes in the tested genes/loci based on current understanding of the disorder. A normal result does not rule out a genetic disorder, as some DNA abnormalities may be undetectable with this technology. Test results should be interpreted in the context of clinical findings, family history, and other relevant data. Inaccurate results may occur if DNA quality is suboptimal or extracted by other laboratories. The assay has limited ability to detect certain variants, such as low-level mosaicism of SNVs (<15% variant allele frequency) and CNVs, low heteroplasmy in mtDNA, and variants in high complexity genomic regions. It cannot detect structural variants, CNVs on chromosomes affected by aneuploidies or large deletions/duplications.

Turnaround time

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations)

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Cardiology or Genetics Clinic are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Gene content

Gene: FBN1
Including MLPA of FBN1

Test details

DNA results are based on the analysis of the coding sequence and 10 base pairs immediately adjacent to each exon of FBN1. In addition, several deep intronic regions are analyzed for the presence of likely pathogenic, pathogenic and/or other clinically relevant variants. This test is performed by oligonucleotide-based target capture (Illumina DNA Prep with Enrichment kit and Twist Custom Panel Probes, Twist Biosciences) followed by next generation sequencing using the NextSeq 2000 instrument (Illumina). Additional Sanger sequencing is performed for relevant regions that have insufficient coverage, and to confirm clinically significant variants and variants of unknown significance when applicable. To detect large genomic deletions and duplications, multiplex ligation-dependent probe amplification (MLPA) using the 2 available MRC Holland MLPA kits for analysis of FBN1 (P065-Marfan 1, P066-Marfan 2) is performed.

Test limitations

This analysis detects >99% of variants within FBN1. Mutations in FBN1 represent the most common cause (70-90%) of classic Marfan syndrome. As this test does not detect all clinically significant variants associated with this disorder, it is also possible that a variant in another gene not tested is present.

Turnaround time

Routine: 10 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations) 

Requisition form

You can find the requisition form for this test here.

Test available as prenatal.

Sample requirements

Blood: EDTA (purple top) tube

Adult only: 1x 10 mL

DNA: 50ng (Minimum concentration 25ng/ul

Test details

The ABI Identifier kit is used to analyze 15 polymorphic markers in prenatal and parental DNA samples to assess whether the prenatal DNA sample extracted from amniocytes or chorionic villi is contaminated with DNA of maternal origin.

Test limitations

This assay is able to detect maternal cell contamination at levels as low as 5%.

Turnaround time

Prenatal: 2 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 1x 10 mL

Infant (<1 yr of age): 1 x3 mL

Products of Conception - restricted service: click here for more details

An intact fetus will not be accepted by the Cytogenetics section of the Genetics Diagnostic Laboratory

Products of Conception (POCs), intrauterine fetal deaths (IUFDs) and stillbirths MUST be sent to a pathology laboratory, where they will be prepared and then automatically transferred to the CHEO Genetics Diagnostic Laboratory for testing. Completed requisitions for both the Pathology AND Genetics Diagnostic Laboratories are required.

DNA: Please contact the laboratory for more information.

Test details

Genomic microarray testing detects copy number variants (CNVs) and is the recommended first-tier test for intellectual disability, developmental delay, autism spectrum disorders, and congenital abnormalities not suggestive of common chromosome aneuploidies. Please review the Microarray testing FAQs prior to ordering testing. The CHEO Genetics Diagnostic Laboratory uses the CytoscanHD assay, which contains approximately 1.9 million copy number oligonucleotide probes and approximately 750,000 SNP probes. The analysis is based upon the human genome build 19 (GRCh37/hg19). Postnatal* samples are analyzed at a resolution of 50kb for copy number gains and losses across the genome with a minimum of 25 oligonucleotide probes. Additionally, long contiguous stretches of homozygosity (LCSH) of 5Mb or more on autosomes are reported if overlapping with a known imprinted region, involving an entire chromosome or more than one region of the same chromosome, or if LCSH represents 5% or more of the autosomal genome. Samples proceeding to microarray testing are analysed at a resolution of 500kb for copy number losses and 1000kb for copy number gains across the genome with a minimum of 25 oligonucleotide probes; regions known or suspected to be clinically significant are analysed at a resolution of 50kb with a minimum of 25 oligonucleotide probes. Additionally, long contiguous stretches of homozygosity (LCSH) of 10Mb or more on autosomes are reported if overlapping with a known imprinted region, involving an entire chromosome or more than one region of the same chromosome, or if LCSH represents 5% or more of the autosomal genome.

*For samples from POC/IUFD/stillbirth, microarray testing is only performed on samples with a normal or uninformative RAD result. Samples proceeding to microarray testing are analysed at a resolution of 500kb for copy number losses and 1000kb for copy number gains across the genome with a minimum of 25 oligonucleotide probes; regions known or suspected to be clinically significant are analysed at a resolution of 50kb with a minimum of 25 oligonucleotide probes. Additionally, long contiguous stretches of homozygosity (LCSH) of 10Mb or more on autosomes are reported if overlapping with a known imprinted region, involving an entire chromosome or more than one region of the same chromosome, or if LCSH represents 5% or more of the autosomal genome.

Test limitations

Copy number variants (CNVs) below the thresholds stated above may not be detected by this analysis. Unless potentially clinically relevant, heterozygous copy number losses implicating autosomal recessive genes (carrier status) are not routinely reported, nor are copy number variants void of known coding genes at the time of reporting. The CytoscanHD assay cannot detect balanced rearrangements (translocations, inversions, insertions) and is not designed to have coverage of all gene exons; it cannot detect sequence variants, imprinting defects, or epigenetic modifications, nor imbalances in regions not represented on the microarray. This assay is not a diagnostic test for uniparental disomy (UPD): it is not able to detect uniparental heterodisomy, and the sensitivity to detect uniparental isodisomy has not been validated. The assay is not designed to detect low-level mosaicism, and the sensitivity to detect mosaicism has not been established. The analysis based on our current understanding of the genome and may not include all genes related to a specific phenotype.

Turnaround time

Expedited: 2 weeks

Routine: 6 weeks

Requisition and more information

You can find the requisition form for this test here.

Find additional information for healthcare providers.

Test available as expedited (including prenatal and newborn) as well as routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

Additional requirements

Copies of the genomic microarray report and all other relevant genetic tests performed on proband need to be attached to the referral when ordering follow-up microarray analysis.

Testing will only be initiated when all necessary samples from family members have been received.

Test details

Microarray follow up testing by fluorescence in situ hybridization (FISH) is the recommended method for familial investigations of CNVs detected by Genomic Microarray. Metaphase FISH testing can detect structural rearrangements such as inversion or translocation that when unbalanced, may cause copy number variants. FISH analysis on interphase nuclei and metaphase chromosomes using appropriate FISH probes (custom RP11 Bacterial Artificial Chromosomes or commercially available probes) are chosen based on the chromosome area of interest.

Test limitations

Testing can only detect abnormalities involving the locus targeted by the FISH probe. Hybridization patterns may influence the interpretation of FISH results and in some instances, reflex to Microarray follow up qPCR testing may be required.

Turnaround time

Expedited: 4 weeks

Routine: 8 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited and routine. Prenatal testing is not available.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

DNA: Please contact the laboratory for more information

Additional requirements

Copies of the genomic microarray report and all other relevant genetic tests performed on proband need to be attached to the referral when ordering follow-up microarray analysis.

Testing will only be initiated when all necessary samples from family members have been received.

Test details

Two custom primer pairs are designed based on the genomic coordinates for each copy number variation to be investigated. Quantification of the genomic region of interest is performed relative to a reference DNA, with a positive and normal control assayed in parallel.

Test limitations

This test cannot detect structural rearrangements and only copy number variations affecting the labeled region can be detected. The sensitivity and specificity of each custom primer has not been established, and the presence of SNPs impeding DNA amplification and affecting quantification cannot be ruled-out. This assay is not designed to detect mosaicism. As such, whenever possible, follow-up testing by fluorescence in situ hybridization (FISH) is the recommended method for testing of CNVs detected by Genomic Microarray.

Turnaround time

Expedited: 4 weeks

Routine: 8 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited (including prenatal and newborn) as well as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

Cultured amniocytes or CVS: 2xT25 flasks

DNA: 3000 – 5000ng (minimum concentration: 200ng/ul)

Additional requirements

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5mL in EDTA tube) also required to rule out maternal cell contamination.

Test details

DNA results are based on analysis of the number of DMPK CTG repeats and in some cases, hybridization of EcoRI digested DNA with the probe pGB2.2. The CTG repeat length is assessed by PCR fragment analysis to identify alleles with less than ~100 repeats, and Southern Blot analysis (BglI digestion and probed with GeneProber GLDM4, Gene Link) to identify alleles with more than ~100 repeats. The analytical sensitivity of this assay to detect CTG repeat expansion is approximately 100%; rare polymorphisms or other technical reasons may result in a false negative result. Almost all individuals with myotonic dystrophy type 1 have a CTG trinucleotide repeat expansion; therefore, the clinical sensitivity of this assay is approximately 100%.

Test limitations

As a small proportion of individuals with symptoms of myotonic dystrophy do not have a CTG expansion, a negative result does not rule out this diagnosis. In those cases, a diagnosis of DM2 should be considered.

Turnaround time

Expedited: 3 weeks

Routine: 8 weeks

Requisition form

You can find the requisition form for this test here.

Test available as routine only.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

DNA: 300ng (minimum concentration: 50ng/ul)

Peripheral blood samples must be received by the Laboratory within 7 days of being drawn to be accepted for this test.

Test details

Regular PCR is performed using primers flanking the repeat motif and repeat-primed PCRs are performed to detect the presence of the expanded allele that is not amplifiable by the regular PCR.

Test limitations

The analytical sensitivity of this assay to detect the CCTG repeat expansion is approximately 100%; however, PCR based assays are unable to size the CCTG repeat expansion and rare polymorphisms or other technical reasons may result in a false negative result.

Turnaround time

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Test available as routine only.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

DNA: 200ng (minimum concentration: 50ng/ul)

Test details

The polymerase chain reaction (PCR) amplification is used to determine the number of PABPN1 GCN repeats.

Test limitations

Rare polymorphisms or other technical reasons may result in a false negative result.

Turnaround time

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited (prenatal and newborn) as well as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

Amniotic Fluid: 1x 20mL

Chorinonic Villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

DNA: 200ng (minimum concentration: 50ng/ul)

Additional requirements

For prenatal samples (familial variant testing only): please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Test details

DNA results are based on analysis using methylation specific multiplex ligation-dependent probe amplification (MLPA) to detect both maternal and paternal copies of the 15q11-q13 region.

Test limitations

This analysis detects all cases of PWS due to deletion, uniparental disomy (UPD), and imprinting mutations; however, it cannot distinguish UPD from an imprinting defect.

Turnaround time

Expedited: 2 weeks

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

Newborn: 2-1 x3 mL

For prenatal samples (amniotic fluid or CVS): see the dedicated Amniotic Fluid and Chorionic Villi Sampling (CVS) sections on the Sample requirements and shipping page.

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Products of Conception - restricted service: click here for more details

An intact fetus will not be accepted by the Cytogenetics section of the Genetics Diagnostic Laboratory

Products of Conception (POCs), intrauterine fetal deaths (IUFDs) and stillbirths MUST be sent to a pathology laboratory, where they will be prepared and then automatically transferred to the CHEO Genetics Diagnostic Laboratory for testing. Completed requisitions for both the Pathology AND Genetics Diagnostic Laboratories are required.

Additional requirements

Contact the laboratory in advance for testing on newborns; testing on newborns is always performed in conjunction with chromosome analysis. RAD is only offered when results of RAD testing are expected to be available before chromosome analysis can be completed.

Samples from POC/IUFD/stillbirth are first tested by RAD; in the event of a normal or uninformative result by RAD, testing will reflex to genomic microarray

Test details

Studies are performed by PCR quantification and allow for enumeration of chromosomes X, Y, 13, 18 and 21 which are commonly implicated in aneuploidies.

Test limitations

This analysis does not detect most structural abnormalities, nor aneuploidies of chromosomes other than 13, 18, 21, X and Y. This is not an assay for the detection of mosaicism, nor fetal-placental discordances due to fetal and/or placental mosaicism including confined placental mosaicism.

Turnaround time

Expedited: 5 days

Routine: 2 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited (including prenatal and newborn) as well as routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

DNA: 200ng (minimum concentration: 50ng/ul)

Additional requirements

For prenatal samples (available only if there is a previous family history): please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Test details

Analysis for deletions and duplications of exons in SMN1 and SMN2 is performed using the multiplex ligation-dependent probe amplification (MLPA) technique. DNA results are based on the analysis of SMN1 exon 7 for a homozygous deletion. In cases where a homozygous deletion is not detected, copy number of the SMN1 gene is determined by dosage analysis. Dosage analysis is also performed to determine carrier status for SMA.

Test limitations

Approximately 95% of individuals with spinal muscular atrophy are homozygous for a deletion in SMN1. Approximately 5% have one deletion of SMN1 and a mutation in the other SMN1 allele. The remainder (<1%) have mutations in both their SMN1 genes. Therefore, a negative result does not rule out SMA in affected individuals or carrier status in unaffected individuals. Carrier status is not disclosed in children.

Turnaround time

Expedited: 2 weeks

Routine: 6 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: 2 x 6 mL EDTA (purple top) tube 

Blood: 3 mL EDTA 

Blood: 2 x 3 mL EDTA 

Cord blood: 3 mL EDTA 

Cultured Amniocytes: 2 x T25 flasks 

Cultured CVS: 2 x T25 flasks 

Direct amniotic fluid: 20 mL 

Direct CVS: 10-20 mg 

Other cultured cells (source to be noted on requisition) 

DNA: 1000ng (minimum concentration: 50ng/ul) 

DNA for familial variant testing: 200ng (minimum concentration: 50ng/ul) 

(For Prenatal/cord blood: separate MCC requisition required) 

Additional requirements

ONLY samples referred through Cardiology or Genetics Clinic are accepted.

For familial variant testing: please attach a copy of the proband's laboratory report (or name of proband for whom testing was previously performed by our laboratory) and indicate relationship to the proband.

For prenatal samples: please notify the laboratory in advance for prenatal studies. Maternal blood sample (5 mL in EDTA tube) also required to rule out maternal cell contamination.

Gene content

Genes: ACTA2, ARIH1, COL3A1, EFEMP2, FBN1, FOXE3, LOX, MYH11, MYLK, PRKG1, ROBO4, SLC2A10, SMAD2, SMAD3, TGFB2, TGFB3, TGFBR1, TGFBR2, and THSD4

Including MLPA of: COL3A1, FBN1, TGFBR2, and TGFBR1

Test details

Genomic DNA is extracted from the specimen using the QIAsymphony DSP DNA Mini Kit. DNA quality and quantity are determined with a Nanodrop spectrophotometer. Genomic DNA is enzymatically fragmented and ligated to adapters using Illumina’s DNA Prep kit. DNA Capture is performed using hybridization-based target capture (Illumina DNA Prep with enrichment kit) with custom oligonucleotide probes (Twist Biosciences) to enrich the sample for regions of interest within the genetic panel selected (visit https://www.cheo.on.ca/GDL). Sequencing and primary analysis is performed on a NextSeq 1000/2000 (Illumina) instrument with use of Illumina’s BaseSpace BCLConvert software to generate FASTQ files. Secondary analysis is performed using Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT platform, including mapping FASTQ files to the human reference genome (Homo sapiens [NCBI] hs37d5 v4 Multigenome) and variant calling (e.g. SNVs and InDels). Tertiary analysis is performed only if quality control metrics, including Q30≥90% and uniformity of coverage ≥98%, are met. Sanger sequencing is performed for any regions of interest that are not captured and/or have insufficient coverage (<20X). Tertiary analysis including variant annotation and filtering is performed using Emedgene software (Illumina), focusing on protein coding exons, exon-intron boundaries (+/- 10 bps) and specific deep intronic variants including FBN1 c.1589-14A>G, c.2678-15C>A, and c.5672-87A>G. Some regions within the tested genes including repetitive DNA sequences, such as microsatellites and minisatellites (PMID 37726397), and regions with high sequence homology with other sequences in the genome, such as MYLK exons 13-18 (c.1652-10 to c.3448+10), are prone to misalignment and therefore are at increased risk of false positive and negative results (PMID 27228465). To detect large genomic deletions and duplications, multiplex ligation-dependent probe amplification (MLPA) using the available kits for analysis of FBN1 (P065/P066), COL3A1 (P155), TGFBR1 and TGFBR2 (P148) is performed. Note that some MLPA kits used as part of this test may contain probes for genes or variants that are not included in our test panels, which could result in incidental findings. Reported variants not meeting internal quality criteria are confirmed with an orthogonal method (Sanger sequencing, long range PCR, qPCR or MLPA). All rare variants are checked for prior reports in the literature, ClinVar, the Genome Aggregation Database (gnomAD), and other relevant sources of information. Variant nomenclature is based on the Human Genome Variation Society recommended guidelines and GRCh37 (hg19) human reference genome assembly. Variant significance is categorized using adaptations of the ACMG/AMP (PMID 25741868) and ClinGen Sequence Variant Interpretation recommendations, and CHEO-specific guidelines. Variants are re-interpreted if/when the same variant is identified in another proband and > 12 months has elapsed since its original evaluation. For missense variants, in silico splicing prediction programs are used when the variant is within 10 nucleotides of an exon/intron junction, and not checked when the variant is elsewhere in an exon. Additional Sanger sequencing is performed for any clinically significant regions that are not captured and/or have insufficient coverage. Sequencing of the last exon in the MYH11 MANE Select transcript (NM_002474.3) is not performed; however, all coding exons (±10 bp) of the MYH11 MANE Plus Clinical transcript (NM_001040113.2) are included in the analysis. In addition, due to technical challenges, sequencing of high GC content regions of TGFBR1 exon 1 and FOXE3 c.26 to c.216 is not performed. If you would like to request coverage of these regions or have questions about the coverage, please contact the laboratory directly. Variants are reviewed/re-interpreted if identified in another proband and the following timeframes have passed since the original evaluation: ≥1 year for variants of uncertain clinical significance (VUCS) or likely pathogenic, and ≥3 years for likely benign or pathogenic variants after specific time periods have elapsed, or substantial novel information has emerged. Sequence variants of unlikely clinical significance are not reported (e.g. likely benign). These variants are available on request. Variant interpretation is carried out in reference to the test ordered and may not be applicable for other disorders.

Test limitations

Mutations in the FBN1 and ACTA2 genes account for 23-27% of TAAD cases, therefore a negative test result does not rule out the diagnosis. This analysis detects >99% of variants within the tested genes.

Turnaround time

Routine: 10 weeks

Familial variant testing: 4 weeks (cannot be expedited; minimum 4 weeks even for STAT/urgent indications including prenatal cases due to testing limitations) 

Requisition form

You can find the requisition form for this test here.

Eligibility requirements for OHIP patients only: Patients must reside in the Champlain or Northern Ontario catchment areas. Samples are otherwise accepted across Canada and Internationally, with the exception of the United States.

Test available as routine only.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2 x 6 mL

Child: 2 x 3 mL

Infant (<1 yr of age): 1 x3 mL

DNA: 200ng (minimum concentration: 25ng/ul)

Test details

Analysis of the F5 p.Arg534Gln (Factor V Leiden) and the F2 c.*97G>A (prothrombin 20210G>A) variants are performed using PCR followed by restriction enzyme digest. Variant nomenclature is based on the Human Genome Variation Society recommendations and protein accession #'s NP00012.2 (F5), and nucleotide accession number NC000011.8 (F2).

Test limitations

Additional inherited and environmental causes of thrombosis are known to exist, therefore, negative results do not eliminate the possibility of thrombophilia in the patient.

Turnaround time

Routine: 10 weeks

Requisition and more information

You can find the requisition form for this test here.

Find more information on Thrombophilia.