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: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2 x3 mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and 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: 1000ng (minimum concentration: 50ng/ul)

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

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

Requisition form

You can find the requisition form for this test here.

Test available as expedited and routine

Sample requirements

Restricted service. Please contact the laboratory prior to sending samples.

Test details

Rearrangements involving the BCL6 locus at 3q27 are seen in a variety of neoplasms including follicular, diffuse large B-cell and high-grade B-cell lymphomas. Rearrangements involving the BCL6 locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Test available as expedited and routine.

Sample requirements

Test details

Rearrangements involving the BCL6 locus at 3q27 are seen in a variety of neoplasms including follicular, diffuse large B-cell and high-grade B-cell lymphomas. Rearrangements involving the BCL6 locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Test available as expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x 1 mL (first draw)

Test details

The BCR-ABL1 gene fusion resulting from the translocation t(9;22)(q34;q11.2) or variant rearrangements involving chromosomes 9 and 22 are seen in chronic myelogenous leukemia (CML), acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia (B-ALL) and other rare leukemias. The BCR-ABL1 gene fusion is detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes. In addition, amplification of ABL1 sometimes seen in T-cell acute lymphoblastic leukemia (T-ALL) can be detected using these probes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2 x3 mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

Requisition form

You can find the requisition form for this test here.

Tests available as expedited and routine.

Sample requirements

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

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

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

Cultured fibroblasts from skin biopsy accepted: please contact the laboratory prior to organizing testing for more details.

Gene content

Lists of the variants outside of coding regions

Additional requirements

Samples are referred through Genetics Clinics, an affiliated site, or a documented mainstreamed provider from The Ottawa Hospital only.

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) including relationship to the proband. Please clearly indicate with the proband’s laboratory report the name, date of birth and MRN/OHIP/RAMQ number of the relevant patient undergoing testing.

Panels available

1. BRCA1/BRCA2 Ashkenazi Jewish mutations panel (3 mutations)

2. Hereditary Breast/ Ovarian/ Prostate Cancer panel (19 genes)

3. Hereditary Pancreatic Cancer Panel (12 genes)

4. Familial variant(s) testing (targeted variant analysis)

Test details

Hereditary Breast/ Ovarian/ Prostate Cancer Panel:

Genomic DNA is enriched for targeted regions using custom designed capture probes (KAPA HyperChoice) and a hybridization-based protocol (KAPA HyperPlus Custom Library, KAPA Biosystems-Roche). 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]) and variant calling including SNVs, InDels, SVs and CNVs. Tertiary analysis including variant annotation and filtering is performed using Emedgene software (Illumina), focusing on protein coding exons, exon-intron boundaries (+/- 20 bps) and certain known likely pathogenic or pathogenic variants outside these regions (for a complete list please contact our laboratory). Exonic deletions and duplications in all targeted genes (except PMS2) are called using Illumina’s DRAGEN Bio-IT and Emedgene pipeline, based on read depth and normalization to a panel of normal samples. Multiplex ligation-dependent probe amplification (MLPA) is performed for CNV analysis for PMS2. All reported variants are confirmed by a second technology including Sanger sequencing, MLPA, long range PCR, or qPCR. 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. Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for SNV, indels <10bp in length and exonic deletions and duplications; however, sensitivity may be reduced for larger or complex insertions and deletions larger than or (greater than 10bp), single exon CNVs, or regions with high pseudogene homology. The following genes and corresponding exons are prone to misalignment due to presence of highly homologous regions in the genome, and therefore, are at increased risk of false results: ATM exon 28, CHEK2 exons 11-15, PTEN exon 9 and PMS2 exons 1-5, 9, 11-15 (PMID 27228465). This assay is not designed and validated for detection of mosaicism. Variant nomenclature is based on the Human Genome Variation Society guidelines. Variant interpretation and classification is based on published guidelines (PMID 25741868), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Groups, and/or CHEO-specific guidelines. Only pathogenic, likely pathogenic, and variants of uncertain clinical significance are reported.

Hereditary Pancreatic Cancer panel:

Genomic DNA is enriched for targeted regions using custom designed capture probes (KAPA HyperChoice) and a hybridization-based protocol (KAPA HyperPlus Custom Library, KAPA Biosystems-Roche). 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]) and variant calling including SNVs, InDels, SVs and CNVs. Tertiary analysis including variant annotation and filtering is performed using Emedgene software (Illumina), focusing on protein coding exons, exon-intron boundaries (+/- 20 bps) and certain known likely pathogenic or pathogenic variants outside these regions (for a complete list please contact our laboratory). Exonic deletions and duplications in all targeted genes (except PMS2) are called using Illumina’s DRAGEN Bio-IT and Emedgene pipeline, based on read depth and normalization to a panel of normal samples. Multiplex ligation-dependent probe amplification (MLPA) is performed for CNV analysis for PMS2. All reported variants are confirmed by a second technology including Sanger sequencing, MLPA, long range PCR, or qPCR. 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. Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for SNV, indels <10bp in length and exonic deletions and duplications; however, sensitivity may be reduced for larger or complex insertions and deletions larger than or (greater than 10bp), single exon CNVs, or regions with high pseudogene homology. The following genes and corresponding exons are prone to misalignment due to presence of highly homologous regions in the genome, and therefore, are at increased risk of false results: ATM exon 28, CHEK2 exons 11-15, PTEN exon 9 and PMS2 exons 1-5, 9, 11-15 (PMID 27228465). This assay is not designed and validated for detection of mosaicism. Variant nomenclature is based on the Human Genome Variation Society guidelines. Variant interpretation and classification is based on published guidelines (PMID 25741868), Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Groups, and/or CHEO-specific guidelines. Only pathogenic, likely pathogenic, and variants of uncertain clinical significance are reported.

BRCA1/BRCA2 Ashkenazi Jewish mutations panel:

DNA results are based on the sequence analysis of exon 2 of BRCA1 to detect the c.68_69delAG (previously 185delAG) variant and the c.5266dupC (previously 5382insC) BRCA1 variant as well as sequence analysis of BRCA2 to detect the c.5946delT (previously 6174delT) BRCA2 variant. A negative result does not rule out a pathogenic variant in either the BRCA1 or BRCA2 genes or in another breast cancer susceptibility gene. Variant nomenclature is based on the Human Genome Variation Society recommended guidelines and GRCh37 (hg19) human reference genome assembly, and nucleotide accession #’s BRCA1 (NM_007294.3) and BRCA2 (NM_000059.3). Sequence variants of unlikely clinical significance are not included in this report but are available upon request.

Test limitations

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for SNV, indels <10bp in length and exonic deletions and duplications; however, sensitivity for indels larger than 10bp but smaller than a full exon may be reduced. Due to the presence of high sequence homology between exons 12-15 of the PMS2 and its pseudogene PMS2CL these regions are at increased risk of false positive and negative results. Although our CNV analysis using NGS data detects most deletions and duplications, in some regions they may not be accurately detected due to sequence paralogy (e.g. pseudogenes, segmental duplications). This assay is not designed and validated for detection of mosaicism.

Turnaround time

Breast/ Ovarian/ Prostate Cancer Panel and Hereditary Pancreatic Cancer Panel:

STAT: 4 weeks

Routine: 8 weeks

Family variant testing/ Ashkenazi Jewish mutations: 4 weeks

More information and requisition form

You can find more information about, as well as the requisition form for this test, here.

Test available as prenatal and 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

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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 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 time

Expedited: 2 weeks

Routine: 8 weeks

Familial variant testing: 4 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Inversions or translocations involving the CBFB locus at 16q22 are commonly seen in acute myeloid leukemia (AML) and are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Fresh lymph node/tumour biopsy: sterile container with culture medium. If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Test details

Rearrangements of the CCND1 (BCL1) locus at 11q13.3 are commonly seen in mantle cell lymphoma and other lymphoproliferative neoplasms. Rearrangements involving the CCND1 (BCL1) locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Aneuploidy of chromosomes 4 and/or 10 is commonly seen in pediatric B-cell acute lymphoblastic leukemia (B-ALL). Aneuploidy involving chromosomes 4 and 10 are detectable using commercially available centromere-specific probes fluorescence in situ hybridization (FISH) on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Eligibility criteria for constitutional testing on adults from Ontario (except tests ordered for Microarray follow-up):
Patients must reside in Champlain region (Eastern Ontario).

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

Note: Testing on POCs, IUFDs and Stillbirths is not available

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Postnatal Tissue (EXCLUDING Products of Conception, Intrauterine Fetal Deaths and Stillbirths):

3-4 mm fresh skin or tissue biopsy (sterile container with culture medium)

For postnatal tissues and oncology lymph nodes/tumour biopsies: If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Test details

Conventional cytogenetic testing, also known as chromosome analysis or karyotyping, is utilized to detect numerical and/or structural chromosome abnormalities. It requires viable dividing cells from sterile samples. Clinical indications for such test include, but are not limited to:

• 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 at time of delivery:
    • Singleton pregnancy: ≥40 years
    • Twin or multiple pregnancies: ≥35 years
  • Positive prenatal screening result (biochemical or NIPT)
  • Fetal ultrasound anomalies
  • Family history of chromosome abnormalities
• Recurrent pregnancy losses (minimum of three miscarriages); specimens from both partners are required
• Screen for familial chromosome abnormalities

Test limitations

Detection of chromosome abnormalities in metaphase cell preparations by conventional banding methods is limited to identifying those that are visible by oil-immersion light microscopic methods (1000x total magnification), following currently accepted cytogenetic processing and analysis standards specific to the sample type and clinical indication. Detection of structural chromosome anomalies is dependent upon the sample type and is limited to approximately 10 Mb in size in postnatal samples. Chromosome analysis cannot rule-out other forms of genetic abnormalities such as molecular defects, point mutations, uniparental disomy or subtelomeric rearrangements, and the detection of tissue-specific mosaicism is limited.

Turnaround time

Prenatal

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

Postnatal

• Newborn: 1 week
• Parents of fetus with abnormal karyotype or couple where partner is pregnant: 1-2 weeks (depending on gestation)
• Routine: 4 weeks

Oncology

• Diagnosis of new leukemia (ALL,AML,CML): 2 weeks
• Other indications: 3 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2X6 mL

Child: 2 x3 mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

Additional requirements

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

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

Requisition form

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

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Cri-du-Chat syndrome have a deletion distal to 5p15.2 on the short arm of chromosome 5. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe. This analysis will also detect deletions limited or extending to the 5p15.31 band.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Deletions or translocations involving the CRLF2 locus at Xp22.33/Yp11.32 can be seen in acute lymphoblastic leukemia (ALL) and are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Monosomy of entire chromosome 7 or deletion of its long arm (deletion 7q) is commonly seen in acute myeloid leukemia (AML), myelodysplastic syndrome (MDS) or inherited bone marrow failure syndromes. Monosomy 7 or deletion 7q is detectable using commercially available locus-specific fluorescence in situ hybridization (FISH) probes targeting the centromere of chromosome 7 and the D7S486 locus at 7q31. In addition, isochromosome 7q sometimes seen in inherited bone marrow failure syndromes can be detected using these probes. Upon request, a commercially available locus-specific FISH probe targeting the centromere of chromosome 8 can also be included to detect trisomy 8.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with DiGeorge/VelocardioFacial syndrome have a deletion of the long arm of chromosome 22 occurring in region 22q11.21, which includes the HIRA (TUPLE1) gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Test limitations

This probe cannot detect distal or “B-D” nested deletions within the 22q11.2 region, which are reported in less than 10% of patients.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Monosomy of entire chromosome 5 or deletion of its long arm (deletion 5q) is commonly seen in acute myeloid leukemia (AML), myelodysplastic syndrome (MDS) or inherited bone marrow failure syndromes. Monosomy 5 or deletion 5q is detectable using commercially available locus-specific fluorescence in situ hybridization (FISH) probes targeting the EGR1 locus at 5q31 and a control locus on the short of chromosome 5.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

The ETV6-RUNX1 gene fusion resulting from the translocation t(12;21)(p13;q22) is commonly seen in pediatric B-cell acute lymphoblastic leukemia (B-ALL) and is detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes. In addition, deletion of 12p13, trisomy 21 or amplification of RUNX1 [“iAMP21”], also seen in pediatric B-ALL, can be detected using these probes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Tissue

Fresh lymph node/tumour biopsy: sterile container with culture medium. If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections: restricted service. Please contact the laboratory prior to sending samples.

Test details

Rearrangements involving the EWSR1 locus at 22q12 are commonly seen in Ewing sarcoma and related-tumours. Rearrangements involving the EWSR1 locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

Child or infant: 2 x 3 mL

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.

Test available as expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Tissue:

Fresh lymph node/tumour biopsy: sterile container with culture medium. If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections: restricted service. Please contact the laboratory prior to sending samples.

Test details

Rearrangements involving FOXO1 (FKHR) locus at 13q14 are commonly seen in Alveolar Rhabdomyosarcomas. Rearrangements involving the FOXO1 (FKHR) locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2 x3 mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Kallmann syndrome have a deletion of the short arm of the X chromosome occurring in region of Xp22.33, which includes the KAL1 gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe. This analysis will detect deletions of the KAL1 gene as well as deletions extending down to the STS gene in Xp22.31.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Rearrangements involving the KMT2A (MLL) locus at 11q23 are seen in acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia (B-ALL) and other rare leukemias. Rearrangements involving the KMT2A (MLL) locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2x 3mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 2x 6 mL

Child: 2x 3mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and routine.

Sample requirements

Blood: EDTA (purple top) tube

Adult: 1x 10 mL

Child: 2x 5mL

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Cultured amniocytes or CVS: 2xT25 flasks

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

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

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

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

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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Miller-Dieker syndrome have a deletion of the short arm of chromosome 17 occurring in region 17p13.3, which includes the PAFAH1B1 (LIS1) gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Prenatal, expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Tissue:

Fresh lymph node/tumour biopsy: sterile container with culture medium. If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections: restricted service. Please contact the laboratory prior to sending samples.

Test details

Rearrangements involving the MYC (C-MYC) locus at 8q24 are seen in a variety of neoplasms including Burkitt and high-grade B-cell lymphomas. Rearrangements involving the MYC (C-MYC) locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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 expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Tissue:

Fresh lymph node/tumour biopsy: sterile container with culture medium. If transit is to be delayed for more than one day, refrigerate sample (in sterile culture media or isotonic saline). Do not freeze. Do not use alcohol, formalin, distilled water or any other type of preservative.

Frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections: restricted service. Please contact the laboratory prior to sending samples.

Test details

Amplification of the NMYC (MYCN) locus at 2p24 is frequently seen in neuroblastoma and other peripheral neuroblastic tumours. Amplification involving the NMYC (MYCN) locus is detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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 and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Test details

Interstitial deletion 4q12 involving the CHIC2 locus is typically associated with cytogenetic rearrangements of the PDGFRA locus and may result in a FIP1L1-PDGFRA gene fusion in myeloid/lymphoid neoplasms with eosinophilia. Rearrangements involving the CHIC2 locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

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

Most individuals with Phelan-McDermid syndrome have a deletion of the long arm of chromosome 22 occurring in region 22q13.33, which includes the SHANK3 gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

The PML-RARA gene fusion resulting from the translocation t(15;17)(q24;q21) is commonly seen in acute myeloid leukemia (AML) and is detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 1 week

Routine: 3 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

Prenatal Samples: click here for more details

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 and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Test details

Rearrangements involving the RARA locus at 17q21 are seen in acute myeloid leukemia (AML) and are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 1 week

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

The RUNX1-RUNX1T1 gene fusion resulting from the translocation t(8;21)(q22;q22) or variant rearrangements is commonly seen in acute myeloid leukemia (AML) and is detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Test available as expedited (including prenatal) and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Individuals with Saethre-Chotzen syndrome have a deletion of the short arm of chromosome 7 occurring in region 7p21.1, which includes the TWIST1 gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Bone marrow: 1x1 mL (first draw)

Test details

Detection of XX/XY chimerism in individuals who have received a bone marrow transplant from an opposite-sex donor can typically be done by using commercially available centromere-specific fluorescence in situ hybridization (FISH) probes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Individuals with Smith-Magenis syndrome have a deletion of the short arm of chromosome 17 occurring in region 17p11.2, which includes the RAI1 gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Sotos syndrome have a deletion of the long arm of chromosome 5 occurring in region 5q35, which includes the NSD1 gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 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: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Steroid Sulfatase Deficiency of X-linked ichthyosis have a deletion of the short arm of the X chromosome occurring in region Xp22.31, which includes the STS gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using commercially available probes. This analysis will detect deletions of the STS gene as well as deletions extending up to the KAL1 gene in Xp22.33.

Turnaround time

Expedited: 2 weeks

Routine: 3 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 expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Test details

Many individuals with XY or XX disorders of sex development have chromosome rearrangements involving the SRY locus in Yp11.31, and mosaic cell lines with a Y chromosome can be seen in some individuals with apparent homogeneous 45,X constitutions. The presence or absence of the SRY gene and Yq12 heterochromatin can typically be detected by fluorescence in situ hybridization (FISH) using commercially available probes on interphase nuclei and metaphase chromosomes.

Test limitations

This test cannot detect point mutations or other molecular defects of the SRY gene, which are reported in some patients with disorders of sex development.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.

Test available as prenatal and 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: 1000ng (minimum concentration: 50ng/ul)

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

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

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.

Test available as expedited and routine.

Sample requirements

Blood: Sodium Heparin (green top) tube

Adult: 1x 10 mL

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

Bone marrow: 1x1 mL (first draw)

Test details

Rearrangements resulting in loss of the TP53 (P53) locus at 17p13.1 are seen in a variety of neoplasms including of lymphoid or myeloid origin. Rearrangements involving the TP53 locus are detectable using commercially available fluorescence in situ hybridization (FISH) probes on interphase nuclei and metaphase chromosomes.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Williams syndrome have a deletion of the long arm of chromosome 7 occurring in region 7q11.23, which includes the ELN gene. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 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

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

Prenatal Samples: click here for more details

Amniotic Fluid: 1x 20mL

Chorionic villi: 10-20mg

Test details

Most individuals with Wolf-Hirschhorn syndrome have a deletion distal to 4p16.3 on the short arm of chromosome 4. This deletion can typically be detected by fluorescence in situ hybridization (FISH) using a commercially available probe.

Turnaround time

Expedited: 2 weeks

Routine: 3 weeks

Requisition form

You can find the requisition form for this test here.