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Test Code D4211
Test Summary

This test analyzes 2 genes associated with tuberous sclerosis.

Turn-Around-Time (TAT)* 2 - 3 weeks
Acceptable Sample Types
Whole Blood (EDTA)
DNA, Isolated
Dried Blood Spots
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
Self (patient) Price $250.00
Institutional Price $950.00
CPT Codes** 81405 (x1), 81406 (x2), 81407 (x1)
*TAT starts after the sample and all required sample information is received at PerkinElmer Genomics.
**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.

This panel analyzes 2 genes associated with tuberous sclerosis. Both sequencing and deletion/duplication (CNV) analysis will be performed on the coding regions of all genes included (unless otherwise marked). All analysis is performed utilizing Next Generation Sequencing (NGS) technology. CNV analysis detects most deletions and duplications of three exons or greater in size. All variants are classified according to ACMG guidelines.

Genetic testing for TSC may be appropriate for individuals with a clinical suspicion of a TSC diagnosis. Significant features of TSC include:

  • Angiofibromas (more than 3) or fibrous cephalic plaque
  • Cardiac rhabdomyoma
  • Cortical dysplasias, including tubers and cerebral white matter migration lines
  • Hyopmelanotic macules (3-5 mm in diameter)
  • Lymphangioleiomyomatosis
  • Multiple retinal nodular hamartomas
  • Renal angiomyolipoma
  • Shagreen patch
  • Subependymal giant cell astrocytoma
  • Subependymal nodules
  • Ungual fibromas

Minor features of TSC include:

  • Confetti skin lesions
  • Dental enamel pits
  • Intraoral fibromas
  • Multiple renal cysts
  • Nonrenal hamartomas
  • Retinal achromic patch

Tuberous Sclerosis (TSC) is a rare genetic condition that causes benign tumors to grow in the brain, kidneys, heart, eyes, lungs, and skin. Other symptoms of TSC include seizures, developmental delay, autism, skin abnormalities, behavioral problems, and kidney disease. TSC is caused by pathogenic mutations in two genes, TSC1 and TSC2. Most cases of TSC arise due to new (de novo) mutations; however, TSC mutations can also be inherited. Genetic testing can help confirm a diagnosis of TSC and help guide medical management. Genetic testing can also provide vital information for other family members.


Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the genes on this panel. Direct sequencing of the amplified captured regions was performed using 2X100bp reads on Illumina next-generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X, and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. Low coverage regions, if any, are limited to ~1% or less of the nucleotides in the test unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. Alignment to the human reference genome (hg19) is performed, and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs are confirmed by Sanger sequence analysis before reporting at the director's discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequencing complexity, or other factors, not all CNVs may be analyzed and/or may be difficult to detect. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.4.12. Secondary and tertiary data analysis is performed using PerkinElmer’s internal ODIN v.1.01 software for SNVs and Biodiscovery’s NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v.3.4.12 for CNV and the absence of heterozygosity (AOH). Genes and/or exons located in pseudogene regions are not covered in this assay.

Whole Blood (EDTA) (Preferred sample type)
Collection Container(s):

EDTA (purple top)


Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
Clotted or hemolyzed samples are not accepted.
DNA, Isolated

Required DNA Quantity by Test Type*:

  • Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
  • Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
  • Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.


Condition: * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping: Ship overnight at ambient temperature.
  • Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
  • Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor prior to submitting a DNA sample from any non-CLIA certified laboratory.
  • Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Dried Blood Spots
Collection Container(s):

Dried blood spot card


Follow kit instructions. Briefly, allow blood to saturate card until indicated areas are filled and blood has soaked through card. Air dry card at ambient temperature for at least 3 hours.

  • NBS: Please contact PKIG to request the StepOne® kit.
  • Gene Sequencing: Please contact PKIG to request the DBS collection kit.
  • For pre-punched DBS: The required minimum 6 punches with 3.2 mm or 4 punches 4.75 mm.
Condition: Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.
Collection Container(s):

Oragene™ Saliva Collection Kit or ORAcollect-Dx kit


Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s instructions. 

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature.
Please contact PerkinElmer to request the saliva collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample.

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