Tuberous Sclerosis Complex Panel, Sequencing and Deletion/Duplication

Last Literature Review: February 2022 Last Update:

Preferred DNA test to confirm clinical diagnosis of TSC

  • Use to confirm diagnosis of TSC in a fetus with suspected cardiac rhabdomyoma on ultrasound
  • Use to confirm diagnosis in a fetus at risk for TSC based on a positive family history

If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.

Tuberous sclerosis complex (TSC) is a multisystem, genetic disorder causing numerous benign tumors as well as cognitive and developmental disabilities. Tumors can occur in the skin, brain, kidneys, and other organs, and can lead to significant health complications. TSC may be life threatening. Nearly all affected individuals have skin findings that develop early in life, which can include pigmentary changes, thickened skin, growths in the nails, and facial angiofibromas. Changes in cognitive ability are common and can present in a variety of ways, including autism spectrum disorder, behavioral change, and cognitive disability. Seizures occur in more than 80% of affected individuals. TSC may be suspected prenatally due to the presence of a fetal cardiac rhabdomyoma, the most common cardiac tumor seen on ultrasound. 

Disease Overview

Diagnostic Criteria

  • TSC should be suspected in individuals with either one major feature or two or more minor features.
  • A definitive diagnosis is established by any of the following:
    • The presence of two major features
    • One major feature with two or more minor features
    • Identification of a pathogenic variant in either TSC1 or TSC2 by molecular genetic testing
Major FeaturesMinor Features

Angiofibromas or a fibrous cephalic plaque

Cardiac rhabdomyoma

Cortical dysplasias

Hypomelanotic macules

Lymphangioleiomyomatosis (LAM)

Multiple retinal nodular hamartomas

Renal angiomyolipoma

Shagreen patch

Subependymal giant cell astrocytoma

Subependymal nodules

Ungual fibromas

“Confetti” skin lesions

Dental enamel pits

Intraoral fibromas

Multiple renal cysts

Nonrenal hamartomas

Retinal achromic patch

Sources: Northrup, 2021 ; Northrup, 2013 

Genetics

Genes Tested

TSC1 and TSC2

Prevalence

1 in 6,000 individuals 

Etiology

Pathogenic variants in either the TSC1 or TSC2 gene

Inheritance

  • Autosomal dominant
  • Approximately 66% are de novo

Genotype-Phenotype Correlation

TSC2 pathogenic variants produce a more severe phenotype and are more likely to be sporadic (de novo) than TSC1 variants. Individuals with TSC2 variants are at a greater risk for renal malignancy, cognitive disability, autism spectrum disorder, and infantile spasm. However, there is variable expressivity and clinical overlap between TSC1 and TSC2 variants.

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as NGS) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Clinical Sensitivity

95% for TSC 

  • TSC1: Approximately 26%
  • TSC2: Approximately 69%
  • Unknown: Approximately 5%

Analytic Sensitivity

For massively parallel sequencing:

Variant ClassAnalytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region (%)Analytic Specificity (NPA) (%)
SNVs>99 (96.9-99.4)>99.9
Deletions 1-10 bpb93.8 (84.3-98.2)>99.9
Insertions 1-10 bpb94.8 (86.8-98.5)>99.9
Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [Single exon]

>99.9
Exon-levelc duplications83.3 (56.4-96.4) [3 exons or larger]>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Results

ResultVariant(s) DetectedClinical Significance
PositiveOne TSC1 or TSC2 pathogenic variant detectedConsistent with a diagnosis of TSC
NegativeNo TSC1 or TSC2 pathogenic variants detectedDiagnosis of TSC is unlikely but not excluded
UncertainTSC1 or TSC2 variant of unknown clinical significance detectedIt is unknown whether variant is benign or pathogenic

Limitations

  • A negative result does not exclude a diagnosis of TSC.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of the targeted genes
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massive parallel sequencing
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive or homologous regions
    • Low-level somatic variants

References