Peroxisomes are intracellular organelles with diverse cellular functions including biosynthesis, catabolism and detoxification of various compounds. Inborn errors of metabolism of peroxisomes function are roughly divided into peroxisome biogenesis disorders and single enzyme or transporter defects. This panel is designed for comprehensive testing for the following peroxisomal disorders:
- Peroxisome biogenesis disorders, also called Zellweger syndrome spectrum (PBD, ZSS) that include Zellweger syndrome (ZS), neonatal adrenoleukodystrophy (NALD), and infantile Refsum disease (IRD).
- X-linked adrenoleukodystrophy and adrenomyeloneuropathy.
- Rhizomelic Chondrodysplasia Punctata, Types 1, 2, and 3.
- Refsum Disease or phytanoyl-CoA hydroxylase deficiency.
- Acyl-CoA oxidase (ACOX1) deficiency.
- D-bifunctional protein (DBP) deficiency
- 2-Methylacyl-CoA racemase (AMACR) deficiency.
- Hyperoxaluria Type 1 or alanine glyoxylate aminotransferase deficiency.
- Mulibrey nanism.
- Sterol carrier protein X (SCP2) deficiency.
- DNM1L-related encephalopathy.
- ABCD3-related congenital bile acid synthesis defect
This test is indicated for:
- Confirmation of a clinical/biochemical diagnosis of peroxisomal disorders.
- Carrier testing in adults with a family history of peroxisomal disorders.
Next Generation Sequencing: In-solution hybridization of all coding exons is performed on the patient's genomic DNA. Although some deep intronic regions may also be analyzed, this assay is not meant to interrogate most promoter regions, deep intronic regions, or other regulatory elements, and does not detect single or multi-exon deletions or duplications. Direct sequencing of the captured regions is performed using next generation sequencing. The patient's gene sequences are then compared to a standard reference sequence. Potentially causative variants and areas of low coverage are Sanger-sequenced. Sequence variations are classified as pathogenic, likely pathogenic, benign, likely benign, or variants of unknown significance. Variants of unknown significance may require further studies of the patient and/or family members.
Copy Number Analysis: Comparative analysis of the NGS read depth (coverage) of the targeted regions of genes on this panel was performed to detect copy number variants (CNV). The accuracy of the detected variants is highly dependent on the size of the event, the sequence context and the coverage obtained for the targeted region. Due to these variables and limitations a minimum validated CNV size cannot be determined; however, single exon deletions and duplications are expected to be below the detection limit of this analysis.
Clinical Sensitivity: Pathogenic variants in the PEX genes account for ~95% of individuals with PBD, ZSS. Pathogenic variants in the promoter region, some pathogenic variants in the introns and other regulatory element pathogenic variants cannot be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient's clinical and/or biochemical phenotype.
Analytical sensitivity for sequence variant detection is ~99%.
Copy Number Analysis: The sensitivity and specificity of this method for CNV detection is highly dependent on the size of the event, sequence context and depth of coverage for the region involved. The assay is highly sensitive for CNVs of 500 base pairs or larger and those containing at least 3 exons. Smaller (< 500 base pairs) CNVs and those that involving only 1 or 2 exons may or may not be detected depending on the sequence context, size of exon(s) involved and depth of coverage.
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
- Individual gene sequencing and deletion/duplication analysis are available for the following genes: ABCD1, PEX1, PEX2, PEX3, PEX5, PEX6, PEX12, PEX14, and PEX26
- Peroxisome Disorders: Deletion/Duplication Panel