Molecular Genetics Infantile Neuroaxonal Dystrophy, PLA2G6, Sequencing

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Test Code:

1682
Department:

Molecular Genetics
Test Synonyms:

INAD • PLA2G6-Related Infantile Neuroaxonal Dystrophy • Seitelberger Disease • NBIA • PLAN • Atypical NAD • Dystonia-parkinsonism
CPT Code(s):

81479

Background:

Infantile neuroaxonal dystrophy (INAD) is a progressive neurodegenerative disorder characterized by infantile or early childhood onset of progressive motor and sensory impairment; atypical INAD presents with later onset and a more protracted course (OMIM#256600). INAD symptoms include regression, truncal hypotonia, spastic tetraparesis, mental retardation, optic atrophy and early death. Common pathologic features include axonal degeneration with spheroid bodies throughout the central and peripheral nervous systems and cerebellar atrophy. Some individuals with INAD show high brain iron accumulation in the globus pallidus. The disease is autosomal recessive and caused by mutations in the PLA2G6 gene.

Reasons for Referral

Confirmation of clinical diagnosis in patients with classic or atypical INAD.
Testing of family members of INAD patients with known mutations.
Prenatal diagnosis of known familial INAD mutations.

Methodology:

Genomic DNA is analyzed using next-generation sequencing (NGS) on the Illumina NextSeq 2000 platform, with target enrichment performed using hybridization-based probes to capture exonic (coding) regions of the gene(s). Single nucleotide variants (SNVs) and small insertions or deletions (INDELs) are identified using the Illumina DRAGEN Enrichment Workflow, executed onboard the NextSeq2000. This pipeline combines software and hardware acceleration to generate high-confidence germline haplotype calls. Clinical and analytical validation of DRAGEN was performed in our laboratory. Based on validation study results, for SNVs, this assay achieves >96% analytical sensitivity and >99% positive predictive value (PPV). For INDELs <50 bp, the analytical sensitivity is >87% and the PPV is >97%. INDELs >50 bp may be detected but the sensitivity for these is reduced.

Exon-level copy number variants (CNVs) are detected using the Germline Copy Number Variation Best Practices pipeline from GATK. A Bayesian model, clinically validated in our laboratory, enables detection of deletions and duplications involving three or more contiguous exons in genes with adequate probe coverage and without complicating factors (e.g. pseudogene homology, short tandem repeats, segmental duplications). Please note that exon-centric microarray remains the gold standard for exonic copy number variant calling. If exon-centric microarray is of interest, please contact the laboratory for additional information.

This test is not designed to detect polynucleotide repeats, low-level mosaicism, structural rearrangements or balanced alterations (e.g. inversions, gene conversion events, translocations, etc.) or variants in difficult regions. Additionally, variants located in regions of insufficient coverage, including introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and of high GC content may not be detected. This test does not provide complete coverage of all exons and noncoding regions may have limited information and ability to interpret. Variants in introns that are greater than 10 bp from the intron-exon junction may be analyzed. Please contact the laboratory if interrogation of intronic sequence greater than 10 bp from the intron-exon boundary is desired.

Specimen Requirements:

Blood: EDTA (purple-top) or ACD (yellow-top) tube

Adult: 6.0 mL
Child: 3.0 mL
Infant: 2.0-3.0 mL

Saliva: 2 ORAgene Saliva Kits (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.

Assisted Saliva: 4 ORAgene Assisted Saliva Kits (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.

Buccal Cells: 4 CytoSoft™ Cytology Brush (Medical Packaging CYB-1) used according to manufacturer instructions. Please contact KDL Client Services for a Buccal Collection Kit for patients that cannot provide a blood sample.

Skin Fibroblast: Punch Biopsy (cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.

Prenatal:

Direct Amniotic Fluid (10-20mL)
Direct CVS
Direct POC
Cultured Amniocytes (2 T-25 flasks)
Cultured CVS (2 T-25 flasks)
Cultured Fetal Tissue: Product of Conception (2 T-25 flasks)
Cord Blood (1-2mL)

DNA: 5-10µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS).

Notice Regarding Molecular Genetic Testing on Prenatal Specimens:

Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood (or saliva) in addition to the fetal specimen. Additional charges apply for the maternal cell rule-out test.

For routine testing of blood and saliva (or DNA extracted from them), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed within the above windows, please contact our lab.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.

Test Performed (Days):

Weekly

Turn Around Time:

14-21 days

Shipment Sensitivity Requirements: