Molecular Genetics Neuroferritinopathy, FTL, Sequencing

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Test Code:

1550
Department:

Molecular Genetics
Test Synonyms:

Neurodegeneration with Brain Iron Accumulation • NBIA • Ferritinopathy • Ferritin Light Chain • FTL1
CPT Code(s):

81479

Background:

NBIA is a group of neurodegenerative diseases caused by iron accumulation in the basal ganglia leading to dystonia, parkinsonism, neurocognitive anomalies, and ophthalmologic disorders. Neuroferritinopathy is caused by mutations in the FTL gene (Ferritin Light chain), and is inherited in an autosomal dominant manner. This disease is characterized by progressive adult-onset chorea or dystonia and cognitive deficits, and shows the presence of focal spherical inclusions in the brain and other organs, including liver and muscle. In addition, mutations in the iron response element (IRE) of the FTL gene cause hereditary hyperferritinemia cataract syndrome (HHCS), a syndrome of early-onset cataract and hyperferritinemia. The IRE is located in the 5’ untranslated region of the FTL mRNA.

Reasons for Referral:

Confirmation of a suspected clinical diagnosis in patients with the hallmark findings of neuroferritinopathy.
Further assessment of patients with clinical diagnosis of idiopathic Neurodegeneration with Brain Iron Accumulation (NBIA) who have had mutations ruled out in other NBIA genes.
Carrier testing of family members of FTL patients with known 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) (Solutions A or B):

Adult: 5 mL
Child: 5 mL
Infant: 2-3 mL

Saliva: 2 ORAgene™ Saliva Collection 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 Collection 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.

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).

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)

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: