Background:
Neurodegeneration with Brain Iron Accumulation (NBIA) is a group of neurodegenerative diseases associated with abnormal iron accumulation in the basal ganglia, most often in the globus pallidus or substantia nigra. Common findings across the NBIA spectrum include progressive dystonia, spasticity, dysarthria, parkinsonism, neuropsychiatric changes, and ophthalmologic changes. The age of onset varies from infancy to late adulthood, and progression can be rapid or slow with long periods of stability. Eleven types and their associated genes have been described. Although cognition is usually spared, cognitive decline or intellectual disability are common in some forms. The diagnosis is suspected when abnormal brain iron accumulation is appreciated on MRI, often in association with other findings. However, both clinical findings and molecular genetic testing establish the diagnosis of specific types of NBIA.
This panel is the most comprehensive clinical NBIA testing panel currently available. It includes genes associated with well-described NBIA disorders, as well as thoughtfully selected genes associated with new emerging phenotypes, related disorders, and disorders with imaging findings that mimic NBIA. The results of each NBIA panel are reviewed by Dr. Susan Hayflick, who discovered many of the genes associated with NBIA, is internationally recognized as a leading expert in these disorders, is actively advancing novel gene therapies, and provides consultation on NBIA disorders to physicians around the world. For consultation by the clinical team, please contact Allison Gregory, MS, CGC by email at gregorya@ohsu.edu or at 503-494-4344.
Reasons for Referral:
- Confirmation of a suspected clinical diagnosis in patients with the hallmark findings of NBIA.
- Further assessment of patients with clinical diagnosis of idiopathic NBIA who have had mutations ruled out in other genes.
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 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.
Neurodegeneration with Brain Iron Accumulation (NBIA) Panel (36 genes):
AP4B1, AP4E1, AP4M1, AP4S, ATP13A2, C19orf12, CACNA1I, CIAO1, COASY, CP, CRAT, DCAF17, FA2H, FTL, FTH1, FUCA1, GTPBP2, KIF1A, KMT2B (MLL4), MECR, PANK2, PDGFB, PDGFRB, PLA2G6, PSEN1, REPS1, SCP2, SLC20A2, SLC39A14, SQSTM1, TRIM32, UBTF, VAC14, VPS13A, WDR45, XPR1
Specimen Requirements:
Blood: EDTA or ACD (Solution 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.
- Please note that buccal samples may yield a limited amount of DNA, and additional specimens may be required for confirmatory or supplementary testing.
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, saliva, and buccal swabs (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:
6-8 weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
- Gregory A. and Hayflick S., 2014. GeneReviews: http://www.ncbi.nlm.nih.gov/books/NBK121988/
- Maio N., Orbach R., Zaharieva I., Töpf A., Donkervoort S., Munot P., Mueller J., Wilis T., Verma S, Peric S., Krishnakumar D., Sudhakar S., Foley A.R., Silverstein S., Douglas G., Pais L., DiTroia S., Grunseich C., Hu Y., Sewry C., Sarkozy A., Straub V., Muntoni F, Rouault T., Bönnemann C.G. Loss of Function of the Cytoplasmic Fe-S Assembly Protein CIAO1 Causes a Neuromuscular Disorder with Compromise of Nucleocytoplasmic Fe-S Enzymes. MedRxiv. 2020 Dec 20. Loss of Function of the Cytoplasmic Fe-S Assembly Protein CIAO1
Additional Info: