Background:
Mitochondrial membrane Protein-Associated Neurodegeneration (MPAN) is characterized by progressive dystonia, spasticity, paraparesis or tetraparesis, optic atrophy, psychiatric changes (ADHD-like behavior, mood swings), and evidence of iron accumulation in both the globus pallidus and substantia nigra on T2-weighted MRI. Onset generally occurs in childhood to early adulthood with slow progression and survival well into adulthood.
MPAN is observed in ~10% of NBIA patients and mutations in c19orf12 are observed in 95% of patients with a clinical diagnosis of MPAN. Mutations in MMIN are observed in ~40% of patients with a negative mutation test for other NBIA-associated genes, eg. PANK2, PLA2G6, CP and FTL (Hartig et al. 2011).
Reasons for Referral:
- Confirmation of a suspected diagnosis in patients with the hallmark findings of MPAN.
- Further assessment of patients with clinical diagnosis of idiopathic Neurodegeneration with Brain Iron Accumulation (NBIA) who do not have an eye-of-the-tiger sign and/or have had mutations ruled out in PANK2 or PLA2G6.
- Carrier testing of family members of MPAN patients with known mutations.
Methodology:
Sequencing using either Sanger Sequencing or Next-Generation Sequencing.
Sanger Sequencing: Sequencing of c19orf12 is carried out by amplification of all exons and intron/exon boundaries followed by bi-directional Sanger sequencing. The sensitivity of full gene sequencing is estimated to be approximately 99% for single nucleotide substitutions and small insertions/deletions. All nucleotide changes are analyzed within the context of current databases and literature to predict pathogenicity.
NGS: Next generation sequencing will analyze the exons or coding regions of c19orf12 using Illumina NextSeq 500/550 technology. Samples are prepared using hybridization probes to enrich exonic regions. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
Exon-level deletion/duplication analysis is performed by running the NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5mL
- Child: 5mL
- Infant: 2-3mL
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.
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 (1-2 mL)
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 outside of 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:
- Keep specimen cold during transit, but do not ship on dry ice.
- Please contact Client Services at (855) 535-1522 for shipping kits and instructions.
- Use the cold pack provided in the KDL shipping kit.
- Ship the specimen via overnight express, using the FedEx priority overnight label provided.
References:
- Hartig MB, Iuso A, Haack T, et al. Absence of an orphan mitochondrial protein, c19orf12, causes a distinct clinical subtype of neurodegeneration with brain iron accumulation. Am J Hum Genet. 2011 Oct 7;89(4):543-50.
Additional Info: