Background:
Pantothenate kinase-associated neurodegeneration (PKAN) (previously known as Hallervorden-Spatz syndrome) is a progressive neurodegenerative disorder with brain iron accumulation. Symptoms include progressive dystonia, dysarthria, rigidity, and retinitis pigmentosa. Classical PKAN has its onset in the first decade of life; atypical PKAN presents with later onset and slower disease progression. The disease is autosomal recessive and is caused by mutations in the pantothenate kinase 2 (PANK2) gene.
Reasons for Referral
- Confirmation of clinical diagnosis in patients with classic or atypical PKAN.
- Carrier testing of family members of PKAN patients.
- Prenatal diagnosis of known familial PKAN mutations.
Methodology:
Next generation sequencing (NGS) will analyze the exons or coding regions of three Autosomal Dominant Osteogenesis Imperfecta-associated genes 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.
Test reporting follows the American College of Medical Genetics (ACMG) guidelines.
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.
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
- 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 CVS or Amniotic Fluid Specimens:
- Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood 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:
- 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:
Additional Info:
Custom sequencing of known familial mutations may be available; each request will be addressed given the specific parameters of each case. Please call Client Services at (855) 535-1522 prior to submitting samples.
Prior to any genetic testing we recommend genetic counseling. To receive forms and information about prenatal diagnostic testing, please contact Client Services.