Molecular Genetics Beta-Propeller Protein-Associated Neurodegeneration (BPAN), WDR45 Sequencing

Test Code:

1080
Department:

Molecular Genetics
Test Synonyms:

WDR45 sequencing • BPAN sequencing • NBIA Sequencing
CPT Code(s):

81479

Background:

Mutations in WDR45 are associated with beta-propeller protein-associated neurodegeneration (BPAN), an X-linked form of neurodegeneration with brain iron accumulation (NBIA). Patients with BPAN have characteristic brain MRI results (including T1 hyperintense and T2 hypointense signals in the substantia nigra), along with global developmental delay in childhood, regression in early adulthood, as well as progressive dystonia, parkinsonism and dementia. Additionally, patients with BPAN have similar phenotypic characteristics to individuals diagnosed with atypical Rett syndrome. If Rett specific mutations are not identified in those patients, WDR45 mutational analysis should be considered. All mutations in WDR45 are suspected to arise de-novo, however due to the X-linked nature of the gene females may have germline or somatic mutations while males will have somatic mutations.

Reasons for Referral:

Individuals with characteristic BPAN brain MRI results
Individuals identified with developmental delay accompanied by seizures and/or disordered sleep
Individuals identified with symptoms of atypical Rett syndrome

Methodology:

Sequencing can be performed by either Sanger Sequencing or Next-Generation Sequencing.

Sanger Sequencing: Sequencing of WDR45 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 (NGS) will analyze the exons or coding regions of the genes using Illumina NextSeq 500/550 technology and preparing samples 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: 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.

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

DNA: 1-2µg at a minimum of 50-100ng/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-T25 flasks)
Cultured CVS
Cultured Fetal Tissue: Product of Conception (2 T-25 flasks)
Cord Blood (1-2mL.)

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, saliva and buccal swabs, 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:

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: