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

Test Code:

1080 • LAB101616 • LAB103682
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:

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 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.

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

DNA: 5-10µg 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 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:

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: