Diagnostic testing:
- Positive newborn screening for PAH deficiency (provide copy of newborn screening results, if available)
- Biochemical analysis indicative for PAH deficiency (provide copy of biochemical results if available)
Carrier testing:
- At least one affected or carrier relative
- Partner is affected or carrier
This test detects sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of PAH (NM_000277.3). Selected known pathogenic non-coding variants are also covered by this assay (ClinVar IDs: 607, 102508).
Targeted regions are enriched using hybridization probes (IDT) and sequencing libraries are prepared using the Illumina DNA Prep with Enrichment kit. Paired-end massively parallel sequencing of 150-bp fragments is performed with an Illumina instrument. Sequences are aligned and compared to reference genome GRCh37. Sample identity is confirmed in parallel using Applied Biosystems™ SNaPshot™ Multiplex Kit. Clinically relevant copy number variants are confirmed by an orthogonal method (gap-PCR, TaqMan, MLPA or microarray).
Based on validation study results, this test achieves >99% analytical sensitivity and specificity for SNVs, indels and CNVs. A negative result does not rule out the possibility that a rare variant not detected by this assay is present in the individual. This test does not detect all possible variants in the gene tested. Unless explicitly specified, only coding exons and flanking intronic regions are covered by this assay. Furthermore, technically challenging variant types, such as large indels, small CNVs, complex rearrangements, low-complexity repeat associated, segmental duplication associated, and postzygotic variants, may not be detected (PMID: 34007000). Interpretation of results is highly dependent on the clinical and demographic information provided.
Only clinically relevant variants are reported. Benign/likely benign variants and variants of uncertain significance with limited evidence for pathogenicity are not reported. Variants of uncertain significance are not reported if the testing indication is carrier status.
Turnaround time: 4-6 weeks
Specimens accepted:
- 2 x 4 mL blood in EDTA tubes (purple top tube) – 2 mL for newborns
- DNA: min 10 ug
- Amniotic fluid: min 10 ml
- Direct CVS: min 10 mg direct villi
- Cultured amniocytes or CVS: 2 x T25 flasks (confluent)
- For any other sample type, contact the laboratory for testing availability
Submit your test request using our molecular genetics requisition.