PGmax^TM - Neonatal Crisis Panel

Due to the genetic heterogeneity of the disorders tested in this panel, the clinical sensitivity of this specific grouping of genes is difficult to estimate. We are currently unaware of any reports in the literature in which these genes have been sequenced together.

PHOX2B has two polyalanine repeat regions in exon 3; expansion of this second polyalanine repeat region results in congenital central hypoventilation syndrome (CCHS; for a review, see Weese-Mayer et al. 2021. PubMed ID: 20301600). In individuals with suspected CCHS, ~90-92% of causative mutations are due to expansions of this repeat region (Weese-Mayer et al. 2021. PubMed ID: 20301600). Note that this repeat expansion screen is only available to tests ordered on the PGnome platform, as these expansions are often undetectable on exome-based panels.

Reporting:

Reports will consist of two different sections:

• Variants in genes known to be associated with phenotype
• Variants in genes possibly associated with phenotype

All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories (Pathogenic, Likely Pathogenic, Variant of Uncertain Significance, Likely Benign and Benign) per ACMG Guidelines (Richards et al. 2015). Pathogenic, Likely Pathogenic and Variants of Uncertain Significance considered to contribute to the proband's phenotype will be reported in the first and second sections.

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).

Exome-wide CNV analysis is included at no additional charge as part of this test.  As part of this analysis, we will report any rare deletions ≥ 250 kb in size and duplications ≥ 500 kb in size. In rare cases, sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size, and inadequate coverage may impact our ability to identify and/or interpret a CNV.

If ordered on the PGnome platform, individuals will be screened for repeat expansions in PHOX2B. Variants in the mitochondrial genome will not be reported at this time.

If a concurrent expedited CMA test is ordered, results will be reported separately from the neonatal crisis test results. For details on our CMA testing, please see the separate CMA test description page.

Limitations and Other Test Notes:

Interpretation of the test results is limited by the information that is currently available. Enhanced interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder accumulate. A negative finding does not rule out a genetic diagnosis.

When sequencing does not reveal any heterozygous differences from the reference sequence, we cannot be certain that we were able to detect both patient alleles. Occasionally, a patient may carry an allele which does not capture or amplify, due to a large deletion or insertion. In these cases, the report will contain no information about the second allele.

For technical reasons, the Newborn Crises test is not 100% sensitive. Some exons cannot be efficiently captured, and some genes cannot be accurately sequenced because of the presence of multiple copies in the genome. Therefore, a small fraction of sequence variants relevant to the patient's health will not be detected.

In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.

In order to offer the fastest possible turnaround time for this test, results of copy number variant (CNV) analysis may be reported at a later date than the results of the sequencing portion of the test.

Tests that meet our eligibility criteria for repeat expansion screening (described above in Testing Strategy) must have locus coverage of at least 20x for data to be considered reliable. This screen may not detect low-level mosaic expansions. Any potential expansions will be confirmed with an appropriate confirmatory repeat expansion test. Only results from the confirmatory repeat expansion test (including repeat count and methylation status, if applicable) will be included in the final report.

We sequence coding exons for most given transcripts, plus ~10 bp of flanking non-coding DNA for each exon. Unless specifically indicated, test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions, uncharacterized alternative exons, chromosomal rearrangements, repeat expansions, epigenetic effects, and mitochondrial genome variants.

In most cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative variants for recessive disorders, we cannot be certain that the variants are on different alleles, unless parental specimens are also tested.

Our ability to detect minor sequence variants due to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient's nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during amplification.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes if taken from whole blood). Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics. However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Genetic counseling to help to explain test results to the patients and to discuss reproductive options is recommended.