Neonatal Crisis Panel

Summary and Pricing

Test Requisition Form

Test Method

Exome Sequencing with CNV Detection
Test Type Test Code Total Price Prenatal
Family - Trio (NICU panel of patient + 2 additional family members) 10066 $2490 Add to Order
Family - Duo (NICU panel of patient + 1 additional family member) 10065 $2290 Add to Order
Patient Only (NICU panel of patient) 7383 $1890 Add to Order
Genes CPT Codes
Genes x(1991) 81161(x1), 81162(x1), 81173(x1), 81175(x1), 81185(x1), 81189(x1), 81222(x1), 81223(x1), 81236(x1), 81238(x1), 81249(x1), 81252(x1), 81259(x1), 81269(x1), 81302(x1), 81304(x1), 81307(x1), 81321(x1), 81323(x1), 81324(x1), 81325(x1), 81363(x1), 81364(x1), 81400(x1), 81403(x10), 81404(x52), 81405(x94), 81406(x110), 81407(x32), 81408(x19), 81479(x3636)
Add-On Testing Option Test Code Price CPT Code
Expedited, Concurrent CMA (patient only) 10064 $1390 81229

For a full list of genes click here.

For a full list of disorders click here.

Pricing Comment

We are happy to accommodate requests for single genes or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered on our PGxome Custom Panel.

Sequencing cost to additional family members beyond trio: $390 (no report).

If report is needed for any additional family members, add $490.

The price to reflex to PGxome is $390.

Turnaround Time

The Neonatal Crisis panel has an expedited turnaround time of 13 calendar days on average, with a preliminary communication within an average of 9 days. This preliminary communication will be either a preliminary report or an update regarding expected TAT for the final report.

We recommend that providers choose expedited shipping to decrease the time samples spend in transit to PreventionGenetics.

Please note that 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.

Although the sensitivity of the NGS-based CNV analysis included along with this sequencing panel is comparable to that of chromosomal microarray (CMA) analysis, we realize that there are circumstances under which a concurrent CMA test may be desired. For those cases, we are able to offer a concurrent expedited CMA with a maximum turnaround time of 10 days (assuming sample quality that meets our requirements for CMA analysis and barring technical difficulties).

 

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Many known monogenic diseases may present early in life as severe neonatal or early childhood (<2 years old) illness. In the United States, such diseases account for ~20% of infant deaths and ~18% of pediatric hospitalizations (Kingsmore. 2012. PubMed ID: 22872815; Saunders et al. 2012. PubMed ID: 23035047). Recent studies have shown that genetic testing in such patients can be a very beneficial first-line test, as the results may provide a comprehensive molecular diagnosis that allows for early intervention for the patient, proper genetic counseling of the family, and may reduce the time spent in the diagnostic odyssey (Kingsmore. 2012. PubMed ID: 22872815; Saunders et al. 2012. PubMed ID: 23035047; Ceyhan-Birsoy et al. 2017. PubMed ID: 28079900).

In recent studies, thorough curation of clinically relevant genes has shown that ~500-1000 genes are typically associated with the majority of the severe infant or early childhood onset genetic disorders (Kingsmore. 2012. PubMed ID: 22872815; Ceyhan-Birsoy et al. 2017. PubMed ID: 28079900). Clinically, such patients may present with a wide-variety of non-specific symptoms, including but not limited to: respiratory distress, hypotonia, gastrointestinal distress, difficulty feeding, failure to thrive, lethargy, seizures, encephalopathy, cardiac defects, organomegaly, unusual facial features, abnormal odor, and metabolic disturbances (Saudubray and Cazorla. 2016). In addition, we have recently updated this test to include disorders that may present prenatally with abnormal ultrasound findings (Pangalos et al. 2016. PubMed ID: 27168972, genes analyzed from the most updated version of the Fetalis pipeline as of October 2018).

Genetics

The majority of the genes in this test have been included in large gene panels designed for testing of disorders with severe neonatal or early childhood onset (Kingsmore. 2012. PubMed ID: 22872815; Ceyhan-Birsoy et al. 2017. PubMed ID: 28079900). In the more recent study by Ceyhan-Birsoy et al. (2017), genes were divided into several categories. For this test, we have included the majority of the genes classified as Category A (genes with definitive or strong evidence to cause a highly penetrant childhood-onset disorder) in their study. In addition, we have included a number of nuclear genes that have been recently associated with mitochondrial disorders (Craven et al. 2017. PubMed ID: 28415858) as well as recently reported genes associated with disorders with a prenatal, neonatal or early-childhood onset and phenotype relevant to this test (Pangalos et al. 2016. PubMed ID: 27168972)..

The full list of genes sequenced in this test is available under the “Summary and Pricing” tab.

Testing Strategy

The Neonatal Crisis Panel offers the traditional Patient Only testing as well as the options of Family testing (e.g., Duo, Trio, etc.). For the highest diagnostic rate, Family - Trio testing is recommended.

For the Neonatal Crisis Panel, we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: 98.9% of target bases are covered at >20x and mean coverage of target bases >100x. Data analysis and interpretation is performed by the internally developed Infinity pipeline. Variant calls are made by the GATK Haplotype caller and annotated using in house software and Jannovar. Common benign, likely benign, and low quality variants are filtered from analysis.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All reported CNVs are confirmed using another technology such as aCGH, MLPA, or PCR.

The report will not include all the observed variants in a patient due to the large number of genes included. However, the list of variants is available, along with our interpretations, upon request. Since this test is performed using exome capture probes, a reflex to exome sequencing may be ordered. Please see the PGxome page (Test #5000) for limitations and reporting criteria for this test.

Clinical Sensitivity

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.

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 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.

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.

Indications for Test

This test is primarily implicated for patients with neonatal, infantile or early childhood onset severe disorders with a suspected genetic cause.

Citations

  • Ceyhan-Birsoy et al. 2017. PubMed ID: 28079900
  • Craven et al. 2017. PubMed ID: 28415858
  • Kingsmore. 2012. PubMed ID: 22872815
  • Pangalos et al. 2016. PubMed ID: 27168972
  • Saudubray and Cazorla. 2016. Clinical Approach to Inborn Errors of Metabolism in Pediatrics. In: Saudubray JM, Baumgartner MR, and Walter J, editors. Inborn Metabolic Diseases: Diagnosis and Treatment. Berlin: Springer, p 8-14.
  • Saunders et al. 2012. PubMed ID: 23035047

Ordering/Specimens

Ordering Options

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details