PGxome® - Whole Exome Sequencing
Test Requisition Form
PGxome® Diagnostic Exome Test
| Name | Test Code | Description | CPT Code(s) | Price | Patient Prompt Pay Price |
|---|---|---|---|---|---|
| Family - Trio | 5300 | WES of patient + 2 additional family members | 81415, 81416(x2) | $2,490 | $2,241 |
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If report is needed for any additional family members, add $590 per family member. |
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| Family - Duo | 5200 | WES of patient + 1 additional family member | 81415, 81416 | $2,490 | $2,241 |
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If report is needed for any additional family members, add $590 per family member. |
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| Patient Only | 5000 | WES of patient | 81415 | $1,890 | $1,701 |
Sequencing cost to additional family members beyond trio: $390 (no report); additional CPT Code 81416
PGxome Sequencing Panel Reflex to PGxome
| Number of Genes Ordered | Pricing | ||
|---|---|---|---|
| 1 - 100 | $1,200 | $1,800 | |
| 101 - 300 | $900 | $1,500 | |
| > 300 | $400 | $1,000 |
What is PGxome Diagnostic?
PGxome is PreventionGenetics' whole exome sequencing (WES) test. The PGxome assesses almost all genes from the human genome including coding regions and adjacent introns. This test is intended for health care providers who are looking for a genetic diagnosis when the clinical phenotype is unclear and/or previous test results have been uninformative. This is important as more than 50% of patients with genetic diseases are not given a specific diagnosis even after repeat clinical examinations and tests (Shashi et al. 2014). The standard clinical practice often involves examinations for specific phenotypes, imaging, biochemical testing for inborn errors of metabolism, genomic tests such as karyotyping or microarrays, and single gene or panel tests (Iglesias et al. 2014). However, patients remain without a genetic diagnosis, and patients and health care providers are caught in a long term diagnosis search, known as a diagnostic odyssey. This can lead to failures in identifying potential treatments and unknown recurrence and prognosis risks (Yang et al. 2013).
Reported diagnostic rates from commercial and academic laboratories have found that WES assays have a ~20-40% positive diagnostic rate, with higher rates being reported from trio analysis (i.e. proband and parents) compared to singleton analysis (Atwal et al. 2014; Iglesias et al. 2014; Farwell et al. 2015). Notably, ~5-7% of individuals who have WES have had dual diagnoses (i.e. two non-overlapping clinical presentations) (Yang et al. 2014; Farwell et al. 2015; Posey et al. 2016). The inclusion of copy number variant (CNV) calling should increase diagnostic rates. One study reported that 30% of genetics diagnoses have only been recently resolved due to new literature reports, highlighting the fast pace of gene-disease discovery and the need of genetic testing laboratories to be current of the medical literature (Yang et al. 2014). The use of a whole exome sequencing test may aid in altering clinical management, predict recurrence and prognosis risks, reduce costs of additional testing, and may offer advantages over traditional molecular tests in certain patients (Valencia et al. 2015).
PGxome - Diagnostic is ideal for individuals with:
- Unresolved genetic testing such as normal karyotyping or microarray analysis, and negative single gene or gene panel sequencing results
- Disorders with significant genetic heterogeneity
- Global developmental delay/intellectual disability, with or without dysmorphic features
- Dysmorphic features, multiple congenital anomalies, or birth defects
TURN AROUND TIME (TAT) 
PGxome Diagnostic has a TAT of 5-7 weeks on average.
Inclusion of detailed clinical notes/completion of the clinical data checklist and a pedigree are required. The ability to select variants that may be involved with the patient’s health problem directly correlates with the quality of clinical information provided.
ORDERING / SPECIMENS
Our PGxome Diagnostic test offers the traditional options of Patient Only testing or Family testing (Duo or Trio). We encourage trio testing for the highest diagnostic yield, and most cost-effective strategy. Please note that trio testing, in addition to filtering for genotype and phenotype:
- Can identify de novo variants regardless of phenotype match or classification
- Allows for more relevant reporting of Variants of Uncertain Significance (VUS)
- Inclusion of relevant variants that may have lacked adequate phenotype support to consider in a singleton
- Exclusion of irrelevant variants based on parental phenotype and inheritance
- Potential increased diagnostic yield for patients with:
- Atypical presentation
- Complex phenotype (ie: dual diagnosis)
- Early developmental stage where phenotype has not evolved.
When ordering family testing (duo or trio) all comparator samples are required to initiate testing. If all required are not received within 21 days the order will be converted to the most cost effective testing strategy with the samples available Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Requirements and Shipping Details
TEST METHODS
For the PGxome 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: >97% 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. CNVs that pass our interval quality metrics are not confirmed using another technology.
REPORTING
Reports will consist of up to six different sections:
Primary Findings (related to the indication for testing)
- Variants in genes known to be associated with phenotype, including VUS
- Variants in genes possibly associated with phenotype, including VUS
Secondary Findings (if opted in on the requisition form)
- Guideline Recommended Genes: Recent recommendations are that labs performing WES or WGS should report pathogenic variants in selected genes that cause (mostly) dominantly inherited disorders (Version 3.2, Miller et al. 2023. PubMed ID: 37347242). These disorders are treatable and/or preventable. Included on this list are some cancer predisposition conditions, heart conditions associated with sudden death, and conditions that could result in severe health consequences if surgery is performed with certain anesthetics. Only pathogenic and likely pathogenic variants are reported.
- Other Predispositions/Diagnoses: This secondary finding option refers to a very broad range of disorders, including adult-onset neurological conditions such as Alzheimer's disease, Parkinson disease, amyotrophic lateral sclerosis (ALS), small vessel disease, and renal disease, among others. Some of these disorders are very serious, leading to death. Treatment or prevention will be effective for some of these disorders but not for others. Knowledge of these predispositions may be useful for the patients and their families (Amendola et al. 2015. Genome Res 25(3):305- 315; Dorschner et al. 2013. Am J Hum Genet 93(4):631-640). If this option is selected, we will report all variants that are likely to result in a Mendelian (single gene) disorder (i.e., one variant in a dominant gene or X-linked gene or two variants in a recessive gene). Many of these conditions have adult onset, and in accordance with current professional guidelines (Borry et al. 2006 Clin Genet 70(5):374-81; Lucassen et al. 2010 British Society for Human Genetics; Fallat et al. 2013 Pediatrics 131(3): 620–2; NSGC Position Statement 2017) we do not recommend release of information about adult-onset conditions to minors (under the age of 18 years). For minors, we recommend that this testing be postponed until the age of 18 years or that access to this portion of their healthcare records be blocked until they reach 18 years. Only pathogenic and likely pathogenic variants are reported.
- Carrier Status: Variants in any gene that relate to an autosomal recessive or X-linked recessive disorder in females will be reported if this option is selected (regardless of the incidence of the condition). Such single recessive, pathogenic variants usually don’t appreciably affect a patient’s health, but may be useful in reproductive planning. In accordance with current professional guidelines Borry et al. 2006. Eur J Hum Genet 14(2):133-8; NSGC Position Statement 2012; Ross et al. 2013 Genet Med 15(3):234-245), we do not recommend release of carrier information to minors (under the age of 18 years), we do not recommend release of carrier information to minors (under the age of 18 years). For minors, we recommend that carrier testing be postponed until the age of 18 years or that access to this portion of their healthcare records be blocked until they reach 18 years. Only pathogenic and likely pathogenic variants are reported.
- PG Discovery (Candidate Genes, Available for Trios with Parents Only): WES provides the opportunity to identify rare variants in candidate genes for which there is limited available evidence. Relevant rare homozygous, hemizygous, compound heterozygous, and/or de novo variants are reported. These genes and variants reported within them will be classified as uncertain significance, and the variants will not be confirmed by a second method (usually Sanger sequencing). Any literature, such as limited animal studies, etc., is referenced where available. Further research is required to understand if any human disease association exists. PreventionGenetics may reach out to request consent for submission of these variants to research programs and databases like GeneMatcher (https://genematcher.org/). Only uncertain variants are reported.
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). Only relevant pathogenic, likely pathogenic, and uncertain variants are reported. Benign and likely benign variants are not reported. Sequencing data is available to the ordering physician upon request.
Nomenclature for sequence variants comes from Human Genome Variation Society (HGVS) (http://www.hgvs.org).
LIMITATIONS AND OTHER TEST NOTES
Interpretation of the test results is limited by the information that is currently available. Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.
Sequencing: 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.
For technical reasons, the PGxome 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.
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 mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
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.
Copy Number Variant Analysis: The PGxome test detects most deletions and duplications including intragenic CNVs and large cytogenetic events; however, aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of 4 exons or larger is >95% but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.
Balanced translocations or inversions are only rarely detected.
Certain types of sex chromosome aneuploidy may not be detected.
In nearly all cases, our ability to determine the exact copy number change within a targeted region is limited.
Our ability to detect CNVs due to somatic mosaicism is limited.
The sensitivity of this test is dependent on DNA quality.
General: 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 specimen arrives at PreventionGenetics.
A negative finding does not rule out a genetic diagnosis.
Genetic counseling to help to explain test results to the patients and to discuss reproductive options is recommended. Results of PGxome testing can be used for both diagnostic and scientific research purposes.
CONTACTS
Genetic Counselors: GC Team - support@preventiongenetics.com
REFERENCES
Amendola L. et al. 2015. Genome Res 25:305- 315. PubMed ID: 25637381
Atwal P.S. et al. 2014. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 717-9. PubMed ID: 24525916
Borry P. et al. 2006. Clin Genet. 70:374-81. PubMed ID: 17026616
Dorschner M. et al. 2013. Am J Hum Genet 93:631-640. PubMed ID: 24055113
Farwell K.D. et al. 2015. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 17: 578-86. PubMed ID: 25356970
Iglesias A. et al. 2014. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 922-31. PubMed ID: 24901346
Lucassen et al. 2010. British Society for Human Genetics PubMed ID:
Miller D. et al. 2023. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PubMed ID: 37347242
Posey et al. 2016. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 18: 678-85. PubMed ID: 26633545
Richards S et al. 2015. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 17: 405-24. PubMed ID: 25741868
Shashi V. et al. 2014. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 176-82. PubMed ID: 23928913
Yang Y. et al. 2013. The New England Journal of Medicine. 369: 1502-11. PubMed ID: 24088041
Yang Y. et al. 2014. JAMA. 312: 1870-9. PubMed ID: 25326635