PGxome® - Whole Exome Sequencing

Test Requisition Form

PGxome® Health Screen Exome Test (Test Code #4000)

Name Test Code Description CPT Code(s) Price
Singleton Pricing 4000 Sequencing and report 81415 $1,490
Couple Pricing 4200 Sequencing and report for each person 81415 (x2) $2,590
Please order through the
Requisition Form

What is PGxome Health Screen?

PGxome is PreventionGenetics' whole exome sequencing (WES) assay. The PGxome assesses almost all genes from the human genome including coding regions and adjacent introns. The PGxome Health Screen is intended for patients who are basically healthy but who want to learn their carrier status for recessive disease, their susceptibility to adult onset disorders, or both.

Although we sequence nearly all human genes, we analyze and report sequence variants and copy number variants (CNVs) only in genes that have been proven with high confidence to be involved in Mendelian (also called single gene) disorders (MacArthur et al. 2014). Our list of "clinically-relevant" genes currently includes about 4800 genes and is updated quarterly. We do not report variants in genes that for technical reasons cannot be accurately sequenced (primarily due to the presence of pseudogenes).

In addition, although we identify and interpret all sequence variants (differences between the patient's sequence and the reference sequence (build hg19)), we report only pathogenic and likely pathogenic variants (Richards et al. 2015).

We have found through our exome sequencing at PreventionGenetics that the average person is a recessive disease carrier for less than five pathogenic or likely pathogenic variants. Note, however, that the average person also carries approximately 75 variants of uncertain significance and thousands of benign variants.

For this test, patients also have the option of receiving results of pathogenic and likely pathogenic variants in genes that predispose to or confirm a diagnosis of adult onset disorders such as cancer and heart disease (Kalia et al. 2016).

TURN AROUND TIME (TAT)

PGxome Health Screen has a TAT of 28 calendar days on average.

ORDERING / SPECIMENS

Singleton Pricing (sequencing and report): $1,490

Couple Pricing (sequencing and report for each person): $2,590

PGxome Health Screen Test Requisition Form (Required)

Test Code: #4000

CPT Code: 81415 (x2 if couple)

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. All reported CNVs are confirmed using another technology such as aCGH, MLPA, or PCR.

REPORTING

Reports will consist of up to three different sections:

  • Carrier Status: Variants in any gene that relate to an autosomal recessive or X-linked recessive disorder (in females) would 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). For minors, we recommend that carrier testing be postponed until the age of 18 years or access to this portion of their healthcare records be blocked until they reach 18 years. Only pathogenic and likely pathogenic variants are reported.
  • Guideline Recommended Genes: The American College of Medical Genetics and Genomics recommends all labs performing WES or WGS report pathogenic variants in specific  genes that cause certain, mostly dominantly inherited disorders (v3.0; Miller et al. 2021. PubMed ID: 34012068). 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 beyond the Recommended Genes above. Examples vary widely and include adult onset neurological conditions such as Alzheimer's disease, Parkinson disease, amyotrophic lateral sclerosis (ALS), and small vessel disease, as well as cancer predispositions and renal conditions, among others. Some of these disorders are very serious, leading to death. While treatment or prevention will be effective for some of these disorders but not others, knowledge of these predispositions may be useful for the patient and their family. (Amendola et al. 2015. Genome Res 25(3):305- 315; Dorschner et al. 2013. Am J Hum Genet 93(4):631-640). Some people may want to know about these disorders while others may prefer not to know. If this option is selected, we will report all pathogenic and likely pathogenic variants in genes 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 this testing be postponed until the age of 18 years or access to this portion of their healthcare records be blocked until they reach 18 years. Only pathogenic and likely pathogenic 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). 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.

Due to 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 causative sequence variants will not be detected. For those planning reproduction, we cannot guarantee a child free of genetic disorders.

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.

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

Geneticist: Diane Allingham-Hawkins, PhD, FCCMG, FACMG - diane.allingham-hawkins@preventiongenetics.com

REFERENCES

Caudle et al. 2016. Genetics in Medicine. PubMed ID: 27441996

Kalia S.S. et al. 2016. Genetics in Medicine: Official Journal of the American College of Medical Genetics. Advance online publication. doi:10.1038/gim.2016.190. PubMed ID: 27854360

MacArthur D.G. et al. 2014. Nature. 508: 469-76. PubMed ID: 24759409

Miller D. et al. 2021. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PubMed ID: 34012068

Richards S. et al. 2015. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 17: 405-24. PubMed ID: 25741868