PGnome® - Whole Genome Sequencing
PGnome® Health Screen
|Name||Test Code||Description||CPT Code(s)||Price||Patient Prompt Pay Price|
|Patient Only||9000||WGS of patient||81425||$2,490||$2,241|
What is PGnome?
PGnome is PreventionGenetics' whole genome sequencing (WGS) test. This test provides hybridization-free/PCR-free sequencing of the full human genome. The primary benefit of PGnome is the detection of more variant types than any other genetic tests and higher sensitivity for single nucleotide variants (SNVs) and structural variants (SVs; defined here as copy number variants plus insertions and inversions) than competing technologies. PGnome is free from artifacts introduced by hybridization or PCR, and it analyzes non-coding portions of the genome not assessed by traditional exome sequencing. Together, these attributes make it more sensitive than whole exome sequencing (WES) for detecting SNVs and SVs.
Highlights of PGnome:
- Higher sensitivity for small CNV detection (~92% for single exon CNVs, ~100% for 2+ exons)
- Detection of repeat expansions in FMR1, c9orf72, and ATXN2
- Structural variants (SVs), including copy numbers gains and losses and complex rearrangements
Why order PGnome?
The PGnome 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. We identify and interpret all sequence variants (differences between the patient's sequence and the reference sequence (build hg19)), but we report only pathogenic and likely pathogenic variants (Richards et al. 2015. PubMed ID: 25741868).
TURN AROUND TIME (TAT)
PGnome Health Screen has a TAT of 5-7 weeks on average.
ORDERING / SPECIMENS
- Singleton – WGS on proband sample only.
Specimen Requirements and Shipping Details
Note that saliva and buccal specimens are not accepted for WGS. DNA from saliva invariably includes microbial and food DNA which interfere with WGS.
PGnome Health Screen will report variants in any gene that relate to an autosomal recessive or X-linked recessive disorder in females 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. Females who opt-in to carrier status findings will also be screened for FMR1 CGG-repeat expansion status. Variants in the mitochondrial genome will not be reported in this category. Patients can also opt-in to either of the secondary findings categories listed below:
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. Individuals will be screened for expansions in FMR1, c9orf72, and ATXN2 if they opt-in to this category. Variants in the mitochondrial genome will not be reported in this category.
Raw sequence data will be provided to the ordering physician upon request.
Sequencing: PGnome uses Illumina short-read next generation sequencing (NGS) technologies. As required, genomic DNA is extracted from patient specimens. Patient DNA is sheared, adaptors are ligated to the fragment ends, and the fragments are sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads. The following quality control metrics are generally achieved for the nuclear genome: >98% of targeted bases are covered at >15x, >96% of targeted bases are covered at >20x. The minimum acceptable average read depth is 35x. 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.
Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (https://www.hgvs.org). All differences from the reference sequences 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. PubMed ID: 25741868). Benign and likely benign variants are not reported.
Structural Variants: Three SV calling algorithms are employed (Lumpy, CNVnator, and Manta) that utilize read depth, SNP information, split reads, and reads which map to two different sites in the genome to detect deletions, duplications, insertions and inversions. The overall sensitivity for deletions, duplications, and inversions is 96%. Sensitivity for detection of insertions (as opposed to duplications) is currently low (~20%). At this time, balanced translocations are not reported. The ability to detect SVs due to somatic mosaicism is limited.
Repeat Expansions: For the repeat expansion screen, individuals with phenotypes and/or family history consistent with ATXN2, c9orf72, and/or FMR1-related disease or who opt-in for ‘Other Predispositions/Diagnoses’ secondary findings will be evaluated for expansions in these genes. In addition, female patients that opt-in for Carrier Status findings will be screened for expansions in FMR1. Our genome test screens for expanded allele repeat sizes in ATXN2, c9orf72, and FMR1 with nearly 100% analytical specificity and sensitivity. Any potential expansions detected by the screening test will be confirmed with the appropriate confirmatory clinical repeat expansion test. Only those expansions that are confirmed will be reported.
LIMITATIONS AND OTHER TEST NOTES
Limitations of NGS: 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 genetic disorders improves.
Sequencing: This test will not cover 100% of the genome. Parts of the genome cannot be readily sequenced with current technology such as some tandem repeats, paralogous genes and other repeat sequences. Therefore, a small fraction of sequence variants relevant to the patient's health will not be detected.
When Next Generation Sequencing (NGS) or Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, 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 for example to a large deletion or insertion.
Detailed variant analysis and interpretation is focused on the coding exons and immediate flanking non-coding DNA (± 10 bp). We do not attempt to interpret every variant outside of coding and immediate flanking regions. When warranted by sequence results (for example a single pathogenic variant in a recessive gene), rare variants within selected genic regions will be investigated.
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.
The ability to detect low-level mosaicism of variants is limited.
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. Genome build hg19, GRCh37 (Feb2009) is used as our reference in nearly all cases.
Structural Variants (SVs): Sensitivity for detection of insertions (as opposed to duplications) is currently low (~20%). At this time, we are not reporting translocations. Our ability to detect SVs due to somatic mosaicism is limited. On occasion, it will not be technically possible to confirm a smaller SV called by NGS. In these instances, the SV will not be included on the report.
Repeat Expansion Screening: Tests that meet our eligibility criteria for repeat expansion screening (described above in Test Methods) 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.
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.
Genetic Counselors: GC Team - email@example.com
Amendola et al. 2015. Genome Res 25(3):305- 315
Borry et al. 2006 Clin Genet 70(5):374-81
Borry et al. 2006. Eur J Hum Genet 14(2):133-8
Dorschner et al. 2013. Am J Hum Genet 93(4):631-640
Fallat et al. 2013 Pediatrics 131(3): 620–2; NSGC Position Statement 2017
Lucassen et al. 2010 British Society for Human Genetics
Miller et al. 2023. PubMed ID: 37347242
NSGC Position Statement 2012
Richards et al. 2015. PubMed ID: 25741868
Ross et al. 2013 Genet Med 15(3):234-245