XomeDx (Whole Exome Sequencing)
XomeDx and XomeDxPlus test reports will include secondary findings, if present in the proband, as published in the American College of Medical Genetics and Genomics Recommendations for Reporting Incidental Findings in Clinical Exome and Genome Sequencing. We actively look for variants in these genes, as recommended by the ACMG, and confirm reportable secondary findings by Sanger sequencing. Patient samples sent for XomeDxSlice will not be evaluated for secondary findings and therefore will not receive secondary findings as part of their result.
GeneDx honors patient preferences and offers the choice to opt-out of receiving secondary findings. If a patient chooses to opt-out, patients must select the opt-out option on the test requisition form.
XomeDx/XomeDxPlus: Whole Exome Sequencing with or without mtDNA Sequencing and Deletion Testing
|Test Name||Description||More Information|
|XomeDx||XomeDx, or whole exome sequencing (WES), can be used to identify the underlying molecular basis of a genetic disorder in an affected individual and is best suited for patients who have a genetic condition that routine genetic testing has not been able to identify. The XomeDx test targets exons, which are the protein-coding regions of the human genome. Exons are captured and sequenced using massively parallel sequencing.|
|XomeDxPlus||XomeDxPlus includes whole exome sequencing as well as mitochondrial genome sequencing and deletion testing. For more information on the mitochondrial genome sequencing and deletion component of the XomeDxPlus testing, please visit our neurology/mitochondrial genetics page on our website. XomeDxPlus is best suited for individuals with clinical features suggesting a mitochondrial disorder.|
|Test Name||Description||More Information|
The XomeDxXpress test is whole exome sequencing with an expedited turnaround time (TAT) of approximately 2 weeks. A verbal result is given within 7 calendar days after the start of testing and will include pathogenic and/or expected pathogenic variants in known disease-causing genes (Human Genome Mutation Database genes). A written report including all clinically relevant, confirmed variants will be reported within approximately 2 weeks after the start of testing. Because of the rapid TAT, blood or DNA samples on the proband and both biological parents must be submitted at the same time, along with clinical information, in order to begin testing. This test requires approval by GeneDx; please email Xpress@GeneDx.com to discuss prior to sending in samples.
Please visit www.genedx.com/xomedxslice or more information on how to order XomeDxSlice
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(A phenotype-driven targeted exome test)
|XomeDxSlice captures and sequences the whole exome, but analysis is targeted to a limited and specific phenotype-driven gene list. The phenotype-driven gene list must be submitted using the XomeDxSlice online submission tool (link) by the ordering provider. Please review the instructions below.
XomeDxSlice is best suited for individuals with a clearly defined, oligogenic phenotype where a comprehensive gene panel is not available, or the patient has a single gene disorder for which clinical testing is not currently available.
|Test Name||Description||More Information|
XomeDxPrenatal is an expedited whole exome sequencing (WES) test for ongoing pregnancies with abnormal fetal ultrasound findings. There are two reporting options that offer patients a choice on the types of results that will be returned: XomeDxPrenatal Targeted and XomeDxPrenatal Comprehensive. Patients have the option of opting out of the ACMG secondary findings.
With a turnaround time (TAT) of 3-4 weeks, the fetal specimen and specimens from both biological parents must be submitted at the same time, along with clinical information, in order to begin testing. This test requires approval by GeneDx before ordering; please e-mail WESPrenatal@genedx.com to discuss cases prior to submitting samples.
GeneDx Policy on Secondardy Findings
GeneDx will report out known or expected pathogenic variants in the genes recommended by the American College of Medical Genetics and Genomics (ACMG). GeneDx is currently evaluating probands for ACMG SF v2.0 (Kalia et al., 2016). The presence or absence of the proband’s identified secondary findings is available for relatives who underwent whole exome sequencing or targeted segregation analysis as part of the proband’s test. ACMG secondary findings are not reported for relatives that opted out of receiving ACMG secondary findings. Variants that may be present in a relative, but are not present in the proband, would not be detected and therefore are not reported. Only variants that have been previously reported and are a recognized cause of the disorder (known pathogenic; KP) or variants that are previously unreported but are of the type which is expected to cause the disorder (expected pathogenic; EP), as specified in the ACMG recommendations are reported (Kalia et al., 2016; Green et al., 2013; Richards et al., 2015). Known or expected pathogenic variants may be present in a portion of the gene not covered by XomeDx and therefore would not be detected. The absence of reportable secondary findings for any particular gene does not mean there are no known or expected pathogenic variants in that gene, or other variants that may confer susceptibility to the disorders listed.
A current list of genes and disorders for which findings may be reported can be found here.
GeneDx offers other services for patients who have undergone XomeDx, XomeDxPlus or XomeDxSlice tests. There is a charge for these services.
|Service Available||Description||More Information|
|GeneDx can provide Mutation-Specific Testing for known familial mutations, in any gene, for families that have had previous XomeDx or XomeDxPlus testing at GeneDx. Mutation-Specific Testing is offered for both symptomatic and asymptomatic individuals, and for dominant or recessive mutations. Mutation-Specific Testing is less costly and more rapid than diagnostic analysis of the whole gene. Pricing is dependent on whether testing is done for one or two mutations. For XomeDx mutation specific testing, please click here to fill out the XomeDx form.||Informed Consent|
Release of Exome Aligned Sequence Data
GeneDx is able to release whole exome sequence (WES) data for individuals who have undergone XomeDx, XomeDxPlus, XomeDxXpress, or XomeDxPrenatal testing. Data is available as CRAM (compressed BAM file) or VCF files with the signed consent of the patient and applicable family members. GeneDx has generated this sequence data using Agilent Technologies SureSelect systems for human exome sequencing to target exon regions. The targeted regions were sequenced using an Illumina HiSeq sequencing system with 100bp paired-end reads. GeneDx has evaluated the data generated by the XomeDx test for the purpose of a genetic diagnosis based on the reported clinical features. GeneDx does not provide interpretation or confirmation by an orthogonal test method for variants unrelated to the patient’s clinical features as indicated to GeneDx at the time of testing. Variants not included in the GeneDx report should be considered research results and should not be used for medical management without appropriate confirmation and interpretation by a qualified genetics provider.
|Required Forms||Additional Forms and Useful Information|
1. When is whole exome sequencing useful?
Whole exome sequencing (WES) is a powerful diagnostic tool in 20-50% of patients (Yang, et al. N Engl J Med. 2013 Oct 17;369(16):1502-11, and GeneDx, unpublished data). GeneDx offers three different whole exome sequencing tests: XomeDx, XomeDxPlus (which includes mitochondrial genome sequencing and deletion testing) and XomeDxSlice (a phenotype-driven targeted exome test).
WES can be used to identify the molecular basis of a genetic disorder in an individual with:
- A genetically heterogeneous disease in which no single gene or group of genes makes up a significant percentage of the mutation spectrum,
- A long differential diagnosis for which sequential genetic testing is cost prohibitive
- An atypical presentation
- No molecular diagnosis after exhausting currently available genetic testing
2. What are the different WES tests that GeneDx offers and how do they differ?
There are three types of XomeDx tests:
- XomeDx is whole exome sequencing (nuclear genes only) with a phenotype-targeted report. Unless the patient opts-out in writing, we will report, if present, known and/or expected pathogenic variants in a specific subset of genes as secondary findings. This policy follows the policy statement by the American College of Medical Genetics and Genomics (ACMG) regarding the reporting of secondary findings in clinical exome sequencing.
- XomeDxPlus is a combined test including whole exome sequencing with sequencing and deletion testing of the mitochondrial genome.
- XomeDxSlice captures and sequences the whole exome, but analysis is targeted to a limited and specific phenotype-driven gene list. A list of genes to be analyzed is determined prior to testing by GeneDx and the ordering provider, please click here.
|Capture and sequencing of the exome (i.e. the exons of 20,000+ nuclear genes). Variants in genes that cause, or may be associated with, the patient’s phenotype are described in each report. All variants included in the report have been confirmed using a different test method.
Variants identified in the proband are evaluated and reported in the familial samples that have been submitted.
Secondary findings as recommended by the ACMG are reported as a default,but patients can opt-out, as indicated below.
|Capture and sequencing of the exome with reporting similar to XomeDx, PLUS sequencing and deletion testing of the mitochondrial genome (mtDNA).
Next generation sequencing of the mitochondrial genome can detect mtDNA mutations as low as 1.5%-5% heteroplasmy and large deletions (2 kb or larger) as low as 15% heteroplasmy.
Targeted testing by Sanger sequencing to determine the presence or absence of a mtDNA variant in the proband’s mother is performed (when a maternal sample has been submitted) and results are included in the proband’s report.
Other aspects of XomeDxPlus, including reporting variants in family members and incidental findings, are the same as XomeDx.
|Capture and sequencing of the exome with targeted analysis of genes chosen based on known associations with the patient’s phenotype.
The gene list must be reviewed and approved by GeneDx prior to the submission of a sample. Submit a gene list online using our online XomeDxSlice tool.
|Singletons are accepted. Sending the proband and both biological parents is strongly recommended, whenever possible. Other relatives that may be helpful for analysis are: affected and/or unaffected siblings, and affected 2nd and 3rd degree relatives.||Same as XomeDx||Proband only|
|Blood: A single tube with 1-5 mL whole blood in EDTA. Ship overnight at ambient temperature, using a cool pack in hot weather. Specimens may be refrigerated for 7 days prior to shipping.
Purified DNA: High quality extracted DNA can be accepted. At least 15ug is requested (with a minimum concentration of 50ng/ul).
We cannot accept buccal brushes for this test.
|Same as XomeDx||Same as XomeDx|
|Medical records, including indication for testing, history and physical exam, review of systems, and results of prior testing performed. Unusual features, even when not the primary indication for referral, are often helpful in making a diagnosis. Please include as much detailed information as you can!||Same as XomeDx||Prior to testing, ordering providers must submit a gene list online based on the patient’s phenotype through our online XomeDxSlice Tool. The gene list will be reviewed and approved or declined by the GeneDx medical specialists within 1-2 business days. Reasons for declining a gene list for XomeDxSlice include: poor coverage, significant homology to other regions of the genome, and the availability of more sensitive testing.
An approved gene list will be emailed to the ordering provider with the average percent coverage at 10X for the genes requested. This email will contain a unique tracking number that must be submitted with the patient’s sample and requisition form.
|Genes listed in Green, et al (2013) will be evaluated and known and/or expected pathogenic mutations will be reported as part of our standard reporting protocol.
Patients may choose not to undergo this part of the analysis and reporting by signing the Request to Opt-Out of Receiving Incidental Findings section of the consent form (Click here to download the requisition).
|Same as XomeDx||Incidental findings are not evaluated or reported in patients who undergo XomeDxSlice testing.
Only the genes agreed upon between the ordering provider and GeneDx will be evaluated and analyzed in XomeDxSlice.
|Whole exome sequencing does not identify some types of mutations (e.g. trinucleotide repeats, some insertions and deletions)
Exome capture and sequencing has areas of low coverage and/or low quality data. Variants in these regions may not be detected.
Pseudogenes or regions of homology may reduce our ability to detect variants.
While we do our best to interpret variants using the literature and a variety of databases, this can be challenging when the scientific data are limited or conflicting.
|The limitations of exome sequencing are the same as XomeDx.
The mtDNA sequencing and deletion test is expected to detect greater than 98% of known pathogenic mutations and deletions of the mitochondrial genome. Very low levels of heteroplasmy may be missed with this test.
|Same as XomeDx. Because the analysis for XomeDxSlice is targeted, variants present in genes not included on the pre-selected gene list will not be identified or reported.
Regions of any given gene not covered by whole exome sequencing will not be filled in with Sanger sequencing.
3. What does GeneDx need to perform XomeDx testing?
- Proband’s specimen (blood, DNA or frozen tissue)
- Completed submission form and consent
- Medical records, including prior test results, consult notes, pedigree, etc.
- Specimens from additional family members, if available.
4. What is the cost of XomeDx?
GeneDx can bill all commercial insurance and the patient is responsible for only the co-pay, co-insurance and unmet deductible as dictated by his or her insurance carrier. GeneDx will perform a benefit investigation and contact the patient if the patient’s out-of-pocket cost is expected to be greater than $100. We will work with the patient if the patient has financial difficulty and offer a financial assistance program based on their income. Additional information can be found on our billing page (www.genedx.com/xomedxbilling).
5. What is the turn-around-time for this test?
6. Whose specimens should be sent for XomeDx and what testing is performed?
Biological parents are typically the most informative samples and are accepted whenever possible. When a trio is sent for XomeDx and XomeDxPlus, whole exome sequencing is always performed on each member of the trio. This improves the sensitivity of the analysis when compared to testing only the proband. In some cases, siblings of the proband will be requested. Sometimes testing distantly-related family members can be helpful. GeneDx will decide, in consultation with the ordering provider, the individuals who can optimize our ability to identify a genetic cause of the patient’s phenotype. We will also discuss the type of testing that is most useful and cost-effective (i.e. whole exome sequencing or variant analysis to determine segregation). All individuals’ samples should be submitted at the beginning of testing. If additional relatives are indicated to be coming separately from the proband, testing will be on hold until all samples are received. In general, only a single report will be issued for the proband. However, the report will describe the inheritance and segregation of variants for all tested individuals.
7. What if extended family members want to be tested for a variant identified in a patient by XomeDx testing?
Family members can be tested for the mutations/variants identified in the initial patient. Please refer to the information about Carrier Testing for details.
8. Can you use WES to screen the parents for carrier status of recessive diseases?
A test designed for universal carrier screening (such as Inherigen by GenPath: Women’s Health) is a better way to obtain this information than reporting them from WES. This recommendation follows the American Academy of Pediatrics (AAP) guidelines recommending carrier testing not be performed on children.
9. How does GeneDx identify variants that are associated with the patient’s phenotype?
WES identifies hundreds of thousands of variants. Variants are filtered using a variety of factors including population frequency, presence of gene and/or mutation in HGMD or other database, inheritance pattern, phenotype, severity of sequence change, and function in pathways.
10. Will GeneDx report the parental genotype when a proband has a mutation or variant associated with the proband’s phenotype?
Yes. The proband’s report will indicate if a parent or other family member who has been tested also has that mutation or variant.
11. Are there any findings that will NOT be reported?
A single report will be issued on the proband (the affected individual in the family). No report will be issued on the parents or other unaffected relatives. Variations known to be benign (not associated with any disease) and/or commonly seen in many other healthy people will not be reported.
If a patient opts-out of receiving secondary findings, we will not analyze or report variants in the ACMG-recommended genes unless they are related to the patient’s phenotype.
12. Will the analysis identify mutations in disease-associated genes that are not associated with the patient’s reported phenotype?
Over 20,000 genes are being analyzed by the XomeDx and XomeDxPlus tests, which may reveal pathogenic variants in genes that may be medically significant, but not associated with the primary reason for having the test. We follow current recommendations of the ACMG and actively look for and report known and/or expected pathogenic variants in the genes outlined in these recommendations. Pathogenic variants will be reported in these associated genes unless the patient chooses to opt-out by selecting the opt-out option in the patient consent box of the test requisition form. In rare cases, GeneDx may also report an incidental finding in a gene that is not one of the genes recommended by the ACMG. These findings are pathogenic variants identified in the coding exons of genes that are considered medically actionable and the results are significant for your health.
13. Are there genes that are not well covered by this method?
Although there are some entire genes that we may not be able to capture and sequence in a particular patient, in general we expect that there may be small portions of different genes that are not amenable to evaluation. Some exons have low or no coverage because no probes are designed or available for these regions. It may be challenging to get good, usable sequence data for some regions.
14. Does WES detect copy number variants?
WES may detect copy number variants (deletions and duplications) that are three exons or larger. Smaller events may also be detected but with less reliability (Retterer et al., Genet Med. 2014 doi:10.1038/gim.2014.160). As with other types of mutations, any mutation that is included in a GeneDx report has been confirmed. The sensitivity of WES to identify CNVs compared with other methods in a diagnostic setting is not known.
15. Is it possible to reflex to XomeDx if XomeDxSlice is negative?
Yes. You will need to submit a completed add-on form for “Reflex to XomeDx”, a completed XomeDx consent document, and submit additional family member samples if possible. For billing information regarding reflex testing to XomeDx if XomeDxSlice is negative, please contact the GeneDx Billing department at 301-519-2100.
16. Will GeneDx offer re-analysis of WES data and what is the cost?
The ordering provider may request a re-analysis of the exome sequencing data for XomeDx and XomeDxPlus one year after the test report was issued. The first re-analysis can be requested at no charge.
17. What platform is GeneDx using?
The exome capture is performed with the Agilent Clinical Research Exome reagents. We are using the Illumina HiSeq 2500 sequencing system for next-generation sequencing.
18. What are the statistics for coverage/quality?
Approximately 95% of the targeted region of an affected individual’s exome will be assessed with the XomeDx test at 10x coverage, while >98% of the target region will be covered at a minimum of 1x. We will provide detailed information about how much of the exome was evaluated in the patient on the report you receive.
19. Can we get access to the aligned sequence data?
The sequence data generated by the XomeDx test can be requested by the ordering health care provider. Please see the Consent for release of aligned sequence data form in the “Additional Forms and Useful Information” above for directions and fees.