XomeDx

For samples arriving on or after May 1, 2013, GeneDx will begin following the recently released American College of Medical Genetics and Genomics Recommendations for Reporting Incidental Findings in Clinical Exome and Genome Sequencing. As recommended by the ACMG, all patient samples sent to GeneDx for XomeDx or XomeDxPlus testing will receive incidental findings, if present in the proband, as part of their result. Patient samples sent for XomeDxSlice will not receive incidental findings as part of their result. GeneDx would like to honor patient preferences and therefore we will offer the choice to opt-out of receiving incidental findings. Please click here for ACMG recommendations on incidental findings.

XomeDx: Whole Exome Sequencing

XomeDx Requisition	XomeDx Family Member Requisition	XomeDx FAQs
Test Info Sheet	Pre-authorization Template	Consent for Release of Raw Data

Clinical Analysis of genetic variation in the context of symptoms and family history

Whole exome sequencing (WES) can be used to identify the underlying molecular basis of a genetic disorder in an affected individual who has exhausted all other currently available genetic testing options. The XomeDx test is different from other types of genetic diagnostic tests in terms of the number of genes that are sequenced simultaneously. The XomeDx test targets the protein-coding regions of the human genome, which represents ~20,000 genes and accounts for approximately ~2% of all human genetic material.¹ To date, exome sequencing has been used to find novel mutations and genes associated with Mendelian disorders, as well as clarify the cause of atypical presentations and rare diseases.^2,3,4

When is whole exome sequencing useful?

XomeDx can be used to identify the underlying molecular basis of a genetic disorder in an affected individual with:

A disease which is highly genetically heterogeneous, and no single gene, or group of genes, makes up a significant percentage of the mutation spectrum.
A long differential diagnosis that makes sequential genetic testing cost prohibitive.
An atypical presentation of disease.
No molecular diagnosis and who has exhausted currently available genetic testing.

XomeDx is most useful in situations in which there are other family members available for inclusion in the analysis and when detailed medical records are included. The sensitivity of the test is greatly increased if samples and clinical information on both parents are submitted with the proband’s sample.

What can I expect an XomeDx report to contain?

There are three types of XomeDx reports:

XomeDx, the phenotype-targeted report.
XomeDxPlus, which includes XomeDx plus mitochondrial genome sequencing.
XomeDxSlice, which includes targeted analysis of a limited gene list determined by GeneDx and the ordering provider (for more information see question 9).

Every XomeDx order will receive an XomeDx phenotype-targeted report, which will include Sanger-confirmed variants that are:

Mutations and VUS in genes definitely related to the affected individual’s phenotype.
Mutations and VUS in genes possibly/probably related to the affected individual’s phenotype.
Mutations in candidate genes with unknown relationship to the affected individual’s phenotype.

Will your analysis identify mutations in disease-associated genes that are not associated with the patient’s reported phenotype?

Due to the fact that many different genes and conditions are being analyzed by the XomeDx test, this test may reveal some incidental findings, and the individual may learn genetic information about themselves or their family that is not directly related to the reason for ordering the WES. Incidental findings are variants, identified by the XomeDx test, in genes that are unrelated to the individual’s clinical features reported to GeneDx at the time of testing.

Will GeneDx report things such as carrier status, risk for developing adult-onset genetic conditions, etc.?

As recommended by the American College of Medical Genetics (ACMG), all patient samples sent to GeneDx for XomeDx or XomeDxPlus testing will receive incidental findings, if present in the proband, as part of their result. Any incidental findings identified in the 57 genes recommended by ACMG will be listed at the end of the report. Patient samples sent for XomeDxSlice will not receive incidental findings as part of their result. GeneDx would like to honor patient preferences and therefore we will offer the choice to opt-out of receiving incidental findings. Patients can choose to opt-out of receiving incidental findings by signing the opt-out option on on page 6 of the submission form. Although these changes will be reported, Sanger confirmation will not be provided.

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 whose samples were also analyzed in order to allow GeneDx to better interpret the results obtained on the proband. Variations known to be benign (not associated with any disease) and/or commonly seen in many other healthy people will not be reported.

What types of mutations are not detected by this methodology?

Similar to other genetic tests, WES has limitations in the types of mutations that it can detect. At this time, WES will not detect a mutation:

That is not located in the 90%-95% of the exome that is covered.
Located in the non-coding regions of the genome. Although not common, mutations can be located in regulatory regions or other parts of the genome not included in this analysis.
Specific types of mutations including:
- Triplet repeats
- Copy number variants
- Some insertions and deletions
- Abnormal methylation

Are there genes that are not well covered by this method?

The XomeDx test attempts to evaluate all of the protein-coding regions (“exons”) of the approximately 20,000 genes in the genome. However, our ability to capture and sequence the entire exome is imperfect. Certain genes have low or no coverage because no probes are designed or available for these regions. At this time we expect to be able to evaluate approximately 90%-95% of an exome. We will provide detailed information about how much of the exome was evaluated on the report you receive. 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.

Does XomeDxPlus include targeted testing for mitochondrial variants in the mother?

Yes, if the mother’s sample is available, we will do targeted testing by capillary sequencing in the mother to determine the presence/absence of any mitochondrial variant identified in the proband. This will be included in the test report.

What is XomeDxSlice?

XomeDxSlice captures and sequences the whole exome, but analysis is targeted to a limited and specific phenotype-driven gene list. The gene list will be discussed and selected by the ordering provider and GeneDx medical specialists prior to the start of testing. Testing is only performed on the proband and does not use family members’ samples for analysis. 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. XomeDxSlice is not a replacement for established panel tests because we expect the sensitivity will be reduced. XomeDxSlice reports will not include any incidental findings. Please call GeneDx to discuss prior to sending a patient’s sample for XomeDxSlice.

Is it possible to reflex to XomeDx if XomeDxSlice is negative?

Yes. You will need to complete an add-on form for “Reflex to XomeDx” and provide parental samples. There is no additional out-of-pocket cost to reflex to XomeDx for insurance bill cases; the institutional cost is the difference between the Slice and the XomeDx ($2,000 for a proband, $6,000 for a trio).

What is the reporting policy with regard to patented genes?

We will report on findings, which meet our reporting criteria, identified in patented genes but we cannot do confirmation by Sanger sequencing or offer carrier testing for any finding in patented genes.

What is the policy with regard to parental samples?

XomeDx includes whole exome sequencing of the entire trio. If only the proband is submitted for analysis, the sensitivity of the test is reduced as compared to having other family members included in the analysis. Parents are typically the most informative samples and are accepted whenever possible. Who else in the family will be tested depends on the family structure and who is affected with the disorder. In some cases, a child with the disorder and both parents will be tested. In others, siblings of the child will be included. Sometimes several more distantly-related family members will need to be tested. GeneDx will decide, in consultation with your doctor, who needs to be tested in order to ensure that there is the greatest chance of identifying the cause of the disorder in the family. All individuals’ samples should be submitted at the beginning of testing. In general, only a single report for the whole family of tested individuals will be issued.

What if extended family members want to be tested?

Family members can be tested for the mutations/variants identified in the initial patient. Please refer to the information about Carrier Testing for pricing.

Can you use WES to screen the parents for all recessive diseases?

A test designed for pan carrier screening (such as Inherigen by GenPath: Women’s Health) is a better way to approach gathering this information than reporting them from WES. This recommendation follows the AAP guidelines saying that carrier testing on children is not recommended.

What is the cost of XomeDx?

GeneDx can bill all commercial insurances and the patient’s out-of-pocket cost will be limited to $1,000* per trio (patient and two family members). Self-Pay or Institutional price is $9,000/trio (or quad if there is an additional affected relative). In the instance when only the proband is available, the cost is $5,000. Currently, GeneDx does not accept Medicare and Medicaid plans for this test. Additional information can be found on our billing page (www.genedx.com/billing).*Except in Florida and Colorado, where the waiver or reduction of co-pay, co-insurance and unmet deductible will be determined based on patient’s financial need.

What is the turn-around-time for this test?

The report will be returned to the ordering physician in approximately 12-16 weeks.

How does GeneDx filter the variants?

WES produces hundreds of thousands of variants. Those variants present at high percentages in 1000Genomes.org are pre-filtered out by our analysis pipeline. The remaining 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.

What platform is GeneDx using?

The exome capture is performed with Agilent SureSelect v4 reagents. We are using the Illumina platform for next-generation sequencing.

What are the statistics for coverage/quality?

It is anticipated that approximately 90-95% 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.

Can we get access to the “raw” data?

The sequence data generated by the XomeDx test can be requested by the ordering health care provider. Please see the Request for Exome Sequence Data consent form for directions and fees.

What samples are accepted for this test?

Blood: A single tube with 2-5 mL whole blood in an EDTA (lavender top) tube. 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).
Other Tissue Types: Please call to discuss an individual case. Brain tissue is not acceptable for testing.
Post-mortem samples will be accepted in the form of blood in an EDTA tube, cultured cells, and product of conception samples, although obtaining useable DNA is not guaranteed. Additionally, DNA (>15ug) can be accepted if not extracted from fixed tissue. For more information, please see our post-mortem sample guide available on our educational resources page.

Are there any samples that will not be accepted?

Buccal brushes, saliva, and paraffin embedded tissue cannot be accepted for this test.

Can a patient submit a sample without a physician’s order?

No. XomeDx results will only be reported to a physician.

Will GeneDx offer a re-analysis plan and what is the cost?

The ordering provider may request a re-analysis of the exome sequencing data generated at the time of testing one year after the test report was issued. The first re-analysis can be requested at no charge. Additional re-analyses on an annual basis can be requested for a fee.

Gene panels vs. whole exome sequencing? Which should be used when?

If a patient has a phenotype for which a specific set of genes has been implicated, and which is available in a gene panel (for example, hypertrophic cardiomyopathy, infantile epilepsy, LongQT syndrome, etc), the costs and sensitivity of using a panel (first) then reflexing in negative cases to WES, vs. starting with WES should be evaluated.

Gene panels include a specified set of genes that are analyzed to “completion” (or “finished”), meaning that an attempt is made to obtain high quality data for virtually every nucleotide in every gene in the panel. As the panel has been carefully designed to reduce the regions of low quality data, the number of amplicons required to complete by Sanger sequencing is relatively small. Thus, the sensitivity of gene panels approaches 99% for sequence based variation (such as single base changes, and small/medium deletions and insertions). Of course, only the genes included on the panel are obtained and evaluated.

In contrast, WES attempts to capture the entire exome without regard to any specific requirements for any particular gene or genes. Depending on the specific sequence, similarity to other genes in the genome, and the presence of pseudogenes, WES will be unable to capture portions of many genes. Finishing is not done when WES is used, as the cost and effort would be prohibitive. Thus, the sensitivity of WES for any specific set of genes is likely to be lower than the sensitivity of a gene panel which includes only those genes. On the other hand, if the patient does not have a mutation in one of the genes on the panel, WES offers the possibility of looking for a mutation in any other gene in the exome.

The physician should consider the several available options: Panel only, panel with reflex to WES, WES first.

References:

Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011 Sep 27;12(11):745-55.
Ku CS, Naidoo N, Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum Genet. 2011 Apr;129(4):351-70. Epub 2011 Feb 18.
Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010 Sep;42(9):790-3. Epub 2010 Aug 15.
Singleton AB. Exome sequencing: a transformative technology. Lancet Neurol. 2011 Oct;10(10):942-6.