XomeDx: Whole Exome Sequencing

XomeDx Requisition

 

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 this test useful?

XomeDx can be used to identify the underlying molecular basis of a genetic disorder in an affected individual primarily in two situations: 1) a patient who has exhausted all other currently available genetic testing options, or 2) a patient with a diagnosis that suggests the involvement of one or more of many different genes, which would, if even available and sequenced individually, be prohibitively expensive. It is helpful if the referring physician or genetic counselor contact the XomeDx staff at GeneDx to discuss a potential patient for XomeDx. We will evaluate the case and determine if there are other tests to do first that might minimize cost and maximize efficiency in obtaining a diagnosis. Our goal is to offer the XomeDx testing service only when clinically appropriate and when the sensitivity is likely to be greater than other diagnostic approaches.

XomeDx is most useful in situations where there are other family members available for inclusion in the analysis. The sensitivity of the test is greatly increased if samples and clinical information on both parents are submitted with the proband’s sample. Sensitivity can be further increased if any other affected relatives or unaffected siblings are also included.

In support of the XomeDx program, GeneDx has:

  1. A state of the art, web-accessible bioinformatics pipeline to identify clinically relevant variants
  2. In-house team of over 30 geneticists and genetic counselors specializing in rare inherited diseases
  3. Case review and management by Sherri Bale, PhD, experienced clinical geneticist.
  4. Cost conscious testing. Dr. Bale will review each case personally and recommend  the most efficient,cost effective, and sensitive approach based on clinical information, family history, and previous testing.

GeneDx also has a wide array of other genetic and genomics testing available:

  • Copy number variant (CNV) analysis at the genomic and exon level (GenomeDx and ExonArrayDx)
  • mtDNA sequencing and deletion analysis
  • Full sequencing for over 400 individual genes involved in rare disorders
  • Cytogenetics (chromosome analysis, FISH)
  • NextGeneration sequencing of multi-gene panels for specific phenotypes, including cardiac, neurologic, metabolic, mitochondrial, and others.

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.

Why should you choose GeneDx over other labs?

When GeneDx performs an XomeDx test to analyze a trio (proband plus parents), the exomes of all three individuals are generated and sequenced. This is in contrast to some other WES providers, who use the proband’s relatives for evaluation of segregation of variants only. Using the exome data from all family members greatly increases the efficiency of the test, controls cost, and reduces the number of variants of unknown significance to be evaluated and reported.

GeneDx uses Sanger sequencing in a new aliquot of DNA prepared from the submitted sample to confirm all findings on the proband that are reported in the final report, thus reducing false positive errors that could lead to incorrect interpretation and unnecessary follow-up studies.

What does the report include?

XomeDx reports will include Sanger-confirmed variants that:

  1. Are disease-causing and occur in a gene known to be associated with the patient’s phenotype
  2. Are classified as “unknown significance” but occur in a gene known to be associated with the patient’s phenotype
  3. Are expected to be deleterious to the resulting protein and occur in genes that are not currently known to be associated with the phenotype but could be hypothesized to be associated based on current knowledge of gene function, pathway, expression, etc.
  4. If there are specific genes unrelated to the phenotype for which the test is being performed and for which the patient requests (and consents) to receive information, known disease-associated variants in those genes can be reported, although Sanger confirmation will not be provided.
  5. As the American College of Medical Genetics develops its recommendations for the reporting of secondary findings resulting from genomics analysis, GeneDx will revise policies to conform with those recommendations.

How does a positive result impact patient care?

Similar to most genetic tests, a positive result can provide information for both the patient and the entire family. A diagnosis can provide prognostic information, allow for tailored health surveillance and prevention, may suggest specific treatments, allow for networking with other patients with a related diagnosis, access to expert clinicians and researchers, and provide important information to identify other family members at risk. A result can allow families to make informed reproductive choices and provides a means to have healthy children who do not have the genetic condition, through the use of prenatal testing or pre-implantation genetic diagnosis.

What is the cost of this test?

GeneDx can bill all commercial insurances and the patient out-of-pocket cost will be limited to $1000* per trio (patient and two family members). Self/Pay or Institutional price is $9,000/trio. In the instance when only the proband is available, the cost is $5,000. Each additional family member included in the test increases sensitivity, and costs $2,500. Currently,GeneDx does not accept Tricare, Medicare and Medicaid plans for this test. Please click here for more information.

*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.

How can Pre-Authorization or Pre-Certification maximize the chance that insurance will cover the testing?

GeneDx has found that the submission of a request for pre-authorization or pre-certification to the patient’s insurance prior to starting the test helps to increase the chance that insurance will cover the testing. A pre-authorization template can be found here. Please complete the information requested in the template, copy and paste on your letterhead, and e-mail the letter to GeneDx (genedx@genedx.com. We will submit the request to the patient’s insurance and notify the referring physician and genetic counselor with the result, usually within a couple of days.

How can this test be ordered?

XomeDx program staff is available to discuss cases, and answer questions about sample submission. Please use the submission form link at the top of this page to obtain required paperwork. Please include a pedigree, medical history, chart notes and summaries, and a list or copies of previous  testing. Please use the Contact Us link on our website, e-mail us at genedx@genedx.com or call GeneDx at (301)-519-2100 if you have any questions.

What are some limitations of this test?

Similar to other genetic tests, this test has several important limitations:

  1. Current exome sequencing procedures do not capture the entire exome. At this time, the efficiency of capture is about 80%-95% and while we keep working to improve the amount of sequence captured for analysis, it is possible that the region of a patient’s mutation could be missed.
  2. The test does not attempt to sequence 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. We may find rare genetic variations that are not interpretable at this time. Even though a lot is known about human genetic variation, there is much more that is not yet known. If we identify rare variations in our analysis that have never been observed before, we may not be able to provide a full interpretation of the data today, although we anticipate that knowledge will continue to become more complete, allowing better data interpretation with time.
  3. 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.

Can the physician get the “raw” data?

Referring physicians should call to discuss data access. There are several methods available to GeneDx to provide access to various forms of the data.

References: 

  1. 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.
  2. Ku CS, Naidoo N, Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum Genet. 2011 Apr;129(4):351-70. Epub 2011 Feb 18.
  3. 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.
  4. Singleton AB. Exome sequencing: a transformative technology. Lancet Neurol. 2011 Oct;10(10):942-6.