Iowa Institute of Human Genetics

  • Whole Exome Sequencing

    Whole Exome Graphic

    The Iowa Institute of Human Genetics (IIHG) provides an integrated Clinical Whole Exome Sequencing test. The exome is the part of the genome that includes all of the exons, and makes up approximately 1% of your DNA. Whole exome sequencing is the analysis of the coding portion of approximately 20,000 genes in the human genome. The IIHG Clinical Whole Exome Sequencing test can be ordered by a physician as a tool in the diagnosis and management of their patients, or to narrow a differential diagnosis for a patient with an undiagnosed genetic disorder.

    Sequencing of parent-child trios is strongly recommended, as parental samples are often necessary for the interpretation of the child’s results. A clinical consent form and detailed clinical information must be submitted with the test request for the sample to be processed. The clinical consent form can be used during the consent process to provide an overview and explanation of exome sequencing to the patient and family. We have developed a custom informatics pipeline for primary gene analysis based on the differential diagnosis and phenotypes reported by the ordering physician. The multidisciplinary IIHG Clinical Exome Interpretation team reviews and interprets all results. The ordering physician receives a report of high-quality clinically relevant results in a customized report for each patient.

    Genetic counseling is highly recommended for anyone undergoing this test. Genetic counseling typically will include an explanation of the test including risks, benefits, and limitations, as well as explanation and completion of the informed consent document. Post-test genetic counseling can aid in patients' understanding of their test results and implications for other family members. Pre- and post- test genetic counseling are available for patients seen at the University of Iowa Hospitals and Clinics regarding the IIHG Clinical Whole Exome Sequencing test and its results.

    Indications for testing

    Common indications for testing include:

    • Diagnostic odyssey patients (those patients with a suspected Mendelian disorder for which the clinician has exhausted other genetic/other testing options and still does not have a diagnosis)
    • Patients with a long list of differential diagnoses (sequential testing is cost prohibitive; use this test to narrow the differential diagnosis)
    • Atypical presentation of disease

    *Please note, currently approximately 25% of patients for whom this test is ordered receive a positive diagnostic result or suspected diagnosis from the test. (Yang, Y., D.M. Muzny, et al. New England Journal of Medicine 2013; 369(16): 1502-1511.).

    Cost

    *Note: Your institution will be billed the fees below

    • Singleton $4000
    • Trios $5500
    • If genetic counseling through the IIHG is requested, there will be a separate charge for genetic counseling.
     

    Billing

    At this time the IIHG only accepts Institutional Billing.

    *Please note: billing information MUST be complete before samples will be processed.

    Turnaround Time

    • Once payment and all required information is received, the turnaround time is 3 months.
    • Testing is not initiated until billing information and a complete clinical history is received.
     

    How to order the test

    To order the test, please complete the following forms which are available on our website:

    In addition, a pedigree must be submitted. For assistance constructing a pedigree, or family history, a brief tutorial can be found at: http://www.medicine.uiowa.edu/humangenetics/DrawPedigree

    Specimen Type

     * All samples must be labeled with the patient’s name, date of birth, and date of collection.  

    The IIHG accepts the following types of specimens:

    • 6 mL whole blood in lavender EDTA tube (3 mL pediatric minimum). Samples must be received within 72 hours of sample collection.
    • 10 µg DNA (A260/A280 1.8-2) resuspended in 0.1mM EDTA (10mM Tris HCl, 0.1mM EDTA, pH 8, Teknova Cat# T0220)
    • Tissue samples only if the clinician contacts the IIHG in advance of tissue collection to make arrangements. Please contact iihg@uiowa.edu or call (319) 335-3688.

    Please note: Specimens for which insufficient quality or quantity of DNA is obtained, an additional sample will be requested. Incorrect handling or shipping of specimens can result in insufficient quality or quantity of DNA.

    Clinical and Family History

    • Whole Exome Sequencing generates thousands of DNA variants. It is impossible to interpret these variants without the patient’s clinical and accurate family history.
    • Both clinical and family history information are necessary to interpret the test results. Samples are not processed until complete clinical and family history information is received.
     

    Methodology

    • Agilent SureSelect v5 exome capture
    • Sequencing on the Illumina HiSeq2000 with 100 base pair (bp) paired-end reads
    • Informatics Analysis
      • Symptom guided analysis for primary findings
      • Custom Galaxy pipeline
      • Regions in candidate genes not captured and not covered sufficiently are analyzed and reported
       
    • Data sensitivity and specificity for exome testing is variable as gene coverage is not uniform throughout the exome. The Agilent SureSelect XT Human All Exon v5 kit captures ~98% of RefSeq coding base pairs, and >94% of the captured coding bases in the exome are covered at our depth-of-coverage minimum threshold (30 reads). All test reports include a summary of candidate gene regions not captured by the testing platform and a summary of regions with less than 40x sequence coverage. In general, >99% of single nucleotide variant calls and small insertion/deletion variant calls are confirmed when compared to an orthogonal technology.
      Detailed capture and coverage metrics for each gene can be found here.
      *Please note, this is an overall assessment and cannot be applied at the individual gene level.
    •  Sanger sequence confirmation is performed on all reported results
     

    Interpretation of Results

    • IIHG Clinical Exome Interpretation team reviews the results. The ordering physician will be invited to attend the results sign out meeting in person or via GoToMeeting.
    • Variants are classified by ACMG guidelines (Richards et al. GenetMed 2008;10:294-300)
     

    Genetic counseling

    • The IIHG can provide pre- and post-test counseling for patients seen at UIHC who undergo Clinical Whole Exome Sequencing testing performed by the IIHG.
    • There will be a separate charge for the genetic counseling appointment.
    • To schedule a genetic counseling appointment please call (319) 335-3688.
     

    Incidental and Secondary findings

    • Incidental findings are variants in genes associated with the patient’s primary condition that are predicted or expected to cause symptoms that differ from the symptoms for which the patient is being tested. For example, if a patient is being tested for genetic causes of hearing loss and a variant is identified in a gene that causes hearing loss but the variant is predicted to cause a syndromic form of hearing loss which also includes infertility, the variant is called an “incidental finding”. It is not possible to predict the symptoms associated with all incidental findings.
      • Patients have the option to learn of incidental findings on the consent form.
       
    • Secondary findings are variants in genes unrelated to the patient’s primary condition. These genes are not included in our analysis.
      • Secondary findings are not reported at this time.
       
    • If your patient is interested in participating in research on secondary findings, please contact the IIHG.
     

    Data Storage

    • The volume of data generated from this test is large. Below is a description of the files the IIHG will keep.
    • Sequence (fastq) and variant (vcf) files are kept for six years
    • The final report is kept indefinitely
    • If the ordering health care provider would like re-analysis of data within 12 months of ordering the original test, the cost is ½ the cost of the test.
    • If the ordering health care provider would like analysis after 12 months, because of the frequency of exome capture platform updates (12-18 months) and pipeline updates (annually), a new test must be ordered.
    • Unless mentioned above, we will not keep data files for more than 1 year
     

    Technical Limitations

    • Whole Exome Sequencing is a targeted capture platform which does not capture the entire exome. Regions not captured by the exome will not be analyzed.
      • Please note, it is important to understand the absence of a reportable variant in a given gene does not mean there are no pathogenic variants in that gene.
       
    • The variant causing the patient’s primary finding may not be detected because: some types of variants are very difficult to identify; and it may not be included in the sequenced/studied region. Typically, single nucleotide variations, and small insertions or deletions (indels) can be detected. Examples of genomic variations that are not reliably detected include;
      • Trinucleotide repeats
      • Genomic rearrangements
      • Large deletions, duplications, and insertions
      • Copy Number Variants (CNV)
      • Regulatory variants
      • Non-coding RNA
      • Gain-of-splice site variants
      • Multi-gene contributions
      • Un-annotated or under-annotated genes
      • Epigenetic/chromatin variations
      • Mutations involved in tri-allelic inheritance
      • Mitochondrial genome mutations
      • Mutations in genes with pseudogenes
       
    • The test cannot predict disease onset or severity
    • If a variant is identified, it may not be recognized as disease-causing because the understanding of the genome is not complete and it is not possible to predict with 100% accuracy the effect of all variants.
    • Interpretation of results is based on the current understanding of the human genome and human health and disease. The test may detect variants of uncertain clinical significance. Efforts will be made to limit these types of results.
    • Test results may be unclear and testing of other family members may be necessary to interpret the patient’s results, however this testing would require the patient’s approval and the consent of their family members.
    • The ability to identify the variant responsible for the condition is highly dependent on the clinical information and family history provided to the laboratory by the ordering physician.
     

    Resources and Education

    The IIHG Genome Resource Center can assist you with the following;

    For assistance determining if the IIHG Clinical Whole Exome Sequencing test is appropriate for your patient

    • Understanding the physician report and results interpretation
    • Answer any questions regarding the IIHG Clinical Whole Exome Sequencing test  
    • To learn more about exome sequencing and the IIHG Clinical Whole Exome Sequencing please check back soon for healthcare provider education resources, including upcoming courses, seminars, or grand rounds presentations. If you would like to schedule an educational event for your department, please contact the IIHG at 319-335-3688 or iihg@uiowa.edu.
    • IIHG Patient Brochures

    Audio Resources

    Courtesy of mendelspod.com

     

    Contact Information

    Iowa Institute of Human Genetics
    University of Iowa
    285 Newton Road, 5296 CBRB
    Iowa City, IA, 52242
    319-335-3688 Tel
    319-335-3484 Fax
    Email: iihg@uiowa.edu
    www.medicine.uiowa.edu/humangenetics