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The exome is comprised of all of the protein-encoding exons in the genome. Even though the exome accounts for only 1 percent of the entire genome, mutations in the exons account for many genetic disorders.
Whole exome sequencing (WES) examines the majority of exons and exon / intron boundaries of most of the genes at one time. This test is different from most genetic tests that analyze only one gene at a time. Approximately 25 percent of individuals who have whole exome sequencing receive a diagnosis or a suspected diagnosis from the test.
Variants that will be discussed in detail in the report:
Variants that will be listed in the report:
Note: Family members who submit samples for comparative analysis will not receive a separate written report.
This laboratory will seek and report pathogenic variants in genes deemed to be of medical value, including those recommended by the American College of Medical Genetics and Genomics (Green et al. 2013).
Secondary findings will not be sought or reported if the patient or patient’s representative chooses not to receive them. For families who choose to receive secondary findings, the patient's report will include this information for all family members who submit blood samples. Family members will not receive a separate report.
ExomeSeq is performed on genomic DNA using the NimbleGen V3 targeted sequence capture method to enrich the whole exome. The whole exome is sequenced on the Illumina HiSeq 2500 sequencing system with 100 base pair (bp) paired-end reads at a minimum coverage of 10X of 95 percent of the target regions. The proband’s exome DNA sequences are mapped and compared to human genome build UCSC hg19 reference sequence.
The laboratory implements dual bioinformatics analyses pipelines that include the use of NextGene V2.3.1 and GATK / Golden Helix V7.7.4 software packages to compare the proband’s sequence to the reference sequence. Assessment of coverage and quality for targeted coding exons of the known protein-coding RefSeq genes is performed. Exome analyses interrogate thousands of genetic variants in a proband and a subset of these is identified as potentially clinically relevant. Sanger sequencing is performed on all variants included in the report.
At least 3 mls whole blood in a lavender top (EDTA) tube. Label the tube with patient’s name, birth date and date of collection. Alternately, 15 mcg of DNA may be submitted.
The time to complete the case preparation and obtain payor precertification is variable. Once payment precertification is obtained, the turnaround time for sequencing and analysis of the exome is three to six months.
It is important to have reliable clinical information and an accurate family history in order to interpret data from whole exome sequencing (WES) correctly. WES testing is most likely to provide a genetic diagnosis when several family members are analyzed at one time. These items must be included in order to begin the WES process:
> Download a Guide for Families to share with your patients.
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