Medical EmExome Array: Deletion/Duplication Analysis
Sanger Confirmation and Interpretation Only
Interpretation Only (Exome or Genome)
* Includes analysis of one phenotype-specific NGS panel.
What is the Medical EmExome?
The human exome is the complete coding (exonic) region of the genome. It is estimated to encompass approximately 1-2% of the genome, yet contains approximately 85% of disease-causing pathogenic variants. Current off-the-shelf exome kits used for clinical exome sequencing cover 92% of the exome. Traditionally, gene discovery has been done in research laboratories; however, now with the ability to sequence nearly the entire coding region of the human genome, it is possible for clinical laboratories to use this information to identify a previously unrecognized cause of disease.
The Medical EmExome is the next level in clinical exome sequencing offered by EGL Genetics (EGL). The exome sequencing design provides >97% coverage of 22,000 genes, with a mean read depth of 100X. Of the ~4600 disease-associated genes analyzed, 3000 have 100% coverage (≥20X) of all exons; twice the number of genes with complete coverage offered by competitors, making it the most comprehensive exome sequencing test available. This is also the highest coverage offered by any clinical exome sequencing performed in a CLIA-/CAP-certified laboratory.
The Medical EmExome also features the EmExome Boost Option, which allows clinicians to choose an EGL gene panel relevant to the patient’s phenotype to ensure coverage of ALL exons, at no additional cost. EGL is the first clinical laboratory to offer near complete coverage of all disease-associated genes with an exome boost option. A research protocol is also available for extended exome and genome testing for the discovery of novel disease genes.
Will EGL release raw exome data?
Yes, upon request.
Will EGL re-analyze data?
Yes, upon request.
What options are available for Medical EmExome testing?
EXOMT - Medical EmExome: Clinical Exome Sequencing, Trios*
EXOME - Medical EmExome: Clinical Exome Sequencing, Proband Only
EXOMA - Medical EmExome: Clinical Exome Sequencing, Additional Family Member
EXODD - Medical EmExome Array: Deletion/Duplication Analysis
EXSAN - Sanger Confirmation and Interpretation Only
EXINT - Interpretation Only (Exome or Genome)
*Includes analysis of one phenotype-specific NGS panel.
Exome, Proband Only
Whole blood (or DNA extracted from whole blood) is needed from the proband and biological parents, as whole exome sequencing is being run on all three individuals.
Whole blood (or DNA extracted from whole blood) from the proband only is needed. Saliva may be submitted on additional family members.
Secondary Findings Options
Carrier status, pharmacogenetic variants, adult-onset medically actionable, adult-onset not currently medically actionable (adults only). Parents have the option to select carrier status and adult-onset actionable disorders.
Carrier status, pharmacogenetic variants, adult-onset medically actionable, adult-onset not currently medically actionable (adults only).
Completed during the analysis.
Done as a final step.
How is the Medical EmExome performed?
Medical EmExome is performed on genomic DNA, using the Agilent V5 Plus designed to target the exome with greater coverage of known disease-associated genes. These targeted regions are then sequenced using the Illumina HiSeq 2500 sequencing system, with 100 basepair (bp) paired-end reads (similar to bidirectional Sanger sequencing) and an average coverage of 100X in the target region. (The target region includes the exon and 10 bp of flanking intronic region). The DNA sequence is mapped to, and analyzed in, comparison with the published human genome build UCSC hg19 reference sequence. The targeted coding exons and splice junctions of the known protein-coding RefSeq genes are assessed for the depth of coverage and data quality threshold values. The Medical EmExome bioinformatics analysis pipeline is used to compare sequence changes in the individual being tested to the reference sequence. All potential positive sequence variants in the proband are confirmed by conventional di-deoxy DNA sequence analysis (Sanger sequencing) using a separate DNA isolation.
The Medical EmExome also features the EmExome Boost Option, which allows clinicians to choose an EGL gene panel relevant to the patient’s phenotype to ensure coverage of ALL exons, at no additional cost.
Targeted sequencing of parental samples for the proband only option will be completed at no additional charge for exome sequencing only if needed (such as a variant of uncertain clinical significance).
The interpretation service is offered for exomes sequenced outside Emory, in either clinical or core laboratories. The exome data is mapped to, and analyzed in, comparison with the published human genome build UCSC hg19 reference sequence. The targeted coding exons and splice junctions of the known protein-coding RefSeq genes are assessed for the depth of coverage and data quality threshold values. The Medical EmExome bioinformatics analysis pipeline is used to compare sequence changes in the individual being tested to the reference sequence.
EGL is committed to ensuring our clients and your patients are kept as up-to-date as possible as it relates to the classification of discovered variants. EGL introduces EmVClass, EGL's Variant Classification Tool, which provides up-to-the-day status updates on all variants that have been seen and analyzed by EGL Genetics. Click the icon below to be redirected to EmVClass.
Chen B, Gagnon M, Shahangian S, Anderson NL, Howerton DA, Boone JD; Centers for Disease Control and Prevention (CDC). Good laboratory practices for molecular genetic testing for heritable diseases and conditions.MMWR Recomm Rep. 2009 Jun 12;58(RR-6):1-37.
Gahl WA, Markello TC, Toro C, Fajardo KF, Sincan M, Gill F, Carlson-Donohoe H, Gropman A, Pierson TM, Golas G, Wolfe L, Groden C, Godfrey R, Nehrebecky M, Wahl C, Landis DM, Yang S, Madeo A, Mullikin JC, Boerkoel CF, Tifft CJ, Adams D; for the NISC Comparative Sequencing Program. The National Institutes of Health Undiagnosed Diseases Program: Insights into rare diseases. Genet Med. 2011 Sep 26.
Maddalena A, Bale S, Das S, Grody W, Richards S; ACMG Laboratory Quality Assurance Committee. Technical standards and guidelines: molecular genetic testing for ultra-rare disorders. Genet Med. 2005 Oct;7(8):571-83.
Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. What can exome sequencing do for you? J Med Genet. 2011 Sep;48(9):580-9.
Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010 Feb;7(2):111-8.
Mattocks CJ, Morris MA, Matthijs G, Swinnen E, Corveleyn A, Dequeker E, Müller CR, Pratt V, Wallace A; EuroGentest Validation Group. A standardized framework for the validation and verification of clinical molecular genetic tests. Eur J Hum Genet. 2010 Dec;18(12):1276-88.
Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet Med. 2008 Apr;10(4):294-300.
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