The CHOP Medical Exome from Exome Panel test is ordered when a clinician is interested in pursuing full exome analysis for a patient who has already had a CHOP Disease/Phenotype Slice Panel. The CHOP Medical Exome from Panel test allows for the sequencing data generated by CHOP Disease/Phenotype panels to be used for a full exome analysis, without having to re-sequence the patient’s DNA. Typically, a new specimen will not be required for the CHOP Medical Exome from Disease/Phenotype Panel test; the laboratory usually already has the patient’s exome sequencing data from a prior exome-based panel, as well as stored DNA. Rarely, the lab will need a new specimen to perform confirmation of identity testing.
1) originally provided consent for testing before 12/8/2020 or
2) wants secondary findings.
(A new consent form is not required for family members who consented to the original analysis on or after 12/8/20, unless they want to receive secondary findings.) Please contact the lab if a relevant family member included in the original analysis that was ordered before 12/8/20 is no longer available to provide consent. The completed form(s) should be uploaded into the electronic medical record of the individual for whom the form was completed.
Clinical History: Please provide a detailed clinical history as the analysis is partially phenotype-driven. NOTE: The clinical indication entered on the Epic order/requisition form guides the phenotype to target for analysis and reporting and the indication will appear on the report. Please be certain to include all key clinical features that should be used for the analysis and avoid abbreviations. Genes of interest (≤10) may also be entered on the Epic order/requisition form to help focus the lab’s analysis.
Familial Member Samples: Please see below for information regarding ordering testing on family members. If not submitted as part of the proband’s original exome analysis, submission of new parental and/or similarly affected family members via the order for Exome, Family Member is highly recommended. For more information contact the lab at 267-426-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
N/A
Volume Required
N/A
Minimum Required
N/A
Phlebotomy Draw
No
Clinical Features
Using existing exome data from a previously performed CHOP exome-based targeted panel, a CHOP Medical Exome analysis is performed. Utilizing a combined variant and phenotype-driven analysis, the CHOP Medical Exome focuses on identifying and reporting sequence and copy number variants that are highly likely to underlie the patient’s reason for study based on our current understanding of Mendelian genetic disorders. The test does not target variants contributing to disorders with multifactorial inheritance. It is an appropriate clinical test for patients with a complex presentation or those that do not have a clear clinical diagnosis, as well as for patients with phenotypes that could be caused by one of several different genes. It is also a useful diagnostic test for disorders in which a gene or genes have been implicated but for which no targeted clinical diagnostic test is available.
Ordering Recommendations
Order the CHOP Medical Exome from a Disease/Phenotype Panel for an individual who received a non-diagnostic (negative or inconclusive) result from a CHOP panel after February 8, 2023.
Order Exome, Family Member for family members undergoing exome sequencing to directly assist in interpretation of the patient's exome sequencing data (typically parents and/or an affected sibling). The test order and the completed consent form should be placed in the family member’s medical record, not the patient’s medical record.
NOTE: Panel reflex can only be performed on Disease/Phenotype panels that were ordered after February 8, 2023. If the CHOP Medical Exome is indicated for a patient who received a non-diagnostic result from a CHOP panel before this date, place a new order for CHOP Medical Exome v4 and Exome v4, Family Member see order: CHOP Medical Exome v4 and Exome, Family Member.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Methodology
Genomic DNA is extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing is performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis are based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequencing and copy number variants. Whole genome sequencing has uniform coverage with a minimum read depth of 20X for at least 90% of the genome. For re-analysis or reflex testing, sequencing data is generated using the methods above.
Reported
42 days
Synonyms
Exome, CHOP Exome, WES, Whole exome sequencing, panel reflex
EGSPR
LIS Mnemonic
EGSPR
Available STAT
Expedited testing is available on request, please contact DGDgeneticcounselor@chop.edu to inquire about process.
CPT Codes
Proband CHOP Medical Exome from Exome Panel:81415
For each family member submitted for exome sequencing, please authorize one unit of81416.
For example, to authorize a proband for the CHOP Medical Exome from Exome Panel analysis and two parents for exome sequencing for comparison purposes, please use the following codes:81415x1,81416x2.
Collection
Collect
The CHOP Medical Exome from Exome Panel test is ordered when a clinician is interested in pursuing full exome analysis for a patient who has already had a CHOP Disease/Phenotype Slice Panel. The CHOP Medical Exome from Panel test allows for the sequencing data generated by CHOP Disease/Phenotype panels to be used for a full exome analysis, without having to re-sequence the patient’s DNA. Typically, a new specimen will not be required for the CHOP Medical Exome from Disease/Phenotype Panel test; the laboratory usually already has the patient’s exome sequencing data from a prior exome-based panel, as well as stored DNA. Rarely, the lab will need a new specimen to perform confirmation of identity testing.
1) originally provided consent for testing before 12/8/2020 or
2) wants secondary findings.
(A new consent form is not required for family members who consented to the original analysis on or after 12/8/20, unless they want to receive secondary findings.) Please contact the lab if a relevant family member included in the original analysis that was ordered before 12/8/20 is no longer available to provide consent. The completed form(s) should be uploaded into the electronic medical record of the individual for whom the form was completed.
Clinical History: Please provide a detailed clinical history as the analysis is partially phenotype-driven. NOTE: The clinical indication entered on the Epic order/requisition form guides the phenotype to target for analysis and reporting and the indication will appear on the report. Please be certain to include all key clinical features that should be used for the analysis and avoid abbreviations. Genes of interest (≤10) may also be entered on the Epic order/requisition form to help focus the lab’s analysis.
Familial Member Samples: Please see below for information regarding ordering testing on family members. If not submitted as part of the proband’s original exome analysis, submission of new parental and/or similarly affected family members via the order for Exome, Family Member is highly recommended. For more information contact the lab at 267-426-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
Unacceptable Conditions
N/A
Volume Required
N/A
Minimum Required
N/A
Phlebotomy Draw
No
Ordering
Clinical Features
Using existing exome data from a previously performed CHOP exome-based targeted panel, a CHOP Medical Exome analysis is performed. Utilizing a combined variant and phenotype-driven analysis, the CHOP Medical Exome focuses on identifying and reporting sequence and copy number variants that are highly likely to underlie the patient’s reason for study based on our current understanding of Mendelian genetic disorders. The test does not target variants contributing to disorders with multifactorial inheritance. It is an appropriate clinical test for patients with a complex presentation or those that do not have a clear clinical diagnosis, as well as for patients with phenotypes that could be caused by one of several different genes. It is also a useful diagnostic test for disorders in which a gene or genes have been implicated but for which no targeted clinical diagnostic test is available.
Ordering Recommendations
Order the CHOP Medical Exome from a Disease/Phenotype Panel for an individual who received a non-diagnostic (negative or inconclusive) result from a CHOP panel after February 8, 2023.
Order Exome, Family Member for family members undergoing exome sequencing to directly assist in interpretation of the patient's exome sequencing data (typically parents and/or an affected sibling). The test order and the completed consent form should be placed in the family member’s medical record, not the patient’s medical record.
NOTE: Panel reflex can only be performed on Disease/Phenotype panels that were ordered after February 8, 2023. If the CHOP Medical Exome is indicated for a patient who received a non-diagnostic result from a CHOP panel before this date, place a new order for CHOP Medical Exome v4 and Exome v4, Family Member see order: CHOP Medical Exome v4 and Exome, Family Member.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Methodology
Genomic DNA is extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing is performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis are based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequencing and copy number variants. Whole genome sequencing has uniform coverage with a minimum read depth of 20X for at least 90% of the genome. For re-analysis or reflex testing, sequencing data is generated using the methods above.
Reported
42 days
Synonyms
Exome, CHOP Exome, WES, Whole exome sequencing, panel reflex
EGSPR
LIS Mnemonic
EGSPR
Available STAT
Expedited testing is available on request, please contact DGDgeneticcounselor@chop.edu to inquire about process.
Result Interpretation
Administrative
CPT Codes
Proband CHOP Medical Exome from Exome Panel:81415
For each family member submitted for exome sequencing, please authorize one unit of81416.
For example, to authorize a proband for the CHOP Medical Exome from Exome Panel analysis and two parents for exome sequencing for comparison purposes, please use the following codes:81415x1,81416x2.
