Collect

Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.

 

Also accepted: saliva*, fresh/frozen tissue, cultured fibroblasts, DNA extracted from a CLIA-certified lab (5µg at a minimum concentration of 85ng/µl)

To request saliva collection kits for CHOP patients/family members, please place an Epic order for DGD Mail Specimen Collection Kit to Patient (Status: Specimen in Lab, Specimen Type: Saliva).

To request saliva collection kits for non-CHOP patients/family members (client cases), please contact  DGDGeneticCounselor@chop.edu.

NOTE: Due to the increased potential for quality/quantity issues of DNA extracted from saliva, blood is still the preferred sample type when feasible, particularly for urgent testing.

Specimen Preparation

Informed Consent: Completed consent forms should be obtained for the proband and any family member(s) whose data will be utilized for analysis. The completed form(s) should be uploaded into the electronic medical record of the individual for whom the form was completed. Consent is available in English and Spanish here: Genomic Diagnostics Requisition Forms | Children's Hospital of Philadelphia (chop.edu). 

Secondary Findings: Families can indicate on the consent form whether they want the laboratory to look for and report secondary findings. The Current Secondary Findings List is available on our website.
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. 

Family Member Samples: For optimal analysis, submission of parental samples (when available) and/or similarly affected family members is highly recommended. Please see the Exome, Family Member order for ordering tests on other family members. 

Unacceptable Conditions

Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens

Storage/Transport Temperature

For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day. 

For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.

Please contact the lab (267-426-1447) with questions regarding non-blood specimens.

Volume Required

2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul

Minimum Required

1 mL of whole blood

Phlebotomy Draw

Yes

Clinical Features

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

Exome Ordering Options:

Use CHOP Medical Exome for patient (proband) to undergo initial exome sequencing.

Use Exome, Family Member for family members undergoing initial 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.

Use DNA Extraction for family members for whom a sample is to be obtained and DNA held for analysis if needed for interpretation (i.e. Sanger sequencing analysis), as determined by the lab (e.g. an affected or unaffected sibling).

Use Sequencing Known Genetic Variant for a family member who would like to be tested for a specific variant listed in the proband's sequencing test result.

Use CHOP Medical Exome Reanalysis (for patient/proband) and Exome Reanalysis, Family Member for reanalysis of data from a CHOP Medical Exome. (Please review the Exome Reanalysis test menu entries to determine which patients/family members are eligible for these testing options and contact the lab regarding any questions prior to ordering reanalysis.)

For more information contact the lab at 267-426-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
 

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
  • EGPRO

LIS Mnemonic

EGPRO

Available STAT

Expedited testing is available on request. Please contact DGDgeneticcounselor@chop.edu to inquire about process.

CPT Codes

Proband-only exome: 81415. For each family member submitted, please authorize one unit of 81416. For example, to authorize a trio exome analysis (two parents and a proband) please use the following codes: 81415x1, 81416x2.
Collection

Collect

Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.

 

Also accepted: saliva*, fresh/frozen tissue, cultured fibroblasts, DNA extracted from a CLIA-certified lab (5µg at a minimum concentration of 85ng/µl)

To request saliva collection kits for CHOP patients/family members, please place an Epic order for DGD Mail Specimen Collection Kit to Patient (Status: Specimen in Lab, Specimen Type: Saliva).

To request saliva collection kits for non-CHOP patients/family members (client cases), please contact  DGDGeneticCounselor@chop.edu.

NOTE: Due to the increased potential for quality/quantity issues of DNA extracted from saliva, blood is still the preferred sample type when feasible, particularly for urgent testing.

Specimen Preparation

Informed Consent: Completed consent forms should be obtained for the proband and any family member(s) whose data will be utilized for analysis. The completed form(s) should be uploaded into the electronic medical record of the individual for whom the form was completed. Consent is available in English and Spanish here: Genomic Diagnostics Requisition Forms | Children's Hospital of Philadelphia (chop.edu). 

Secondary Findings: Families can indicate on the consent form whether they want the laboratory to look for and report secondary findings. The Current Secondary Findings List is available on our website.
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. 

Family Member Samples: For optimal analysis, submission of parental samples (when available) and/or similarly affected family members is highly recommended. Please see the Exome, Family Member order for ordering tests on other family members. 

Unacceptable Conditions

Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens

Storage/Transport Temperature

For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day. 

For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.

Please contact the lab (267-426-1447) with questions regarding non-blood specimens.

Volume Required

2-3 mL of blood or 3 ug of DNA with a concentration of at least 50 ng/ul

Minimum Required

1 mL of whole blood

Phlebotomy Draw

Yes
Ordering

Clinical Features

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

Exome Ordering Options:

Use CHOP Medical Exome for patient (proband) to undergo initial exome sequencing.

Use Exome, Family Member for family members undergoing initial 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.

Use DNA Extraction for family members for whom a sample is to be obtained and DNA held for analysis if needed for interpretation (i.e. Sanger sequencing analysis), as determined by the lab (e.g. an affected or unaffected sibling).

Use Sequencing Known Genetic Variant for a family member who would like to be tested for a specific variant listed in the proband's sequencing test result.

Use CHOP Medical Exome Reanalysis (for patient/proband) and Exome Reanalysis, Family Member for reanalysis of data from a CHOP Medical Exome. (Please review the Exome Reanalysis test menu entries to determine which patients/family members are eligible for these testing options and contact the lab regarding any questions prior to ordering reanalysis.)

For more information contact the lab at 267-426-1447 or by sending an email to DGDGeneticCounselor@chop.edu.
 

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
  • EGPRO

LIS Mnemonic

EGPRO

Available STAT

Expedited testing is available on request. Please contact DGDgeneticcounselor@chop.edu to inquire about process.
Result Interpretation
Administrative

CPT Codes

Proband-only exome: 81415. For each family member submitted, please authorize one unit of 81416. For example, to authorize a trio exome analysis (two parents and a proband) please use the following codes: 81415x1, 81416x2.

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