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: Consent forms should be obtained for the proband and a consent form should also be obtained for each family member data will be utilized for exome reanalysis if the family member: Consent is available in English and Spanish here: Genomic Diagnostics Requisition Forms | Children's Hospital of Philadelphia (chop.edu) 
 
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

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 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 Exome DNA Extract for family member(s) 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.

Synonyms

  • Exome, WES, Family member exome, exome trio, trio
  • EGFAM

LIS Mnemonic

EGFAM

Available STAT

No

CPT Codes

81416
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: Consent forms should be obtained for the proband and a consent form should also be obtained for each family member data will be utilized for exome reanalysis if the family member: Consent is available in English and Spanish here: Genomic Diagnostics Requisition Forms | Children's Hospital of Philadelphia (chop.edu) 
 
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

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

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 Exome DNA Extract for family member(s) 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.

Synonyms

  • Exome, WES, Family member exome, exome trio, trio
  • EGFAM

LIS Mnemonic

EGFAM

Available STAT

No
Result Interpretation
Administrative

CPT Codes

81416

×
Learn More Remind Me Later Dismiss