Collect

CHOP Medical Exome Reanalysis should be considered for individuals who have had the CHOP Medical Exome signed out more than one year prior to ordering the reanalysis and/or has a significantly different indication for study compared to the initial exome analysis (e.g. a newly emerging phenotype). Typically, a new specimen will not be required for the CHOP Medical Exome Reanalysis test, as the laboratory should already have the patient’s exome sequencing data as well as stored DNA. Rarely, the lab will need a new specimen to perform confirmation of identity 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

N/A

Storage/Transport Temperature

N/A

Volume Required

N/A

Minimum Required

N/A

Phlebotomy Draw

No

Clinical Features

Utilizing a combined variant and phenotype-driven analysis, the CHOP Medical Exome Reanalysis 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

A reanalysis of CHOP Medical Exome data can be ordered for anyone who has previously had a CHOP Medical Exome analysis. This option is typically recommended if it has been more than a year since the original analysis and/or the patient has developed additional symptoms/features.
 
Exome Reanalysis for exomes ordered before February 8, 2023 (v1, v2, and v3) will not be available on the Exome v4 bioinformatic pipeline. Exome reanalysis for exomes ordered before February 8, 2023 (v1, v2, and v3) will utilize the Exome v3 bioinformatic pipeline. Exome reanalysis for exomes ordered after February 8, 2023 (v4) will utilize the Exome v4 pipeline. The ordering process is the same regardless of date of original exome.
What to order for Family Members being included in the patient’s (proband’s) exome reanalysis:
 
Order Exome DNA Extract for a family member who is not undergoing exome analysis but wants to submit a sample for Sanger analysis. New family members (who were not submitted with the patient’s original CHOP Medical Exome) can only be submitted for Sanger sequencing (via the Exome DNA Extract order). They cannot undergo full exome analysis as a part of the proband’s reanalysis.

Order Exome Reanalysis, Family Member for family members who were included in the patient’s original CHOP Medical Exome analysis and are now undergoing reanalysis of existing exome data to directly assist in interpretation of the patient's exome sequencing data (typically parents and/or an affected sibling). The test order should be placed in the family member’s medical record, not the patient’s medical record.

NOTE:  If you are ordering initial exome sequencing for a proband, see order https://www.testmenu.com/chop/Tests/785130.

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 reanalysis, CHOP Medical Exome reanalysis, WES, Whole exome sequencing, exome, reanalysis
  • EGSFMRE

LIS Mnemonic

EGSFMRE

Available STAT

No

CPT Codes

There is no additional code/charge for reanalysis of data from family members who were submitted for exome sequencing as part of the patient’s/proband’s original CHOP Medical Exome.
Collection

Collect

CHOP Medical Exome Reanalysis should be considered for individuals who have had the CHOP Medical Exome signed out more than one year prior to ordering the reanalysis and/or has a significantly different indication for study compared to the initial exome analysis (e.g. a newly emerging phenotype). Typically, a new specimen will not be required for the CHOP Medical Exome Reanalysis test, as the laboratory should already have the patient’s exome sequencing data as well as stored DNA. Rarely, the lab will need a new specimen to perform confirmation of identity 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

N/A

Storage/Transport Temperature

N/A

Volume Required

N/A

Minimum Required

N/A

Phlebotomy Draw

No
Ordering

Clinical Features

Utilizing a combined variant and phenotype-driven analysis, the CHOP Medical Exome Reanalysis 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

A reanalysis of CHOP Medical Exome data can be ordered for anyone who has previously had a CHOP Medical Exome analysis. This option is typically recommended if it has been more than a year since the original analysis and/or the patient has developed additional symptoms/features.
 
Exome Reanalysis for exomes ordered before February 8, 2023 (v1, v2, and v3) will not be available on the Exome v4 bioinformatic pipeline. Exome reanalysis for exomes ordered before February 8, 2023 (v1, v2, and v3) will utilize the Exome v3 bioinformatic pipeline. Exome reanalysis for exomes ordered after February 8, 2023 (v4) will utilize the Exome v4 pipeline. The ordering process is the same regardless of date of original exome.
What to order for Family Members being included in the patient’s (proband’s) exome reanalysis:
 
Order Exome DNA Extract for a family member who is not undergoing exome analysis but wants to submit a sample for Sanger analysis. New family members (who were not submitted with the patient’s original CHOP Medical Exome) can only be submitted for Sanger sequencing (via the Exome DNA Extract order). They cannot undergo full exome analysis as a part of the proband’s reanalysis.

Order Exome Reanalysis, Family Member for family members who were included in the patient’s original CHOP Medical Exome analysis and are now undergoing reanalysis of existing exome data to directly assist in interpretation of the patient's exome sequencing data (typically parents and/or an affected sibling). The test order should be placed in the family member’s medical record, not the patient’s medical record.

NOTE:  If you are ordering initial exome sequencing for a proband, see order https://www.testmenu.com/chop/Tests/785130.

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 reanalysis, CHOP Medical Exome reanalysis, WES, Whole exome sequencing, exome, reanalysis
  • EGSFMRE

LIS Mnemonic

EGSFMRE

Available STAT

No
Result Interpretation
Administrative

CPT Codes

There is no additional code/charge for reanalysis of data from family members who were submitted for exome sequencing as part of the patient’s/proband’s original CHOP Medical Exome.

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