Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 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
Clinical Features
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous autosomal recessive condition caused by biallelic pathogenic mutations in genes associated with ciliary development or motility. PCD is characterized clinically by chronic respiratory distress, chronic nasal and ear infections, bronchiectasis, retention of mucus within the respiratory tract, situs abnormalities, and decreased or absent sperm motility in males [GeneReviews 2019, PMID: 20301301].
Performing Lab
Division of Genomic Diagnostics
Performed
Monday to Friday, 9:00am to 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity for comprehensive next generation sequencing panels is not yet well-established and is dependent on the panel's gene content and the patient's clinical features. The estimated detection rates for pathogenic variants that can be identified for probands with primary ciliary dyskinesia is ~60-70% based on the gene content of this panel. While most pathogenic variants associated with PCD are sequence variants, pathogenic deletions and duplications have been reported rarely in DNAH5, CCDC40, SPAG1, ZMYND10, ARMC4, and DNAAF1 [GeneReviews 2019, PMID: 20301301].
Utility
The clinical utility of the assay is to support a clinical diagnosis of the disease, to facilitate genetic counseling, to assess the risk to other first degree relatives, and to facilitate testing of at-risk family members. Molecular confirmation of a diagnosis may help guide recommendations for medical management and screening, and may help avoid unnecessary procedures.
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 is based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
Primary Ciliary Dyskinesia (PCD) is a disorder caused by alterations in genes associated with ciliary development or motility. There are currently over 30 genes which have been associated with PCD, with the majority of individuals with a molecularly confirmed diagnosis of PCD having biallelic alterations in the DNAH5, DNAH11, CCDC39, or DNA11 genes. This panel includes sequence and copy number analyses of the following genes and regions of interest: CCDC39, CCDC40, CCDC65, CCDC103, CCNO, CFAP298, CFAP300, CFTRφ, DNAAF1, DNAAF2, DNAAF3, DNAAF4, DNAAF5, DNAAF6, DNAAF11, DNAH1, DNAH5, DNAH6, DNAH8, DNAH9, DNAH11, DNAI1, DNAI2, DNAJB13, DNAL1, DRC1, GAS8, INVS, MCIDAS, NME8, ODAD1, ODAD2, ODAD3, ODAD4, OFD1, RPGR, RSPH1, RSPH3, RSPH4A, RSPH9, SPAG1, and ZMYND10.
φ Deep intronic variants c.3718-2477 and c.1680-886A>G and the intron 8 poly T tract in CFTR are included in the analysis.
CPT Codes
81223, 81479
Collection
Collect
Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA and saliva are also acceptable.
Specimen Preparation
Please provide detailed clinical history and features. For more information contact the lab at 6-1447 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
Clinical Features
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous autosomal recessive condition caused by biallelic pathogenic mutations in genes associated with ciliary development or motility. PCD is characterized clinically by chronic respiratory distress, chronic nasal and ear infections, bronchiectasis, retention of mucus within the respiratory tract, situs abnormalities, and decreased or absent sperm motility in males [GeneReviews 2019, PMID: 20301301].
Performing Lab
Division of Genomic Diagnostics
Performed
Monday to Friday, 9:00am to 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity for comprehensive next generation sequencing panels is not yet well-established and is dependent on the panel's gene content and the patient's clinical features. The estimated detection rates for pathogenic variants that can be identified for probands with primary ciliary dyskinesia is ~60-70% based on the gene content of this panel. While most pathogenic variants associated with PCD are sequence variants, pathogenic deletions and duplications have been reported rarely in DNAH5, CCDC40, SPAG1, ZMYND10, ARMC4, and DNAAF1 [GeneReviews 2019, PMID: 20301301].
Utility
The clinical utility of the assay is to support a clinical diagnosis of the disease, to facilitate genetic counseling, to assess the risk to other first degree relatives, and to facilitate testing of at-risk family members. Molecular confirmation of a diagnosis may help guide recommendations for medical management and screening, and may help avoid unnecessary procedures.
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 is based on the GRCh38 reference sequence. Sequencing data is processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
Primary Ciliary Dyskinesia (PCD) is a disorder caused by alterations in genes associated with ciliary development or motility. There are currently over 30 genes which have been associated with PCD, with the majority of individuals with a molecularly confirmed diagnosis of PCD having biallelic alterations in the DNAH5, DNAH11, CCDC39, or DNA11 genes. This panel includes sequence and copy number analyses of the following genes and regions of interest: CCDC39, CCDC40, CCDC65, CCDC103, CCNO, CFAP298, CFAP300, CFTRφ, DNAAF1, DNAAF2, DNAAF3, DNAAF4, DNAAF5, DNAAF6, DNAAF11, DNAH1, DNAH5, DNAH6, DNAH8, DNAH9, DNAH11, DNAI1, DNAI2, DNAJB13, DNAL1, DRC1, GAS8, INVS, MCIDAS, NME8, ODAD1, ODAD2, ODAD3, ODAD4, OFD1, RPGR, RSPH1, RSPH3, RSPH4A, RSPH9, SPAG1, and ZMYND10.
φ Deep intronic variants c.3718-2477 and c.1680-886A>G and the intron 8 poly T tract in CFTR are included in the analysis.
