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
Alport syndrome is a syndromic form of hearing loss characterized by kidney dysfunction, such as hematuria, leading to end stage renal disease (ESRD), high frequency progressive sensorineural hearing loss and the absence or presence of ocular abnormalities, such as anterior lenticonus [Kashtan 2015, PMID: 20301386].
Performing Lab
Division of Genomic Diagnostics
Performed
Monday to Friday, 9:00am to 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity of comprehensive next generation sequencing and deletion/duplication analysis is not yet well-established, and dependent on the patient's clinical features. The estimated detection rate for pathogenic variants that can be identified for probands meeting the clinical diagnostic criteria for Alport syndrome based on the gene content of this panel is ~99% [Kashtan 2015, PMID: 20301386]. A majority of variants causing Alport syndrome are sequence variants, although it is estimated that multiexon deletions occur in ~10% of females whose family histories are consistent with X-linked Alport Syndrome [Kashtan 2015, PMID: 20301386].
Utility
The clinical utility of the assay is to support a clinical diagnosis of the disease, facilitate genetic counseling, and 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
The Alport Syndrome panel includes sequence and copy number analyses of the following genes: COL4A3, COL4A4, COL4A5, and COL4A6. Alport syndrome is genetically heterogeneous conditions with alterations seen in the following genes: COL4A5 (Collagen, type IV, Alpha-5 on Xp22.3; OMIM# 301050); COL4A3 (Collage, type IV. Alpha-3 on 2q36.3; OMIM# 104200) and COL4A4 (Collagen, type IV, Alpha-4 on 2q36.3; OMIM# 203780). Depending on the gene, pathogenic alterations are inherited in X-linked (80%), autosomal recessive (15%) and autosomal dominant (5%) manners. Penetrance of this condition is currently unknown, though is more complete in the X-linked and autosomal recessive types and decreased in the dominant form. There is variability expressivity in terms of the severity and onset of each of the hallmark features which depends somewhat on the implicated gene. Anterior lenticonus, which is pathognomonic for Alport is more often identified in individuals with pathogenic variants in COL4A5. The majority of variants for all genes are inherited from a parent, though some occur de novo. Genetic testing is necessary to establish which gene (and thus which inheritance pattern) is implicated and which other family members may be at risk.
CPT Codes
81407, 81408, and 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
Alport syndrome is a syndromic form of hearing loss characterized by kidney dysfunction, such as hematuria, leading to end stage renal disease (ESRD), high frequency progressive sensorineural hearing loss and the absence or presence of ocular abnormalities, such as anterior lenticonus [Kashtan 2015, PMID: 20301386].
Performing Lab
Division of Genomic Diagnostics
Performed
Monday to Friday, 9:00am to 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity of comprehensive next generation sequencing and deletion/duplication analysis is not yet well-established, and dependent on the patient's clinical features. The estimated detection rate for pathogenic variants that can be identified for probands meeting the clinical diagnostic criteria for Alport syndrome based on the gene content of this panel is ~99% [Kashtan 2015, PMID: 20301386]. A majority of variants causing Alport syndrome are sequence variants, although it is estimated that multiexon deletions occur in ~10% of females whose family histories are consistent with X-linked Alport Syndrome [Kashtan 2015, PMID: 20301386].
Utility
The clinical utility of the assay is to support a clinical diagnosis of the disease, facilitate genetic counseling, and 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
The Alport Syndrome panel includes sequence and copy number analyses of the following genes: COL4A3, COL4A4, COL4A5, and COL4A6. Alport syndrome is genetically heterogeneous conditions with alterations seen in the following genes: COL4A5 (Collagen, type IV, Alpha-5 on Xp22.3; OMIM# 301050); COL4A3 (Collage, type IV. Alpha-3 on 2q36.3; OMIM# 104200) and COL4A4 (Collagen, type IV, Alpha-4 on 2q36.3; OMIM# 203780). Depending on the gene, pathogenic alterations are inherited in X-linked (80%), autosomal recessive (15%) and autosomal dominant (5%) manners. Penetrance of this condition is currently unknown, though is more complete in the X-linked and autosomal recessive types and decreased in the dominant form. There is variability expressivity in terms of the severity and onset of each of the hallmark features which depends somewhat on the implicated gene. Anterior lenticonus, which is pathognomonic for Alport is more often identified in individuals with pathogenic variants in COL4A5. The majority of variants for all genes are inherited from a parent, though some occur de novo. Genetic testing is necessary to establish which gene (and thus which inheritance pattern) is implicated and which other family members may be at risk.
