Skin biopsy or two T25 flasks of cultured fibroblasts from skin*
Blood – 2-3 mL in an EDTA (purple top) tube.
Bone Marrow - 2-3 mL in an EDTA (purple top) tube.
Saliva – please contact the lab regarding the availability of collection kits by emailing DGDGeneticCounselor@chop.edu.
DNA – 3 ug of DNA with a concentration of at least 50 ng/ul
*If the individual being tested has suspected or confirmed myelodysplasia or leukemia/lymphoma, or if the individual is the recipient of a donor (allogeneic) bone marrow transplant, cultured fibroblasts from skin are the preferred specimen to assess for constitutional genetic variants.
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
The Fanconi Anemia NGS Panel is a next generation sequencing (NGS) panel designed to identify underlying genetic variants associated with Fanconi anemia and other chromosomal breakage disorders. These disorders are typically associated with multiple congenital and developmental abnormalities, predisposition to malignancy, and risk for bone marrow failure.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity for comprehensive sequencing and copy number analysis is not yet well-established and is dependent on the panel's gene content and the patient's clinical features. The estimated detection rates are provided for pathogenic variants that can be identified for probands meeting the clinical diagnostic criteria for specific disorders based on the gene content of this panel: >95% for Fanconi anemia [Shimamura 2010, PMID: 20417588], 90-97% for ataxia-telangiectasia [Cavalieri 2008, PMID: 17910737; GeneReviews 2016, PMID: 20301790], 87-93% for Bloom syndrome [German 2007, PMID: 17407155] and >95% for Nijmegen breakage syndrome [GeneReviews 2022, PMID: 20301355].
Utility
These disorders are typically associated with multiple congenital and developmental abnormalities, predisposition to malignancy, and risk for bone marrow failure. Identification of the underlying causative mutation of these disorders has critical implications in confirming an accurate diagnosis, providing personalized approaches to treatment, and for family genetic counseling.
Genomic DNA was extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing was performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis were based on the GRCh38 reference sequence. Sequencing data was processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
The Fanconi Anemia NGS Panel includes sequence and copy number analyses of the following genes: ATM, BLM, BRCA1, BRCA2, BRIP1, DDX11, ERCC4, ESCO2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, LIG4, NBN, NHEJ1, PALB2, RAD51, RAD51C, and SLX4.
CPT Codes
81209, 81163, 81242, 81307, 81408, 81479
Collection
Collect
Skin biopsy or two T25 flasks of cultured fibroblasts from skin*
Blood – 2-3 mL in an EDTA (purple top) tube.
Bone Marrow - 2-3 mL in an EDTA (purple top) tube.
Saliva – please contact the lab regarding the availability of collection kits by emailing DGDGeneticCounselor@chop.edu.
DNA – 3 ug of DNA with a concentration of at least 50 ng/ul
*If the individual being tested has suspected or confirmed myelodysplasia or leukemia/lymphoma, or if the individual is the recipient of a donor (allogeneic) bone marrow transplant, cultured fibroblasts from skin are the preferred specimen to assess for constitutional genetic variants.
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
The Fanconi Anemia NGS Panel is a next generation sequencing (NGS) panel designed to identify underlying genetic variants associated with Fanconi anemia and other chromosomal breakage disorders. These disorders are typically associated with multiple congenital and developmental abnormalities, predisposition to malignancy, and risk for bone marrow failure.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
28 days
Detection Rate
The clinical sensitivity for comprehensive sequencing and copy number analysis is not yet well-established and is dependent on the panel's gene content and the patient's clinical features. The estimated detection rates are provided for pathogenic variants that can be identified for probands meeting the clinical diagnostic criteria for specific disorders based on the gene content of this panel: >95% for Fanconi anemia [Shimamura 2010, PMID: 20417588], 90-97% for ataxia-telangiectasia [Cavalieri 2008, PMID: 17910737; GeneReviews 2016, PMID: 20301790], 87-93% for Bloom syndrome [German 2007, PMID: 17407155] and >95% for Nijmegen breakage syndrome [GeneReviews 2022, PMID: 20301355].
Utility
These disorders are typically associated with multiple congenital and developmental abnormalities, predisposition to malignancy, and risk for bone marrow failure. Identification of the underlying causative mutation of these disorders has critical implications in confirming an accurate diagnosis, providing personalized approaches to treatment, and for family genetic counseling.
Genomic DNA was extracted from patient tissue following standard DNA extraction protocols. Whole genome sequencing was performed on the Illumina NovaSeq 6000 platform using the Illumina DNA PCR-Free Library Prep with 150bp paired-end reads. Mapping and analysis were based on the GRCh38 reference sequence. Sequencing data was processed using the Dragen pipeline (Illumina) to call both sequence and copy number variants.
Molecular Testing Notes
The Fanconi Anemia NGS Panel includes sequence and copy number analyses of the following genes: ATM, BLM, BRCA1, BRCA2, BRIP1, DDX11, ERCC4, ESCO2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, LIG4, NBN, NHEJ1, PALB2, RAD51, RAD51C, and SLX4.
