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Test Code IPFGP Idiopathic Pulmonary Fibrosis Gene Panel, Varies


Ordering Guidance


Patients who have had a previous bone marrow transplant from an allogenic donor should not have testing performed on blood, bone marrow, or saliva because any results generated will reflect the genome of the donor rather than the recipient. Testing on patients who have an active hematologic malignancy or hematologic disorder with clonal proliferation may identify both somatic mutations and germline variants, which may result in test failure or necessitate follow-up testing to determine whether the detected variant is germline or somatic. For these patients, testing a skin biopsy or cultured fibroblasts is recommended. For instructions for testing patients who have received a bone marrow transplant or have an active hematologic disorder, call 800-533-1710. For more information see Cautions.

 

Customization of this panel and single gene analysis for any gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies. To modify this panel via CGPH, use the Inborn Errors of Immunity/Bone Marrow Failure/Telomeropathy/Pulmonary Fibrosis/Very Early Onset IBD/Pancreatitis disease state for step 1 on the Custom Gene Ordering Tool.

 

Targeted testing for familial variants (also called site-specific or known variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.



Additional Testing Requirements


For cord blood specimens: Maternal cell contamination (MCC) studies are available. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on both the cord blood and maternal specimens under separate order numbers. Cord blood testing will proceed without MCC studies, but results may be compromised if MCC is present.



Specimen Required


Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

Specimen Type: Skin biopsy

Supplies: Fibroblast Biopsy Transport Media (T115)

Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin.

Specimen Volume: 4-mm Punch

Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours

Additional Information:

1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.

2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical and Molecular Testing, Tissue. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Source: Skin

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy from another laboratory. Cultured cells from a prenatal specimen will not be accepted.

Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours

Additional Information:

1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.

2.A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical and Molecular Testing, Tissue. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Extracted DNA

Container/Tube:

Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base

Acceptable: Matrix tube, 1 mL

Collection Instructions:

1. The preferred volume is at least 100 mcL at a concentration of 75 ng/mcL.

2. Include concentration and volume on tube.

Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated

Additional Information: DNA must be extracted in a CLIA-certified laboratory, or equivalent, and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.

 

Specimen Type: Bone marrow aspirate

Container/Tube:

Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD)

Specimen Volume: 2 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send bone marrow specimen in original tube. Do not aliquot.

3. Label specimen as bone marrow.

Specimen Stability Information: Ambient 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1.Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2.To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

Specimen Type: Cord blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Green top (sodium heparin)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send cord blood specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen

 

Specimen Type: Blood spot

Supplies: Card-Blood Spot Collection (Filter Paper) (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: PerkinElmer 226 filter paper or blood spot collection card

Specimen Volume: 2 to 5 Blood spots

Collection Instructions:

1. An alternative blood collection option for a patient older than 1 year is a fingerstick. For detailed instructions, see How to Collect a Dried Blood Spot Sample.

2. Let blood dry on the filter paper at ambient temperature in a horizontal position for a minimum of 3 hours.

3. Do not expose specimen to heat or direct sunlight.

4. Do not stack wet specimens.

5. Keep specimen dry

Specimen Stability Information: Ambient (preferred)/Refrigerated

Additional Information:

1. Blood spot specimens are acceptable but not recommended. Multiple extractions will be required to obtain sufficient yield for supplemental analysis, and there is significant risk for test failure due to insufficient DNA.

2. Due to lower concentration of DNA yielded from blood spot, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.

3. For collection instructions, see Blood Spot Collection Instructions

4. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777)

5. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800)

 

Specimen Type: Saliva

Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.

Supplies: Saliva Swab Collection Kit (T786)

Specimen Volume: 2 Swabs, use 2 kits for collection

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient (preferred) 30 days/Refrigerated 30 days

Additional Information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.


Forms

1. New York Clients-Informed consent is required.

Document on the request form or electronic order that a copy is on file. The following documents are available:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Congenital Neutropenia, Bone Marrow Failure, Telomere Defects, and Pulmonary Fibrosis (IPF) Patient Information

Useful For

Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of familial idiopathic pulmonary fibrosis

 

Establishing a diagnosis of familial idiopathic pulmonary fibrosis associated with known causal genes

 

Identifying variants within genes known to be associated with inherited risk for idiopathic pulmonary fibrosis, allowing for predictive testing of at-risk family members and/or determination of targeted management (anticipatory guidance, management changes, specific therapies)

Genetics Test Information

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 27 genes associated with heritable forms of idiopathic pulmonary fibrosis: ABCA3, ACD, AP3B1, CTC1, DKC1, HPS1, HPS4, NAF1, NHP2, NOP10, PARN, POT1, RNF168, RPA1, RTEL1, SFTPA1, SFTPA2, SFTPB, SFTPC, STN1, STING1, TERC, TERT, TINF2, USB1, WRAP53, and ZCCHC8. See Targeted Genes and Methodology Details for Idiopathic Pulmonary Fibrosis Gene Panel and Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling for familial pulmonary fibrosis.

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CULFB Fibroblast Culture for Genetic Test Yes No
MATCC Maternal Cell Contamination, B Yes No

Testing Algorithm

Skin biopsy:

For skin biopsy or cultured fibroblast specimens, fibroblast culture will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

 

Cord blood:

For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.

Method Name

Sequence Capture and Amplicon-Based Next-Generation Sequencing (NGS), followed by Sanger Sequencing/Quantitative Real-Time Polymerase Chain Reaction (qPCR) as needed.

Reporting Name

Pulmonary Fibrosis Gene Panel

Specimen Type

Varies

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Clinical Information

Pulmonary fibrosis is characterized by irreversible, progressive damage and scarring of tissue around and between alveoli in the lungs. Causes include certain medications, chest radiation treatment, long term exposure to toxins, pollutants or other environmental triggers, and autoimmune disease. When none of these causes is identified, pulmonary fibrosis is described as "idiopathic". The histologic pattern "usual interstitial pneumonia" is associated with the clinical diagnosis of idiopathic pulmonary fibrosis (IPF). Although IPF is considered a disease of unknown cause, some factors increase the risk for IPF, such as age and smoking. A subset of individuals with IPF may carry genetic variants that predispose them to disease.

 

When IPF occurs at a younger age than expected (ie, before age 50 years), affects more than one individual in a family, or presents with other clinical features (eg, bone marrow failure, macrocytosis, cryptogenic cirrhosis or portal hypertension, premature graying of hair, abnormal nails, skin pigmentation, or bleeding), genetic testing may be considered.

 

This panel assesses 27 genes associated with the following heritable causes of pulmonary fibrosis.

 

Disorders of Surfactant Dysfunction

Surfactant is a lipoprotein complex secreted by alveolar cells that reduces the surface tension of fluids coating the lung. It is essential for alveolar stability and lung function. Genes important for surfactant production and metabolism include ABCA3, SFTPA1, SFTPA2, SFTPB, and SFTPC. In neonates and infants, inborn errors of pulmonary surfactant metabolism present as severe respiratory insufficiency or failure. However, individuals with disease-causing variants in these genes can present with pulmonary fibrosis at any age, from infancy to late adulthood. While these conditions are not associated with extrapulmonary features, they can cosegregate with lung adenocarcinoma in some families.

 

Telomere Biology Disorders

Telomeres are protective DNA repeats at the ends of chromosomes that protect the chromosome from shortening and damage caused by cellular replication. Genes involved in telomere synthesis, maintenance, and elongation include ACD, CTC1, DKC1, NAF1, NHP2, NOP10, PARN, POT1, RPA1, RTEL1, STN1, TERC, TERT, TINF2, WRAP53, and ZCCHC8. Although idiopathic pulmonary fibrosis is the one of the most common manifestations of telomere biology disorders (TBDs), these conditions often cause extrapulmonary features and are highly pleiotropic. Dyskeratosis congenita, for example, is characterized by reticular skin pigmentation, nail dystrophy, and oral mucosal leukoplakia, and often causes bone marrow failure. Cerebroretinal microangiopathy with calcifications and cysts (aka Coats plus syndrome), which is associated with CTC1 and STN1, is characterized by retinal telangiectasia exudates, leukodystrophy, intracranial calcifications and cysts. Of note, TBDs characterized by short telomeres show genetic anticipation with each generation potentially presenting with earlier and/or more severe disease phenotype.

 

Hemansky-Pudlak syndrome, types 1, 2, and 4

Hermansky-Pudlak syndrome (HPS) is a multisystem disorder with 10 different subtypes that is primarily characterized by skin, hair, and eye hypopigmentation and bleeding diathesis caused by platelet dysfunction. Some individuals with HPS types 1 and 4 also have granulomatous inflammation of the bowel. HPS types 1, 2, and 4, which are caused by disease-causing variants in HPS1, AP3B1, and HPS4 respectively, are associated with pulmonary fibrosis that typically presents at 30 to 40 years of age. Almost all individuals with HPS1 develop pulmonary fibrosis.

 

This panel also includes genes associated with 3 rare syndromic monogenic disorders for which pulmonary fibrosis have been reported: RIDDLE syndrome (RNF168) (increased radiosensitivity, mild immunodeficiency, dysmorphic features, and learning difficulties); STING-associated vasculopathy with onset in infancy (STING1) (SAVI; systemic inflammation, small vessel vasculopathy, progressive lung disease); and poikiloderma with neutropenia (USB1).

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(1) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Cautions

Clinical Correlations:

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.

 

To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact Mayo Clinic Laboratories genetic counselors at 800-533-1710.

 

Technical Limitations:

Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.

 

This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.

 

Deletion/Duplication Analysis:

This analysis targets single and multi-exon deletions/duplications; however, in some instances single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.

 

This test is not designed to detect low levels of mosaicism or to differentiate between somatic mutations and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.

 

Genes may be added or removed based on updated clinical relevance. For the most up to date list of genes included in this test and for detailed information regarding gene-specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.

 

If the patient has had an allogeneic hematopoietic stem cell transplant or a recent non-leukocyte reduced blood transfusion, results of tests performed on blood, bone marrow, or saliva specimens may be clinically inaccurate due to the presence of donor DNA. Test orders for blood, bone marrow, or saliva will be canceled by the laboratory if there is a history of an allogeneic hematopoietic stem cell transplant. Similarly, blood, bone marrow, and saliva results may be impacted by presence of active hematologic malignancy or hematologic disorder with clonal proliferation. Call Mayo Clinic Laboratories for instructions for testing a skin biopsy or fibroblast culture for patients who have received a bone marrow transplant or have an active hematologic disorder.

 

Reclassification of Variants:

Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages healthcare professionals to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.

 

Variant Evaluation:

Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(1) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.

 

Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.

 

Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. These findings will be carefully reviewed to determine whether they will be reported.

Method Description

Next-generation sequencing (NGS) and/or Sanger sequencing is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions/insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. See Targeted Genes and Methodology Details for Idiopathic Pulmonary Fibrosis Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)

 

Genes analyzed: ABCA3, ACD, AP3B1, CTC1, DKC1, HPS1, HPS4, NAF1, NHP2, NOP10, PARN, POT1, RNF168, RPA1, RTEL1, SFTPA1, SFTPA2, SFTPB, SFTPC, STN1, STING1, TERC, TERT, TINF2, USB1, WRAP53, and ZCCHC8

Day(s) Performed

Varies

Report Available

28 to 42 days

Specimen Retention Time

Whole blood: 28 days (if available); Saliva: 30 days (if available); Extracted DNA: 3 months; Blood spots: 1 year (if available)

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
IPFGP Pulmonary Fibrosis Gene Panel 105259-6

 

Result ID Test Result Name Result LOINC Value
621590 Test Description 62364-5
621591 Specimen 31208-2
621592 Source 31208-2
621593 Result Summary 50397-9
621594 Result 82939-0
621595 Interpretation 69047-9
621596 Additional Results 82939-0
621597 Resources 99622-3
621598 Additional Information 48767-8
621599 Method 85069-3
621600 Genes Analyzed 82939-0
621601 Disclaimer 62364-5
621602 Released By 18771-6
MG157 Is this Bone Marrow 31208-2