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HelpTest ID GNF7 Factor VII Deficiency, F7 Gene, Next-Generation Sequencing, Varies
Ordering Guidance
Special coagulation testing for factor VII (FVII) activity should be performed prior to any genetic testing. For assessment of FVII activity, order F_7 / Coagulation Factor VII Activity Assay, Plasma.
This test should only be considered if clinical and family history, initial coagulation screens, and/or initial activity tests indicate a diagnosis of FVII deficiency (see Testing Algorithm).
If genetic testing for hereditary bleeding disorders using a larger panel is desired, both a 6-gene focused bleeding panel and a 25-gene comprehensive bleeding panel are available. For more information see GNBLF / Bleeding Disorders, Focused Gene Panel, Next-Generation Sequencing, Varies or GNBLC / Bleeding Disorders, Comprehensive Gene Panel, Next-Generation Sequencing, Varies.
Testing for the F7 gene as part of a customized panel is available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.
Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the F7 gene. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.
Additional Testing Requirements
All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen as this must be a different order number than the prenatal specimen.
Shipping Instructions
Specimen preferred to arrive within 96 hours of collection.
Necessary Information
Rare Coagulation Disorder Patient Information is required. Testing may proceed without the patient information; however, the information aids in providing a more thorough interpretation. Ordering providers are strongly encouraged to fill out the form and send with the specimen.
Specimen Required
Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. For instructions for testing patients who have received a bone marrow transplant, call 800-533-1710.
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube:
Preferred: Lavender top (EDTA)
Acceptable: Yellow top (ACD)
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 (preferred) 4 days/Refrigerated
Prenatal Specimens
Due to its complexity, consultation with the laboratory is required for all prenatal testing; call 800-533-1710 to speak to a genetic counselor.
Specimen Type: Amniotic fluid
Container/Tube: Amniotic fluid container
Specimen Volume: 20 mL
Specimen Stability Information: Refrigerated (preferred)/Ambient
Additional information:
1. A separate culture charge will be assessed under CULAF / Culture for Genetic Testing, Amniotic Fluid.
2. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Chorionic villi
Container/Tube: 15-mL tube containing 15 mL of transport media
Specimen Volume: 20 mg
Specimen Stability Information: Refrigerated
Additional Information:
1. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing.
2. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Acceptable:
Specimen Type: Confluent cultured cells
Container/Tube: T-25 flask
Specimen Volume: 2 Flasks
Collection Instructions: Submit confluent cultured cells from another laboratory.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Additional Information:
All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Forms
1. Rare Coagulation Disorder Patient Information (T824) is required.
2. 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)
3. If not ordering electronically, complete, print, and send an Coagulation Test Request (T753) with the specimen.
Useful For
Evaluating factor VII deficiency (FVIID) in patients with a personal or family history suggestive of FVIID
Confirming an FVIID diagnosis with the identification of known or suspected disease-causing alterations in the F7 gene
Determining the disease-causing alterations within the F7 gene to delineate the underlying molecular defect in a patient with a laboratory diagnosis of FVIID
Identifying the causative alterations for genetic counseling purposes
Prognosis and risk assessment based on the genotype-phenotype correlations
Carrier testing for close family members of an individual with a diagnosis of FVIID
Genetics Test Information
This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in the F7 gene associated with factor VII deficiency (FVIID), a rare bleeding disorder. See 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 FVIID.
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| CULFB | Fibroblast Culture for Genetic Test | Yes | No |
| CULAF | Amniotic Fluid Culture/Genetic Test | Yes | No |
| MATCC | Maternal Cell Contamination, B | Yes | No |
Testing Algorithm
The clinical workup for factor VII deficiency (FVIID) should begin with special coagulation testing for factor VII (FVII) activity.
Genetic testing for F7D is indicated if:
-FVII activity is less than 65% of normal (Note: reference range may vary depending on the locally established reference range)
-Acquired causes of F7D have been excluded (eg, vitamin K deficiency, use of vitamin K antagonists such as warfarin, liver disease, sepsis)
For prenatal specimens only:
-If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture/genetic test will be added at an additional charge.
-If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture for genetic test will be added at an additional charge.
For any prenatal specimen that is received, maternal cell contamination testing will be performed at an additional charge.
Method Name
Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing
Reporting Name
F7 Gene, Full Gene NGSSpecimen Type
VariesSpecimen Minimum Volume
Whole blood: 1 mL; Amniotic fluid: 10 mL; Other specimen types: See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Varies | ||
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Clinical Information
Factor VII deficiency (FVIID) is a rare hereditary bleeding disorder associated with germline variants in the F7 gene. It is inherited in an autosomal recessive manner with variable expressivity; both male and female individuals may be affected. The estimated prevalence is 1 in 500,000 individuals.(1)
FVIID is characterized by a deficiency or reduced activity of clotting factor VII. The symptoms and severity of FVIID are highly variable. Individuals with mild disease do not typically experience spontaneous bleeding but may have prolonged bleeding after trauma or surgery. For those with severe disease, symptoms include epistaxis, menorrhagia, easy bruising, gum bleeding, and post-surgical bleeding. Onset can occur within the first 6 months of life and include life-threatening intracranial and gastrointestinal hemorrhages. Joint and muscle bleeds are less common. FVIID does not protect against venous thromboembolism.(2-4)
In many cases of FVIID, there is no consistent correlation between FVII plasma levels and disease severity.(1,4,5) However, good correlation has been demonstrated between FVII levels and genotype. Individuals with homozygous or compound heterozygous disease-causing variants in the F7 gene have been found to have significantly lower FVII levels than those individuals with heterozygous or no detectable F7 variants.(6)
Causes of acquired (nongenetic) FVIID should be excluded prior to genetic testing, including vitamin K deficiency, use of vitamin K antagonists such as warfarin, liver disease, and sepsis.(7,8)
The United Kingdom Haemophilia Centre Doctors' Organization provides guidelines regarding diagnosis and management for individuals with inherited bleeding disorders, including F7D.(9)
Reference Values
An interpretive report will be provided.
Interpretation
All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(10) 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 the 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 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.
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 blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.
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 providers 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.(10) 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.
Clinical Reference
1. Palla R, Peyvandi F, Shapiro AD: Rare bleeding disorders: diagnosis and treatment. Blood. 2015 Mar;125(13):2052-2061
2. Lapecorella M, Mariani G, International Registry on Congenital Factor VII Deficiency: Factor VII deficiency: defining the clinical picture and optimizing therapeutic option. Haemophilia. 2008 Nov;14(6):1170-1175
3. Napolitano M, Siragusa S, Mariani G: Factor VII deficiency: Clinical phenotype, genotype and therapy. J Clin Med. 2017 Mar 28;6(4):38
4. Mariani G, Herrmann FH, Schulman S, International Factor VII Deficiency Study Group, et al: Thrombosis in inherited factor VII deficiency. J Thromb Haemost. 2003 Oct;1(10):2153-2158.
5. de Moerloose P, Schved J-F, Nugent D: Rare coagulation disorders: fibrinogen, factor VII and factor XIII. Haemophilia 2016. Jul;22 Suppl 5:61-65
6. Quintavalle G, Riccardi F, Rivolta GF, et al: F7 gene variants modulate protein levels in a large cohort of patients with factor VII deficiency. Results from a genotype-phenotype study. Thromb Haemost. 2017 Aug 1;117(8):1455-1464
7. da Silva VA, Silva SS, Martins FF: Acquired deficiency of coagulation factor VII. Rev Bras Hematol Hemoter. 2015 Jul- Aug;37(4):269-271
8. Mulliez SM, Devreese KM: Isolated acquired factor VII deficiency: a review of the literature. Acta Clin Belg. 2016 Apr;71(2):63-70
9. Mumford AD, Ackroyd S, Alikhan R, et al: Guideline for the diagnosis and management of the rare coagulation disorders: a United Kingdom Haemophilia Centre Doctors' Organization guideline on behalf of the British Committee for Standards in Haematology. Br J Haematol. 2014 Nov;167(3):304-326
10. Richards S, Aziz N, Bale S, et al; ACMG Laboratory Quality Assurance Committee: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424
Method Description
Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the F7 gene, 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-based quantitative method is performed to test for the presence of deletions and duplications in the F7 gene.
There may be regions of the F7 gene 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.(Unpublished Mayo method)
The reference transcript for F7 is NM_000131.4. Reference transcript numbers may be updated due to transcript re-versioning. Always refer to the final patient report for gene transcript information referenced at the time of testing. Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.
Day(s) Performed
Varies
Report Available
28 to 42 daysTest 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
88233-Tissue culture, skin, solid tissue biopsy (if appropriate)
88240-Cryopreservation (if appropriate)
88235-Amniotic fluid culture (if appropriate)