Test Catalog

Test Id : F10NG

Factor X Deficiency, F10 Gene, Next-Generation Sequencing, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Genetic confirmation of a factor X deficiency diagnosis with the identification of a known or suspected pathogenic alterations in the F10 gene

 

Carrier testing for close family members of an individual with a factor X deficiency diagnosis

 

This test is not intended for prenatal diagnosis.

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test detects pathogenic alterations within the F10 gene to delineate the underlying molecular defect in a patient with a laboratory diagnosis of factor X deficiency, a rare bleeding disorder.

 

The gene target for this test is:

Gene name (transcript): F10 (GRCh 37 [hg19] NM_000504)

Chromosomal location: 13q34

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Genetic testing for factor X deficiency (F10D) should only be considered after coagulation screening is performed and if factor X activity is less than 65% of normal (Note: reference ranges may vary depending on the locally established reference range).

 

Genetic testing for F10D is indicated if:

-Factor X clotting activity is reduced (less than 80% of normal)

-Acquired causes of factor X deficiency have been excluded (eg, liver disease, warfarin therapy, vitamin K deficiency, systemic amyloidosis, and inhibitors)

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Custom Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing when appropriate

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

F10 Gene, Full Gene NGS

Aliases
Lists additional common names for a test, as an aid in searching

Factor 10 Deficiency

Factor X Deficiency

Stuart-Prower Factor deficiency

F10D

F10

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Genetic testing for factor X deficiency (F10D) should only be considered after coagulation screening is performed and if factor X activity is less than 65% of normal (Note: reference ranges may vary depending on the locally established reference range).

 

Genetic testing for F10D is indicated if:

-Factor X clotting activity is reduced (less than 80% of normal)

-Acquired causes of factor X deficiency have been excluded (eg, liver disease, warfarin therapy, vitamin K deficiency, systemic amyloidosis, and inhibitors)

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

The clinical workup for factor X deficiency (F10D) begins with special coagulation testing for factor X. Order F_10 / Coagulation Factor X Activity Assay, Plasma.

Shipping Instructions

Ambient and refrigerated specimens must arrive within 7 days of collection, and frozen specimens must arrive within 14 days.

 

Collect and package specimen as close to shipping time as possible.

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
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD) or light-blue top (3.2% sodium citrate)

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: Ambient (preferred)/Refrigerated/Frozen

 

Specimen Type: Extracted DNA

Container/Tube: 1.5- to 2-mL tube

Specimen Volume: Entire specimen

Collection Instructions:

1. Label specimen as extracted DNA and source of specimen.

2. Provide indication of volume and concentration of the DNA.

Specimen Stability: Frozen (preferred)/Refrigerated/Ambient

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

1. Rare Coagulation Disorder Patient Information (T824) is required. Fax the completed form to 507-284-1759.

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 a Coagulation Test Request (T753) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Blood: 1 mL

Extracted DNA: 100 mcL at 50 ng/mcL concentration

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Gross hemolysis OK
Gross lipemia OK

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Ambient (preferred) 7 days
Frozen 14 days
Refrigerated 7 days

Useful For
Suggests clinical disorders or settings where the test may be helpful

Genetic confirmation of a factor X deficiency diagnosis with the identification of a known or suspected pathogenic alterations in the F10 gene

 

Carrier testing for close family members of an individual with a factor X deficiency diagnosis

 

This test is not intended for prenatal diagnosis.

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test detects pathogenic alterations within the F10 gene to delineate the underlying molecular defect in a patient with a laboratory diagnosis of factor X deficiency, a rare bleeding disorder.

 

The gene target for this test is:

Gene name (transcript): F10 (GRCh 37 [hg19] NM_000504)

Chromosomal location: 13q34

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

Genetic testing for factor X deficiency (F10D) should only be considered after coagulation screening is performed and if factor X activity is less than 65% of normal (Note: reference ranges may vary depending on the locally established reference range).

 

Genetic testing for F10D is indicated if:

-Factor X clotting activity is reduced (less than 80% of normal)

-Acquired causes of factor X deficiency have been excluded (eg, liver disease, warfarin therapy, vitamin K deficiency, systemic amyloidosis, and inhibitors)

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Factor X (FX) deficiency (F10D) is a bleeding diathesis of variable severity that may appear at any age, although more severely affected patients, who typically have FX activity less than 1%, present early in life. Symptoms include umbilical stump bleeding, intracranial hemorrhage, gastrointestinal bleeding, joint bleeds, and hematomas. The most severe clinical symptoms are uncommon in a patient with FX activity levels greater than 2%. Regardless of disease severity, the most common bleeding symptom is nose bleeds. Menorrhagia occurs in more than half of women with F10D but miscarriages are not common. Antepartum and postpartum hemorrhage are reportedly common in women with F10D and also has been reported in heterozygous females.

 

F10D is estimated to affect 1 in 1,000,000 people. If genetic, F10D is inherited in an autosomal recessive manner. Both males and females may be affected.

 

Hereditary F10D results from defects in the concentration or function of coagulation FX, a vitamin-K dependent protein synthesized in the liver that is essential for stopping blood loss after injury. FX circulates in blood plasma as an inactive zymogen. It is activated by either the intrinsic or extrinsic pathway and is the most important activator of prothrombin, which has multiple roles in the hemostatic response to injury.

 

The F10 gene produces coagulation FX. Alterations in the F10 gene can interfere with the production of coagulation FX, leading to lower levels of the factor in blood (type I F10D) or dysfunctional factor protein that is produced in normal amounts (type II F10D). The bleeding tendency in F10D is variable and does not always correlate with circulating FX antigen levels. In general, however, lower FX activity levels predict a higher risk for bleeding. FX activity of less than 1% of normal is associated with severe F10D, activity of 1% to 5% of normal is associated with moderate disease, and a FX activity of 6% to 10% is associated with mild disease. Of note, normal, full-term newborn infants or healthy premature infants may have decreased levels (greater than or equal to 15% to 20% of normal), which may not reach adult levels for greater than or equal to 180 days after birth.

 

Acquired deficiency of FX is more common than hereditary F10D. Causes of acquired (non-genetic) F10D that should be excluded prior to genetic testing include liver disease, warfarin therapy, vitamin K deficiency, and (rarely) inhibitors. Acquired isolated F10D is seen in 6% to 14% of individuals with primary amyloidosis. Other conditions associated with acquired isolated F10D include underlying malignancy, especially acute myeloid leukemia, and respiratory infection. Conditions associated with acquired F10D should be considered prior to genetic testing.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

An interpretive report will be provided.

 

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics (ACMG) recommendations as a guideline. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

 

Consultations with the Mayo Clinic Special Coagulation Clinic, Molecular Hematopathology Laboratory, or Thrombophilia Center are available for DNA diagnosis cases. This may be especially helpful in complex cases or in situations where the diagnosis is atypical or uncertain.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Clinical:

Some individuals may have a variant that is not identified by the methods performed. The absence of a variant, therefore, does not eliminate the possibility of factor X deficiency or a related disorder. This assay does not distinguish between germline and somatic alterations, particularly with variant allele frequencies significantly lower than 50%. Test results should be interpreted in context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

Technical Limitations:

Next-generation sequencing (NGS) may not detect all types of genetic variants. Additionally, rare variants (ie, polymorphisms) may be present that could lead to false-negative or false-positive results. Therefore, test results should be interpreted in the context of activity and antigen measurements, clinical findings, family history, and other laboratory data. If results do not match clinical findings, consider alternative methods for analyzing these genes, such as Sanger sequencing or large deletion/duplication analysis. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

If multiple alterations are identified, NGS is not able to distinguish between alterations that are found in the same allele ("in cis") and alterations found on different alleles ("in trans"). This limitation may complicate diagnosis or classification and has implications for inheritance and genetic counseling. To resolve these cases, molecular results must be correlated with clinical history, activity and antigen measurements, and family studies.

 

Unless reported or predicted to cause disease, alterations found deep in the intron or alterations that do not result in an amino acid substitution are not reported. These and common alterations (ie, polymorphisms) identified for this patient are available upon request.

 

Reclassification of Variants Policy:

At this time, it is not standard practice for the laboratory to systematically review likely pathogenic variants or variants of uncertain significance that are detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Brown DL, Kouides PA: Diagnosis and treatment of inherited factor X deficiency. Haemophilia. 2008 Nov;14(6):1176-1182

2. Karimi M, Menegatti M, Afrasiable A, et al: Phenotype and genotype report on homozygous and heterozygous patient with congenital factor X deficiency. Haematologica. 2008 Jun;93(6):934-938

3. Lee G, Duan-Porter W, Metjian AD: Acquired, non-amyloid related factor X deficiency: review of the literature. Haemophilia. 2012 Sep;18(5):655-663

4. Mumford AD, Ackroyd S, Alikhan R, et al: Guidelines for the diagnosis and management of the rare coagulation disorders: a United Kingdon Haemophilia Centre Doctors' Organization guidelines on behalf of the British Committee for Standards in Haematology. Br J Haematol. 2014 Nov;167(3):304-326

5. Nance D, Josephson NC, Paulyson-Nunez K, et al: Factor X deficiency and pregnancy: preconception counseling and therapeutic options. Haemophilia. 2012 May;18(3):e277-285

6. Palla R, Peyvandi F, Shapiro AD: Rare bleeding disorders: diagnosis and treatment. Blood. 2015 Mar;125(13):2052-2061

7. Menegatti M, Peyvandi F: Factor X deficiency. Semin Thromb Hemost. 2009 Jun;35(4):407-415

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing (NGS) and/or Sanger sequencing are performed.

 

Regions of homology, high guanine-cytosine (GC)-rich content, and repetitive sequences may not provide accurate sequence. Therefore, all reported alterations detected by NGSin these regions are confirmed by an independent reference method. However, this does not rule out the possibility of a false-negative result in these regions.

 

Sanger sequencing is used to confirm alterations detected by NGS when appropriate.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

21 to 28 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole Blood: 2 weeks; DNA: Indefinitely

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81479

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports