Coagulation Factor Deficiency Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits

NextGen Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1379 F10 81479 Add to Order
F11 81479
F12 81479
F13A1 81479
F13B 81479
F2 81479
F5 81479
F7 81479
F8 81407
F9 81238
FGA 81479
FGB 81479
FGG 81479
GGCX 81479
LMAN1 81479
MCFD2 81479
SERPINE1 81479
SERPINF2 81479
VKORC1 81479
VWF 81408
Full Panel Price* $640.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1379 Genes x (20) $640.00 81238, 81407, 81408, 81479(x17) Add to Order
Pricing Comments

We are happy to accommodate requests for single genes or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered on our PGxome Custom Panel.

Targeted Testing

For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity

Analytical sensitivity should be high because ~95% of pathogenic variants reported are detectable by this method. The exception is the F8 gene which has inversions in ~40% of cases of hemophilia A which are not detected by this method.

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Del/Dup via aCGH

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
600 F10$990.00 81479 Add to Order
F11$990.00 81479
F12$990.00 81479
F13A1$990.00 81479
F13B$990.00 81479
F2$990.00 81479
F5$990.00 81479
F7$990.00 81479
F8$990.00 81406
F9$990.00 81479
FGA$990.00 81479
FGB$990.00 81479
FGG$990.00 81479
GGCX$990.00 81479
LMAN1$990.00 81479
MCFD2$990.00 81479
SERPINE1$990.00 81479
SERPINF2$990.00 81479
VKORC1$990.00 81479
VWF$990.00 81479
Full Panel Price* $1490.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (20) $1490.00 81406, 81479(x19) Add to Order
Pricing Comments

# of Genes Ordered

Total Price









Over 100

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Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity

For coagulation deficiency genes, large deletions are represent 5% of causative variants in the F10, 2% in F11, 3% in F13A1, 2% in F5, 2% in F7, 6% in F8, 3% in F9, 15% in FGA, and 5% in VWF (Human Gene Mutation Database).

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Clinical Features

The coagulation factor deficiency panel includes testing for a large group of inherited bleeding disorders including three types of hemophilia (F9), von Willebrand disease (VWD) and rare bleeding disorders (RBD). RBDs include inherited deficiencies in fibrinogen, factor (F) II, FV, FV +FVIII, FVII, FX, FXI, FXII, FXIII, plasminogen activator inhibitor, alpha-s-plasmin inhibitor, and combined factor deficiencies (Othman 2013; Peyvandi et al. 2012). Hemophilia A, B, and VWD disease make up ~95% of bleeding disorders due to coagulation factor deficiencies. RBDs occur in one of 500,000 people and equally affect males and females, unlike Hemophilia A and B which arises in males. Symptoms among the various coagulation factor deficiencies range greatly, yet are often phenotypically similar between the specific disease states (Peyvandi et al. 2013). These disorders are also mirror symptoms of many inherited platelet defect disorders (Watson et al. 2013; Diz-Küçükkaya 2013). Bleeding episodes can range from mild with individuals being asymptomatic until incursion of trauma or surgery to severe with life threatening hemorrhages. The coagulation cascade works concurrently to mitigate bleeding through formation of fibrin clots at sites of injury. Each coagulation factor often has its own biochemical assay to assess its function which means diagnosis, especially of RBDs, may be cumbersome. Genetic testing provides a means to examine multiple coagulation factor genes simultaneously to quickly identify potential causes to disease (Peyvandi et al. 2013).


Hemophilia A and B are inherited through an X-linked recessive manner through pathogenic variants in the F8 and F9 genes respectively and primarily affect males. VWD is inherited in both autosomal dominant and recessive manners through pathogenic variants in the VWF gene. RBDs are all inherited in an autosomal recessive manner with deficiencies in FVII, FXI, or FV accounting for ~80% of cases. RBD genes include FGA, FGB, FGG, F2, F5, F7, F10, F11, F12, F13A1, F13B, MCFD2, LMAN1, SERPINE1, SERPINF2, GGCX, and VKORC1 (Othman 2013; Peyvandi et al. 2012). See individual test descriptions for additional information on the molecular biology of each gene.

Testing Strategy

For this NGS test, the full coding regions plus ~10bp of non-coding DNA flanking each exon are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing.

This panel provides 100% coverage of the aforementioned regions of the indicated genes. We define coverage as > 20X NGS reads for exons and 0-10 bases of flanking DNA, > 10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Patients exhibiting excessive bleeding while having normal platelet counts and function are ideal candidates. This test especially aids in a differential diagnosis of similar phenotypes, rules out particular syndromes, and provides the analysis of multiple genes simultaneously. Individuals who are suspected of any of these disorders, especially if clinical diagnosis is unclear and individuals who have been found to be negative by mutation analysis for a single gene test are candidates.


Official Gene Symbol OMIM ID
F10 613872
F11 264900
F12 610619
F13A1 134570
F13B 134580
F2 176930
F5 612309
F7 613878
F8 300841
F9 300746
FGA 134820
FGB 134830
FGG 134850
GGCX 137167
LMAN1 601567
MCFD2 607788
SERPINE1 173360
SERPINF2 613168
VKORC1 608547
VWF 613160
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Afibrinogenemia, congenital AR 202400
Anti-Plasmin Deficiency, Congenital AR 262850
Factor V And Factor VIII, Combined Deficiency Of, 1 AR 227300
Factor V And Factor VIII, Combined Deficiency Of, 2 AR 613625
Factor V Deficiency AR 227400
Factor VII Deficiency AR 227500
Factor X Deficiency AR 227600
Factor XII Deficiency Disease AR 234000
Factor XIII, A Subunit, Deficiency Of AR 613225
Factor XIII, B Subunit, Deficiency Of AR 613235
Hemophilia A, Congenital AD 134500
Hereditary Factor IX Deficiency Disease XL 306900
Hereditary Factor XI Deficiency Disease AR 612416
Plasminogen Activator Inhibitor Type 1 Deficiency AR 613329
Prothrombin Deficiency, Congenital AR 613679
Vitamin K-Dependent Clotting Factors, Combined Deficiency Of, 1 AR 277450
Vitamin K-Dependent Clotting Factors, Combined Deficiency Of, 2 AR 607473
Von Willebrand Disease, Recessive Form AR 277480
Von Willebrand Disease, Type 1 AD 193400
Von Willebrand Disease, Type 2 AD, AR 613554

Related Tests

Anti-Plasmin Deficiency via SERPINF2 Gene Sequencing with CNV Detection
Combined Factor V and Factor VIII Deficiency via MCFD2 Gene Sequencing with CNV Detection
Combined Factor V and Factor VIII Deficiency via the LMAN1 Gene
Congenital Factor XIII Deficiency via F13B Gene Sequencing with CNV Detection
Congenital Factor XIII deficiency via the F13A1 Gene
Congenital Fibrinogen Deficiency via FGA Gene Sequencing with CNV Detection
Congenital Fibrinogen Deficiency via the FGB Gene
Congenital Fibrinogen Deficiency via the FGG Gene
Factor VII Deficiency via F7 Gene Sequencing with CNV Detection
Factor X Deficiency via the F10 Gene
Hemophilia A via F8 Gene Sequencing with CNV Detection
Hemophilia B via F9 Gene Sequencing with CNV Detection
Neonatal Crisis Sequencing Panel with CNV Detection
von Willebrand Disease Types 1, 2, and 3 via the VWF Gene


Genetic Counselors
  • Diz-Küçükkaya R. 2013. Hematology. 2013: 268-75. PubMed ID: 24319190
  • Human Gene Mutation Database (Bio-base).
  • Othman M. 2013. Seminars in Thrombosis and Hemostasis. 39: 575-8. PubMed ID: 23982907
  • Peyvandi F. et al. 2012. Haemophilia. 18 Suppl 4: 148-53. PubMed ID: 22726099
  • Peyvandi F. et al. 2013. Blood. 122: 3423-31. PubMed ID: 24124085
  • Watson S.P. et al. 2013. Journal of thrombosis and haemostasis : JTH. 11 Suppl 1: 351-63. PubMed ID: 23516995
Order Kits

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~10 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are often covered by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~10 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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