Coagulation Factor Deficiency Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: HE0501

The Blueprint Genetics Coagulation Factor Deficiency Panel is a 16 gene test for genetic diagnostics of patients with clinical suspicion of hemophilia A, hemophilia B, rare bleeding disorder or Von Willebrand disease.

Inheritance pattern in these coagulation factor deficiencies may be autosomal recessive, autosomal dominant or X-linked. This panel is included in the Bleeding Disorder/Coagulopathy Panel and Comprehensive Hematology Panel.

About Coagulation Factor Deficiency

Coagulation Factor Deficiencies refers to a heterogenous group of inherited bleeding disorders. The most common coagulation factor deficiencies are hemophilias (A and B), and von Willebrand disease (VWD), accounting together for 95% of bleeding disorders. The clinical presentation of inherited bleeding disorders can be highly variable and the severity of the clinical manifestations depends on the biological activity of the coagulation factor. The diseases are characterized by abnormal bleeding of variable severity occurring either spontaneously or in association with an invasive procedure. Age of onset in hemophilia is in infancy. In VWD, the symptoms can begin at any age. Hemophilia A and B and are inherited in an X-linked recessive manner through mutations in the F8 and F9 genes, respectively. The diseases primarily affect males, but female carriers of the disease-causing mutations may also manifest generally milder forms of the disease. VWD is inherited in both autosomal dominant and recessive manners and the causative gene is VWF. Rare bleeding disorders (RBDs) include inherited deficiencies of coagulation factors fibrinogen, factor (F)II, FV, combined FV and FVIII, FVII, FX, FXI, FXIII, and congenital deficiency of vitamin K-dependent factors (VKCFDs). RBDs are autosomal recessive conditions and deficiencies in FVII and FXI together account for 64% of cases (PMID: 25712993). The associated genes are FGA, FGB, FGG, F2, F5, F7, F10, F11, F13A1, LMAN1 and VKORC1. The prevalence of hemophilia is estimated at 1:12,000 and the prevalence of symptomatic VWD that requires specific treatment is estimated at between 1:50,000 and 1:8,500.

Availability

Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.

Genes in the Coagulation Factor Deficiency Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
F2Thrombophilia due to thrombin defect, Prothrombin deficiency, congenitalAD/AR1466
F5Factor V deficiency, Thrombophilia due to activated protein C resistanceAD/AR18162
F7Factor VII deficiencyAR23304
F8*Hemophilia AXL2763074
F9Hemophilia B, Warfarin sensitivity, Thrombophilia, due to factor IX defectXL1091260
F10Factor X deficiencyAR15147
F11Factor XI deficiencyAD/AR35250
F12AngioedemaAD/AR553
F13A1Factor XIIIA deficiencyAR20165
FGAAfibrinogenemia, congenital, Dysfibrinogenemia, congenital, Hypodysfibrinogenemia, congenital, Familial visceral amyloidosisAD/AR9140
FGBAfibrinogenemia, congenital, Dysfibrinogenemia, congenital, Hypodysfibrinogenemia, congenitalAD/AR688
FGGAfibrinogenemia, congenital, Hypodysfibrinogenemia, Dysfibrinogenemia, congenital, Hypodysfibrinogenemia, congenitalAD/AR5127
GGCXPseudoxanthoma elasticum-like disorder with multiple coagulation factor deficiency, Vitamin K-dependent clotting factors, combined deficiencyAD/AR/Digenic1338
LMAN1Combined factor V and VIII deficiencyAR537
VKORC1Drug metabolism, VKORC1-related, Vitamin K-dependent clotting factors, combined deficiencyAD/AR533
VWF*Von Willebrand diseaseAD/AR38857
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Blueprint Genetics offers a comprehensive coagulation factor deficiency panel that covers classical genes associated with congenital factor II deficiency, congenital factor V deficiency, congenital factor VII deficiency, congenital factor X deficiency, congenital factor XI deficiency, hemophilia A, hemophilia B, hereditary combined deficiency of vitamin K-dependent clotting factors, rare bleeding disorder, severe hemophilia A, severe hemophilia B, Von Willebrand disease and Von Willebrand disease type 1. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Coagulation Factor Deficiency Panel

ICD-10Disease
D68.0Von Willebrand disease
D66Hemophilia A
D67Hemophilia B

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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