Fanconi Anemia 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: HE0301

The Blueprint Genetics Fanconi Anemia Panel is a 22 gene test for genetic diagnostics of patients with clinical suspicion of Fanconi anemia or Nijmegen breakage syndrome.

Fanconi anemia (FA) is primarily an autosomal recessive genetic disorder although X-linked inheritance is observed in 2% of FA cases caused by FANCB mutations. Eighty to 90 percent of the cases of FA are due to mutations in FANCA, FANCC and FANCG. This panel is included in the Anemia Panel, Bone Marrow Failure Syndrome Panel and Comprehensive Hematology Panel.

About Fanconi Anemia

FA is a rare, inherited blood disorder that leads to bone marrow failure. The genetic defect in FA affects a cluster of proteins responsible for DNA repair. It is clinically defined by pancytopenia in the first decade of life and increased risk of cancer, most often acute myeloid leukemia. Over half of the FA patients have congenital defects such as short stature, abnormalities of the skin, cardiac, kidney and limb malformations especially radius aplasia are frequent. Mild microcephaly usually without intellectual disability is observed in 10%-25% of cases. Endocrine problems are common as well. Affected adults are also at high risk for non-hematologic malignancies. Allogeneic stem cell transplantation is the only treatment allowing long-term outcome. Fanconi anemia occurs in 1 in 160,000 individuals worldwide. It is more common among people of Ashkenazi Jewish descent, the Roma population of Spain, and black South Africans. Syndromes establishing differential diagnostic challenges include Seckel syndrome, Bloom syndrome and more common Nijmegen breakage syndrome (1:100,000 live births).

Availability

Results in 3-4 weeks.

Genes in the Fanconi Anemia Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ATMBreast cancer, Ataxia-TelangiectasiaAD/AR455853
ATRCutaneous telangiectasia and cancer syndrome, Seckel syndromeAD/AR613
BLMBloom syndromeAR5392
BRCA2Fanconi anemia, Medulloblastoma, Glioma susceptibility, Pancreatic cancer, Wilms tumor, Breast-ovarian cancer, familialAD/AR25141791
BRIP1Fanconi anemia, Breast cancerAD/AR8787
CXCR4Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndromeAD414
ERCC4Fanconi anemia, Xeroderma pigmentosumAR1137
FANCAFanconi anemiaAR33474
FANCBFanconi anemiaXL714
FANCCFanconi anemiaAR3434
FANCD2*Fanconi anemiaAR1049
FANCEFanconi anemiaAR39
FANCFFanconia anemiaAR68
FANCGFanconi anemiaAR1173
FANCIFanconi anemiaAR827
FANCLFanconi anemiaAR615
FANCMFanconi anemiaAR113
NBNBreast cancer, Nijmegen breakage syndromeAD/AR5762
PALB2Fanconi anemia, Pancreatic cancer, Breast cancerAD/AR237223
RAD51CFanconi anemia, Breast-ovarian cancer, familialAD/AR4986
SLX4Fanconi anemiaAR831
XRCC2Hereditary breast cancerAD/AR313
  • * 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 Fanconi anemia panel that covers classical genes associated with Bloom syndrome, Fanconi anemia and Nijmegen breakage syndrome. 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.

Find more info in Support
Download PDF

Full service only

Choose an analysis method

$ $ 1400
$ $ 1000
$ $ 1600

Extra services

$ 500
Total $
Order now

ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Fanconi Anemia Panel

ICD-10Disease
D61.0Fanconi anemia

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.