Publications about genetic testing for metabolic disorders
  1. NGS panel - Genetic testing for Fanconi anemia

Fanconi anemia

March 18, 2018

Disease summary

Fanconi Anemia (FA) is a rare inherited chromosome breakage syndrome characterized by physical abnormalities, bone marrow failure, and increased risk for development of various malignancies. FA is the most common genetic cause of aplastic anemia and one of the most common genetic causes of hematologic malignancy. Many different genes, mostly involved in DNA repair, are underlying FA and they account for different phenotypic complementation groups, including FANCA, FANCB, FANCC, FANCD1 (BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (BRIP1), FANCL, FANCM and FANCN (PALB2) genes (Table 1).

FA-associated proteins (namely: FANCA, FANCB, FANCE, FANCF, FANCG, and FANCL) are assembled in a nuclear “FA core” complex, a multi-subunit ubiquitin ligase complex (see Figure 1). Additional FA proteins (FANCD2 and FANCI) are associated with the FA core complex, and after ubiquitination by ubiquitin ligase FANCL they are translocated to nuclear foci that include the “DNA repair” proteins BRCA2, RAD51, NBS1, and others (Figure 1). The latest proteins actively participate in DNA repair and therefore, when they carry a pathogenic variant, the DNA repair function is missing and as a result the DNA is no longer stable and tumors can develop.

 

Autosomal recessive, autosomal dominant (RAD51), X-linked (FANCB)

1/100,000 1; carrier frequency is 1/100 in Ashkenazi Jewish, Spanish Gypsy, and black South African 1, 2

Clinical symptoms:

Fanconi anemia is suspected in individuals with the following clinical features 1, 4, 10, 15:

  • Abnormal skin pigmentation with café au lait spots is present in about 40% of all FA-affected cases, commonly associated with generalized hypopigmentation1
  • Malformations of the skeletal system are commonly present (in ~35% of cases1) in form of absent thumbs, absent or hypoplastic radii followed by weak pulse, congenital hip dislocation and syndactyly (in about 5% of FA-cases)1
  • Short stature, pre-  or postnatal accompanied with low birth weight in majority of affected
  • Microcephaly or CNS-anomalies in 20% of FA-cases1
  • Ocular anomalies (in 20% affected) including cataract, microphthalmia, strabismus, astigmatism, ptosis and others.
  • Gastrointestinal and urinary system anomalies, including renal anomalies, hypospadias and cryptorchidism in man and small ovaries in females.
  • Progressive bone marrow failure manifested as thrombocytopenia, leukopenia, anemia, macrocytosis and/or increased fetal hemoglobin levels.
  • Increased risk of malignancy, including the following:

              o    Adult-onset aplastic anemia.

              o    Myelodysplastic syndrome (MDS).

              o    Acute myelogenous leukemia (AML): the relative risk for AML is ~500 times higher than in   non-affected people 3, 4

              o    Solid tumors (early-onset) that may be the first manifestation of disease, including squamous cell carcinomas of the head and neck (most common form. With the incidence >700 times higher compared to normal population 1, 5), esophagus, and vulva; cervical cancer and liver tumors.

Diagnostic criteria for Fanconi anemia 1, 4, 10, 15:

  • The diagnosis of FA is established in a proband with increased chromosome breakage and radial forms on cytogenetic testing of lymphocytes with diepoxybutane (DEB) and mitomycin C (MMC).
  • Biallelic pathogenic variants in one of the dozen genes known to cause autosomal recessive FA (BRCA2, BRIP1, ERCC4, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, PALB2, RAD51C, SLX4, UBE2T, XRCC2).
  • A heterozygous pathogenic variant in RAD51, known to cause autosomal dominant FA
  • A hemizygous pathogenic variant in FANCB, known to cause X-linked FA.

Treatment options:

  • Allogeneic hematopoietic stem cell transplant is the only curative treatment for patients with Fanconi anemia 1, 20.
  • Alternative treatments are beneficial and include administration of oral androgens (improvement of blood counts in 50% of FA-patients), administration of G-CSF (granulocyte-colony stimulating factor) and others 1, 20.
  • Chromosome breakage syndromes, such as Bloom syndrome or ataxia-telangiectasia
  • Nijmegen breakage syndrome (NBS)
  • Seckel syndrome
  • Neurofibromatosis 1 (NF1)
  • TAR syndrome (thrombocytopenia with absent radii)
  • VACTERL association

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for Fanconi anemia using NGS Panel Genomic:

Step 1: Whole genome sequencing from a single filter card (drop of blood), covering the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Fanconi anemia panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no pathogenic variant is identified in Step1, continue with bioinformatics analysis covering genes that are either implicated or associated with overlapping phenotype or similar pathways.   

  • Individuals with a positive family history of Fanconi anemia.
  • Individuals with most common symptoms of Fanconi anemia (regardless of family history).

Confirmation of a clinical diagnosis through genetic testing of Fanconi anemia can allow for genetic counseling and may direct medical management.


Figure 1:
Schematic presentation of the Fanconi anemia DNA repair pathway: DNA damage activates Fanconi anemia complex which includes the Fanconi anemia-associated proteins FANCA, FANCB, FANCE, FANCF, FANCG and subsequently FANCL. FANCL is a ubiquitin ligase and it ubiquitinate FANCD2 and FANCI. This FANCD2/FANCI ubiquitinated/activated complex further activates “DNA repair proteins” associated with Fanconi anemia: BRCA2, RAD51, BRCA1, NBS1 and PCNA, subsequently leading to DNA repair.


Overview of the genes in CENTOGENE´s Fanconi anemia panel

Gene Complementation group OMIM Chromosomal locus Frequency of mutations
FANCA FA-A 607139 16q24.3 60%-70% 1, 9
FANCB FA-B 300515 Xp22.2 2%1, 9
FANCC FA-C 613899 9q22.3 14%1, 9
BRCA2
FANCD1
FA-D1 600185 13q13.1 3%1, 9
FANCD2 FA-D2 613984 3q25.3 3%1, 9
FANCE FA-E 613976 6p21.31 3%1, 9
FANCF FA-F 613897 11p15 2%1, 9
FANCG FA-G 602956 9p13 10%1, 9
FANCI FA-I 611360 15q26.1 1%1, 9
BRIP1
FANCJ
FA-J 605882 17q23.2 2%1, 9
FANCL FA-L 608111 2p16.1 13 variants reported 10
FANCM FA-M 609644 14q21.3 1 family reported 11
PALB2
FANCN
FA-N 610355 16p12.1 14 variants reported 12
RAD51C
FANCO
FA-N 602774 17q22 1 family 13
SLX4
FANCP
FA-P 613278 16p13.3 Rare 14
ERCC4
FANCQ
FA-Q 133520 16p13.12 Rare 1
XRCC2
FANCR
FA-U 179617 15q15.1 Rare 1
UBE2T
FANCT
FA-T 510538 1q32.1 Rare 1

Allogeneic hematopoietic stem cell transplant is the only curative treatment for patients with Fanconi anemia20. However, alternative treatments are beneficial and include administration of oral androgens (improvement of blood counts in 50% of FA-patients), administration of G-CSF (granulocyte-colony stimulating factor), and others20.

CENTOGENE offers the Fanconi anemia panel, including full gene sequencing (genes: BRCA2, BRIP1, ERCC4, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, PALB2, RAD51C, SLX4, UBE2T, XRCC2) and deletion/duplication analysis of selected genes (FANCD2, BRIP1, FANCB, PALB2, BRCA2, FANCA, RAD51C). In addition, any of the genes in the Fanconi anemia panel can also be ordered individually, for full gene sequencing and deletion/duplication analysis.