Fanconi Anemia via the BRCA2/FANCD1 Gene

Fanconi Anemia (FA) is an inherited anemia associated with bone marrow failure (aplastic anemia), however, the clinical features of FA can expand well beyond hematologic anomalies. FA is also characterized by a range of physical abnormalities, pancytopenia, and predisposition to certain cancers - particularly acute myelogenous leukemia (AML), gynecologic and GI tract cancers, and cancers of the head and neck (Auerbach. 2009. PubMed ID: 19622403). FA patients are up to 800 fold more susceptible to AML than the general population with a median age of onset of 13 years (Rosenberg et al. 2003. PubMed ID: 12393424). Physical abnormalities include radial ray defects (absent thumb or radius), skin pigmentation defects, short stature, microphthalmia, renal and urinary tract defects, genital defects (males in particular), gastrointestinal malformations (atresia), congenital heart disease, hearing and central nervous system defects, and general developmental delay (Tischkowitz and Hodgson. 2003. PubMed ID: 12525534; Dokal. 2000. PubMed ID: 11030042). About one-third of FA patients have no obvious physical abnormalities and are diagnosed only after a family member is diagnosed, or after developing hematologic anomalies such as thromobocytopenia, leukopenia, and anemia (Giampietro et al. 1997. PubMed ID: 8986277).

A hallmark of FA is hypersensitivity of chromosomes to inter cross-strand linkage (ICL) agents such as diepoxybutane (DEB) or mitomycin C (MMC) (Sasaki and Tonomura. 1973. PubMed ID: 4352739). Exposure of primary cell cultures from FA patients to DEB or MMC results in chromosomal aberrations (breaks, radials, rearrangements) due to deficient DNA repair mechanisms that require functional products of the Fanconi anemia genes. For example, the FANCA, -B, -C, -E, -F, -G, -L, and -M proteins are part of a nuclear core complex that regulates monoubiquitination of the FANCD2 and FANCI proteins (ID complex) during S-phase and after exposure to DNA crosslinking agents (Moldovan and D'Andrea. 2009. PubMed ID: 19686080). In unaffected individuals, ubiquitination helps localize the ID complex to sites of DNA damage and facilitate repair, but in FA patients, this mechanism is impaired (Grompe and van de Vrugt. 2007. PubMed ID: 17488615; Smogorzewska et al. 2007. PubMed ID: 17412408).

FA is a genetically heterogeneous disorder. To date, 22 FA or FA-like genes have been discovered. Inheritance is primarily autosomal recessive or X-linked, however a case of heterozygous FA-like syndrome was associated with a dominant-negative variant in the RAD51 (FANCR) gene (Ameziane et al. 2015. PubMed ID: 26681308). Approximately 86% of all cases are attributed to variants in three genes: FANCA (~ 60%), FANCC (~ 16%), and FANCG (~ 10%) (Auerbach. 2009. PubMed ID: 19622403). Since variants in FANCA are the most common cause of FA, it is important to note that large deletions make up over one-third of all reported pathogenic variants in FANCA. In the United States, the carrier frequency for Fanconi anemia is estimated at 1 in 181, and the incidence rate is estimated at 1 in 131,000 (http://www.fanconi.org/; Rosenberg et al. 2011. PubMed ID: 21739583). Nearly 95% of all FA cases are attributed to variants in eight genes, FANCA, -C, -G, -D1 (aka BRCA2), -D2, -E, -F, and –L that are either part of the core complex required for ID complex ubiquitination and facilitation of DNA repair or function directly in ICL recognition and repair (Grompe and van de Vrugt. 2007. PubMed ID: 17488615). FA is phenotypically diverse even among related patients that harbor the same variants; null alleles however are reported to result in more severe phenotypes (Faivre et al. 2000. PubMed ID: 11110674). FA affects males and females roughly equally and affects all ethnic groups.

Heterozygous pathogenic variants in BRCA2/FANCD1 are most commonly associated with an increased risk for developing breast and ovarian cancer (Wooster et al. 1995. PubMed ID: 7524414; Pruthi et al. 2010. PubMed ID: 21123638), whereas biallelic variants in BRCA2/FANCD1 are associated with FA (Howlett et al. 2002. PubMed ID: 12065746). BRCA2/FANCD1 is a tumor suppressor that plays a large role in DNA repair and genome stability. Over 4,800 unique pathogenic variants have been reported for the BRCA2/FANCD1 gene; however, only around 40 unique pathogenic variants have been reported in patients with FA (https://databases.lovd.nl/shared/genes/BRCA2). Variants associated with FA include primarily small deletions or duplications resulting in premature protein termination or splice site variants; pathogenic missense variants in BRCA2/FANCD1 are a rare cause of FA. Gross deletions and duplications in BRCA2/FANCD1 have been reported as risk factors for breast and ovarian cancer, but have not been reported in patients with FA. In contrast with other FA subtypes, pathogenic variants in BRCA2/FANCD1 are associated with a high rate of spontaneous chromosomal aberration and earlier onset of both leukemias and solid tumors (Wagner et al. 2004; Hirsch et al. 2004. PubMed ID: 8524414; Alter et al. 2006. PubMed ID: 16825431).

Pathogenic variants in the BRCA2/FANCD1 gene ccount for <5% of all Fanconi anemia (FA) cases (Auerbach. 2009. PubMed ID: 19622403).

Gross deletions and duplications in the BRCA2/FANCD1 gene have been reported as risk factors for breast and ovarian cancer, but have not yet been reported in patients with FA (The Rockefeller University Fanconi Anemia Mutation Database; Human Gene Mutation Database).

This test provides full coverage of all coding exons of the BRCA2/FANCD1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.