Purpose: Fanconi anemia is a genetically heterogeneous chromosomal breakage disorder exhibiting a high degree of clinical variability. Clinical diagnoses are confirmed by testing patient cells for increased sensitivity to crosslinking agents. Fanconi anemia complementation group assignment, essential for efficient molecular diagnosis of the disease, had not been validated for clinical application before this study. The purpose of this study was (1) confirmation of the accuracy of Fanconi anemia complementation group assignment to Group A (FANCA) and (2) development of a rapid mutation detection strategy that ensures the efficient capture of all FANCA mutations. Methods: Using fibroblasts from 29 patients, diagnosis of Fanconi anemia and assignment to complementation Group A was made through breakage analysis studies. FANCA coding and flanking sequences were analyzed using denaturing high pressure liquid chromatography, sequencing, and multiplex ligation-dependent probe amplification. Patients in which two mutations were not identified were analyzed by cDNA sequencing. Patients with no mutations were sequenced for mutations in FANCC, G, E, and F. Results: Of the 56 putative mutant alleles studied, 89% had an identifiable FANCA pathogenic mutation. Eight unique novel mutations were identified. Conclusion: Complementation assignment to Group A was validated in a clinical laboratory setting using our FANCA rapid molecular testing strategy. Genet anconi anemia (FA; MIM no. 227650), the most common inherited bone marrow disorder, has an overall prevalence of 1-5 per million and an estimated carrier frequency of 1 in 200 to 1 in 300 in most populations. 1,2 Demonstrating either an autosomal or X-linked recessive mode of inheritance, FA is characterized by childhood progressive bone marrow failure and predisposition to acute myelogenous leukemia; older patients are at increased risk for squamous cell carcinomas of the head, neck, and genitourinary tract. [3][4][5][6][7] Congenital abnormalities are present in approximately 70% of FA patients and may include radial ray defects; café au lait spots or hypopigmentation; short stature; microphthalmia; malformations of kidneys, gastrointestinal tract, and heart; mental retardation; and hearing defects. 8 Because of the high degree of phenotypic variability exhibited by FA patients, diagnosis may be difficult on the basis of clinical manifestations alone. Because FA patient-derived lymphocytes and fibroblasts exhibit hypersensitivity to DNA crosslinking agents such as diepoxybutane (DEB) 9 and mitomycin C (MMC), 10 resulting in a high rate of chromosomal breakage and radial formation, analysis on the basis of this hypersensitivity has been routinely used to confirm clinical diagnosis.Molecular diagnosis of FA has been challenging because of the genetic heterogeneity associated with the disease; FA is multigenic, with 13 complementation groups and associated genes having been characterized (A, B, C, D1, D2, E, F, G, I, J, L, M, N). [11][12][13][14][15][16][17][18][19][20][21][...