Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes

Elizabeth K. Flynn, Aparna Kamat, Francis P. Lach, Frank X. Donovan, Danielle C. Kimble, Narisu Narisu, Erica Sanborn, Farid Boulad, Stella M. Davies, Alfred P. Gillio, Richard E. Harris, Margaret L. Macmillan, John E. Wagner, Agata Smogorzewska, Arleen D. Auerbach, Elaine A. Ostrander, Settara C. Chandrasekharappa

Research output: Contribution to journalArticle

20 Scopus citations

Abstract

Fanconi anemia (FA) is a rare recessive disease resulting from mutations in one of at least 16 different genes. Mutation types and phenotypic manifestations of FA are highly heterogeneous and influence the clinical management of the disease. We analyzed 202 FA families for large deletions, using high-resolution comparative genome hybridization arrays, single-nucleotide polymorphism arrays, and DNA sequencing. We found pathogenic deletions in 88 FANCA, seven FANCC, two FANCD2, and one FANCB families. We find 35% of FA families carry large deletions, accounting for 18% of all FA pathogenic variants. Cloning and sequencing across the deletion breakpoints revealed that 52 FANCA deletion ends, and one FANCC deletion end extended beyond the gene boundaries, potentially affecting neighboring genes with phenotypic consequences. Seventy-five percent of the FANCA deletions are Alu-Alu mediated, predominantly by AluY elements, and appear to be caused by nonallelic homologous recombination. Individual Alu hotspots were identified. Defining the haplotypes of four FANCA deletions shared by multiple families revealed that three share a common ancestry. Knowing the exact molecular changes that lead to the disease may be critical for a better understanding of the FA phenotype, and to gain insight into the mechanisms driving these pathogenic deletion variants. We report results from screening 202 Fanconi anemia (FA) families for large deletions. High-resolution analysis of the deletion boundaries identified by aCGH, accompanied by subsequent cloning and sequencing of the breakpoints, revealed that 52 FANCA deletionends, and one FANCC deletion end extended beyond thegene boundaries, potentially affecting neighboring geneswith phenotypic consequences. We also gainedinsight into the location and potential mechanisms driving the intrachromosomal breakage events, in addition to identifying conserved deletions and their likely origin.

Original languageEnglish (US)
Pages (from-to)1342-1353
Number of pages12
JournalHuman mutation
Volume35
Issue number11
DOIs
StatePublished - Nov 1 2014

Keywords

  • ArrayCGH
  • FANCA
  • FANCB
  • FANCC
  • FANCD2
  • Fanconi anemia

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  • Cite this

    Flynn, E. K., Kamat, A., Lach, F. P., Donovan, F. X., Kimble, D. C., Narisu, N., Sanborn, E., Boulad, F., Davies, S. M., Gillio, A. P., Harris, R. E., Macmillan, M. L., Wagner, J. E., Smogorzewska, A., Auerbach, A. D., Ostrander, E. A., & Chandrasekharappa, S. C. (2014). Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes. Human mutation, 35(11), 1342-1353. https://doi.org/10.1002/humu.22680