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Nicchia E, Greco C, De Rocco D, et al. Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology. Mol Genet Genomic Med. 2015;3(6):500-12doi: 10.1002/mgg3.160.
Nicchia, E., Greco, C., De Rocco, D., Pecile, V., D'Eustacchio, A., Cappelli, E., Corti, P., Marra, N., Ramenghi, U., Pillon, M., Farruggia, P., Dufour, C., Pallavicini, A., Torelli, L., & Savoia, A. (2015). Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology. Molecular genetics & genomic medicine, 3(6), 500-12. https://doi.org/10.1002/mgg3.160
Nicchia, Elena, et al. "Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology." Molecular genetics & genomic medicine vol. 3,6 (2015): 500-12. doi: https://doi.org/10.1002/mgg3.160
Nicchia E, Greco C, De Rocco D, Pecile V, D'Eustacchio A, Cappelli E, Corti P, Marra N, Ramenghi U, Pillon M, Farruggia P, Dufour C, Pallavicini A, Torelli L, Savoia A. Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology. Mol Genet Genomic Med. 2015 Jul 02;3(6):500-12. doi: 10.1002/mgg3.160. eCollection 2015 Nov. PMID: 26740942; PMCID: PMC4694132.
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Mol Genet Genomic Med. 2015 Jul 02;3(6):500-12. doi: 10.1002/mgg3.160. eCollection 2015 Nov.

Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology.

Molecular genetics & genomic medicine

Elena Nicchia, Chiara Greco, Daniela De Rocco, Vanna Pecile, Angela D'Eustacchio, Enrico Cappelli, Paola Corti, Nicoletta Marra, Ugo Ramenghi, Marta Pillon, Piero Farruggia, Carlo Dufour, Alberto Pallavicini, Lucio Torelli, Anna Savoia

Affiliations

  1. Department of Medical Sciences University of Trieste Trieste Italy.
  2. Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy.
  3. Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy.
  4. Pediatrics Unit San Gerardo Hospital Monza Italy.
  5. Pediatric Hematology Unit Santobono Pausilipon Hospital Naples Italy.
  6. Department of Pediatric and Public Health Sciences University of Torino Torino Italy.
  7. Pediatric Onco-Haematology Clinic University of Padua Padua Italy.
  8. Pediatric Onco-Hematology ARNAS Civico Hospital Palermo Italy.
  9. Department of Life Sciences University of Trieste Trieste Italy.
  10. Department of Mathematics and Geosciences University of Trieste Trieste Italy.
  11. Department of Medical SciencesUniversity of TriesteTriesteItaly; Institute for Maternal and Child Health - IRCCS Burlo GarofoloTriesteItaly.

PMID: 26740942 PMCID: PMC4694132 DOI: 10.1002/mgg3.160

Abstract

Fanconi anemia (FA) is a rare bone marrow failure disorder characterized by clinical and genetic heterogeneity with at least 17 genes involved, which make molecular diagnosis complex and time-consuming. Since next-generation sequencing technologies could greatly improve the genetic testing in FA, we sequenced DNA samples with known and unknown mutant alleles using the Ion PGM (™) system (IPGM). The molecular target of 74.2 kb in size covered 96% of the FA-coding exons and their flanking regions. Quality control testing revealed high coverage. Comparing the IPGM and Sanger sequencing output of FANCA,FANCC, and FANCG we found no false-positive and a few false-negative variants, which led to high sensitivity (95.58%) and specificity (100%) at least for these two most frequently mutated genes. The analysis also identified novel mutant alleles, including those in rare complementation groups FANCF and FANCL. Moreover, quantitative evaluation allowed us to characterize large intragenic deletions of FANCA and FANCD2, suggesting that IPGM is suitable for identification of not only point mutations but also copy number variations.

Keywords: Fanconi anemia; copy number variations; diagnosis; ion PGM system; next‐generation sequencing; point mutations

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