title: Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology.
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.
authors.affiliation: Department of Medical Sciences University of Trieste Trieste Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Nicchia
authors.affiliation: Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Greco
authors.affiliation: Department of Medical Sciences University of Trieste Trieste Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: De Rocco
authors.affiliation: Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy.
authors.forename: Vanna
authors.initials: V
authors.lastname: Pecile
authors.affiliation: Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy.
authors.forename: Angela
authors.initials: A
authors.lastname: D'Eustacchio
authors.affiliation: Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Cappelli
authors.affiliation: Pediatrics Unit San Gerardo Hospital Monza Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Corti
authors.affiliation: Pediatric Hematology Unit Santobono Pausilipon Hospital Naples Italy.
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Marra
authors.affiliation: Department of Pediatric and Public Health Sciences University of Torino Torino Italy.
authors.forename: Ugo
authors.initials: U
authors.lastname: Ramenghi
authors.affiliation: Pediatric Onco-Haematology Clinic University of Padua Padua Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Pillon
authors.affiliation: Pediatric Onco-Hematology ARNAS Civico Hospital Palermo Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Farruggia
authors.affiliation: Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Dufour
authors.affiliation: Department of Life Sciences University of Trieste Trieste Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pallavicini
authors.affiliation: Department of Mathematics and Geosciences University of Trieste Trieste Italy.
authors.forename: Lucio
authors.initials: L
authors.lastname: Torelli
authors.affiliation: Department of Medical SciencesUniversity of TriesteTriesteItaly; Institute for Maternal and Child Health - IRCCS Burlo GarofoloTriesteItaly.
authors.forename: Anna
authors.initials: A
authors.lastname: Savoia
keywords: Fanconi anemia; copy number variations; diagnosis; ion PGM system; next‐generation sequencing; point mutations