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

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)500-12
Number of pages13
JournalMolecular genetics & genomic medicine
Volume3
Issue number6
DOIs
Publication statusPublished - Nov 2015

Keywords

  • Journal Article

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