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 PGMTM 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.
