Dysfunctional DNA repair pathway via defective FANCD2 gene engenders multifarious exomic and transcriptomic effects in Fanconi anemia

Using next-gen sequencing, we show that a clinically-derived FA cell line continued to accumulate genetic variants, especially INDELs, relative to its retrovirally corrected cell line. About 65% of SNPs and 55% of INDELs were found to be commonly present in both the FA dysfunctional and retrovirally corrected cell lines, showing their common origin. Furthermore, the variant analysis comparing biological replicates indicated that new high impact mutations, such as deletion of start codons, introduction of premature stop codons, and missense mutations, have continued to accumulate during a single 30-hour culture. A FANCD2-corrected sample contained 27 new high impact mutations, compared to its biological replicate. These genetic modifications had a dramatic effect on the transcriptome, with statistically significant changes in the expression of 270 genes. These genetic and transcriptomic variants significantly impacted pathways and molecular functions, spanning a diverse spectrum of disease phenotypes/symptoms, consistent with the disease diversity seen in FA patients.