Targeted Resequencing of 30 Genes Improves the Detection of Deleterious Mutations in South Indian Women with Breast and/or Ovarian Cancers

Background: We earlier used PCR-dHPLC for mutation analysis of BRCA1 and BRCA2. In this article wereport application of targeted resequencing of 30 genes involved in hereditary cancers. Materials and
Methods:A total of 91 patient samples were analysed using a panel of 30 genes in the Illumina HiScan SQ system. CLCBiowas used for mapping reads to the reference sequences as well as for quality-based variant detection. All thedeleterious mutations were then reconfirmed using Sanger sequencing. Kaplan Meier analysis was conductedto assess the effect of deleterious mutations on disease free and overall survival.
Results: Seventy four of the91 samples had been run earlier using the PCR-dHPLC and no deleterious mutations had been detected while17 samples were tested for the first time. A total of 24 deleterious mutations were detected, 11 in BRCA1, 4 inBRCA2, 5 in p53, one each in RAD50, RAD52, ATM and TP53BP1. Some 19 deleterious mutations were seen inpatients who had been tested earlier with PCR-dHPLC [19/74] and 5/17 in the samples tested for the first time,Together with our earlier detected 21 deleterious mutations in BRCA1 and BRCA2, we now had 45 mutationsin 44 patients. BRCA1c.68_69delAG;p.Glu23ValfsX16 mutation was the most common, seen in 10/44 patients.Kaplan Meier survival analysis did not show any difference in disease free and overall survival in the patientswith and without deleterious mutations.
Conclusions: The NGS platform is more sensitive and cost effective indetecting mutations in genes involved in hereditary breast and/or ovarian cancers.