Clinical and molecular collaboration studies: i)comparison of CNV by NGS&MLPA in hereditary breast and ovarian cancer ii)effective covid-19 sampling and storage

Abstract

HBOC syndrome, as the focus of the study in chapter one, represents a significant concern in cancer genetics. HBOC is primarily associated with mutations in the BRCA1 and BRCA2 genes. In this context, the study aims to enhance the detection of CNVs, crucial genetic alterations often observed in malignancies, including HBOC. The research assesses the efficacy of NGS for CNV detection, comparing it against the established Multiplex Ligation-Dependent Probe Amplification (MLPA) method. In this study, 1276 cases were examined using targeted NGS panels. Of these, 691 cases were further validated through MLPA, encompassing 61 calls in 58 NGS-CNV positive and 630 NGS-CNV negative cases. The findings revealed a considerable disparity: 46% of NGS-CNV positive calls were consistent with MLPA results, while 54% displayed discrepancies. Two cases identified as single nucleotide variations (SNVs) by NGS were found to be CNVs by MLPA. Interestingly, 2-3% of the cases showed MLPA-confirmed CNV regions in the BRCA1/2 genes. Notably, while the NGS-CNV algorithm had a high rate of false positives, it did not yield false negatives. The instances where NGS indicated negative but MLPA showed positive was due to SNVs at MLPA probe binding sites. The study concludes that NGS-CNV analysis shows promising diagnostic capabilities in detecting CNVs, specifically for negative CNV cases. However, false positives and the necessity for confirmation through alternative methods highlight the need for an integrated approach in clinical diagnostics. This ensures more accurate and reliable detection of CNVs, which is crucial for understanding and treating HBOC. Chapter Two focuses on PCR tests, which have been widely adopted as an essential diagnostic tool for identifying SARS-CoV-2 infections during the COVID-19 pandemic. However, proper handling and storage of collected samples are essential to confirm the precision and reliability of test results. Understanding the impact of sample storage conditions on PCR assay performance is critical to maintaining the effectiveness of test protocols. Moreover, this thesis investigates the effectiveness of using saliva samples as an alternative to oro-nasopharyngeal swabs for the detection of SARS-CoV-2, the virus responsible for COVID-19, through reverse transcription-polymerase chain reaction (RT-PCR) testing.