Assessment of National External Quality Assurance Programme of Pakistan as a tool for improving quality of lab results among participating laboratories.

OBJECTIVE: To assess the impact of the National External Quality Assessment Programme of Pakistan NEQAPP in improving the quality of laboratory results among the participating laboratories. METHODS: The cross-sectional observational study was conducted from July to December 2020 at the Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan, in association with the National Quality Assurance Programme of Pakistan. A survey questionnaire was developed and sent to the participating laboratories via email. Frequencies of their responses were calculated and data was analysed using SPSS 21. RESULTS: Of the 150 laboratories approached, 145(96.6%) responded. Among them, 140 (96.6%) laboratories were satisfied by the information provided on the programme's portal, 123(84.8%s) were pleased with the responsiveness of the programme manager, 140(96.6%) reported quality of services had improved after participation in the programme, 129(89%) indicated that the clinician's confidence had enhanced, and 122(84%) said the participation in the programme had improved the credibility of their respective of laboratories. CONCLUSIONS: The National External Quality Assessment Programme of Pakistan was found to have significantly contributed in improving the quality of laboratory results among the participating laboratories.

Targeted Next-generation Sequencing for Reliable Detection of Genetic Status in Breast Cancer.

OBJECTIVE: To test the germline oncogenic mutations in BRCA1 and BRCA2 genes, associated with triple-negative breast cancer (TNBC) patients under study, by targeted sequencing of their DNA with next-generation sequencing (NGS) platform. STUDY DESIGN: Cross-sectional observational study. PLACE AND DURATION OF STUDY: Histopathology Department, Armed Forces Institute of Pathology (AFIP) Rawalpindi, Pakistan from May to June 2020. METHODOLOGY: Peripheral blood of 14 women (aged ≤60) with triple negative breast carcinoma (TNBC) was taken with the consent of performing germline genetic testing. Targeted NGS was performed for all coding regions and splicing sites of BRCA1 and BRCA2 genes, using AmpliSeq for Illumina BRCA Panel and Illumina MiSeq sequencer (placed at AFIP). Analysis and interpretation of the sequencing results have been done by using Illumina bioinformatics tools and external databases. RESULTS: Two hundred and fifty-four variants were detected in BRCA1 and BRCA2 genes, having variant quality score of 100 in all cases under study. As a result, two pathogenic variants and three variants of uncertain significance were interpreted in this germline pipeline. Cases with pathogenic variants had early onset breast cancer with age less than 35. CONCLUSION: Germline variants in BRCA were detected in the known cases of TNBC, which will not only identify the most prevalent mutations in this region; but will also make them a candidate to receive targeted therapies, which was previously not possible without genetic testing. Moreover, this study further validates the importance of early BRCA genetic screening in young patients, who have positive family history of breast carcinoma. Key Words: Breast cancer, Triple negative, Next-generation sequencing, BRCA1, BRCA2.