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Home > Bioinformatics and Experimental Analysis of the Genetic and Non-Genetic Basis of Breast Cancer in Pakistani Population

Bioinformatics and Experimental Analysis of the Genetic and Non-Genetic Basis of Breast Cancer in Pakistani Population

Thesis Info

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Author

Raisa Bano

Program

PhD

Institute

Capital University of Science & Technology

City

Islamabad

Province

Islamabad.

Country

Pakistan

Thesis Completing Year

2019

Thesis Completion Status

Completed

Subject

Bio sciences

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/11649/1/Raisa%20Bano_Biosci_2019_CUST_30.04.2019.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676725618721

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Breast cancer is a multifactorial and complex disorder. It is posing serious public health concerns and its incidence rate is on the rise in Pakistan. It is therefore of prime importance to identify genetic and/or non-genetic factors contributing towards the development and progression of breast cancer. The present investi gation is a case-control study including 1000 cases and 1000 age matched con trols of the same ethnic background. Individuals were recruited on the basis of a predefined inclusion and exclusion criteria. All participants were in-person di rectly interviewed after signing an informed consent document. Peripheral blood samples were collected from all the participants along with personal identifiers, demographic characteristics and family history of cancer and other diseases. Vital status/survival status of the patients was determined for up to a maximum of 47 months to record the censored data. We analyzed our sequenced variants and clinico-pathologic features for their possible association with the disease risk by using unconditional logistic regression. Association of the variables was measured with ORs and corresponding 95% confidence intervals. Overall survival of the patients was assessed using Kaplan-Meier curve. Cox proportional hazard model was used to calculate risk ratios and to adjust for potential confounders. A total of thirteen variants were reported in BRCA1 and BRCA2 genes respec tively including three novel variants (Exon3 -37insC, Exon3 -215T<C and Exon14 102-103insTC) in BRCA1 and five novels (exon8 +87insA, exon20 +318T<A, exon19 -351-353delTCT, exon16 -17G<T and exon27 T129A) in BRCA2. Five out of thirteen variants were the in silico identified, HapMap confirmed, pathogenic and previously reported in other populations. Their contribution towards disease risk was tested in our sampled population and it was observed that rs28897686 polymorphism of BRCA1 and rs28897743 of BRCA2 were observed positively asso ciated, while rs28897696 and rs1060915 polymorphisms of BRCA1 and rs4987049 SNP of BRCA2 were found not associated with the disease risk. Five of the eight novel variants, two in BRCA1 (-37insC exon 3 and 102-103insTC exon 14) and three in BRCA2 (+87insA exon 8, -351-353delTCT exon 19 and T129A exon 27) xii were observed only in the breast cancer cases and found completely absent in the controls while the rest of 3/8 of the novel variants (BRCA1 -215T<C exon 3, BRCA2 +318T<A exon 20 and BRCA2 -17G<T exon 16) were found highly significantly associated with breast cancer risk. Pairwise Linkage Disequilibrium analysis showed that the strong LD (D0=0.52) exists in between rs28897696 and -215T<C exon 3 variant of BRCA1 and LD (D0=0.43) in between rs28897743 and -17G<T exon 16 of BRCA2. We also examined the cross-sectional associations of life style, reproductive and socio-demographic risk factors with breast cancer density in Pakistani women. Mean age of cases and controls at recruitment was 50.58±10.68 and 54.78±14.52 years while mean BMI for cases and controls was 26.07±4.04 and 25.05±4.25, respectively. Among the patients 60.70% were married, 46.50% were nulliparous, 16.90% had≥4 children, 39.90% women breast fed their children, 88.90% were nonsmokers and 67.90% were physically active. Post-menopausal women diagnosed with breast cancer accounted for 52.30%. In the current data set, 31.70% patients had at least a blood relative diagnosed with some type of cancer, 22.80% patients were diagnosed with other types of medical complications including high blood pressure, diabetes etc. Significant association between age and breast cancer was observed. Overweight (BMI≥25) and obese (BMI≥30) females have approximately 1.5 times more risk of having breast cancer (Overweight; OR = 1.52, 95% CI: 1.28-1.81 and Obese; OR = 1.41, 95% CI: 1.14-1.74). It was also observed that unmarried women were at more than two fold higher risk. Similarly use of oral contraceptives and smoking were also significantly associated with increasing risk of breast cancer. Individuals who were physically inactive were recorded to be 1.27 times more likely to develop breast cancer. We have found approximately 1.34 fold increase in the disease risk among the postmenopausal patients (OR = 1.34, 95% CI: 1.14-1.58). Breast cancer patients were observed having an overall median survival time of 33 months (95% CI: 28-34). In this present study we attempted to define the genetic and non-genetic basis responsible for breast cancer incidence among Pakistani population. It can be concluded that there is a significant contribution of BRCA1 and BRCA2 genetic alterations in breast cancer pathogenesis. It is hoped that our findings will be of great importance to establish adequate evidence-based awareness and preventative measures against breast cancer in Pakistani women.
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