Comparison of the Diagnostic Accuracy of Next Generation Sequencing and Microarray Resequencing Methods for Detection of BRCA1 and BRCA2 Gene Mutations

Download

10.12996gmj.2018.32.pdf

Date

2018-4-1

Author

Bahsi, Taha
Ergun, Sezen Güntekin
Ergun, Mehmet Ali
Perçin, E. Ferda

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

241
views

168
downloads

Objective: Breast cancer constitutes 29 % of estimated new cases of cancer in women, and it is also one of the major cause of death in all cancer types. In this study, DNA samples of familial breast cancer patients with BRCA1 and BRCA2 mutations which had been analyzed using conventional DNA sequencing method, were also analyzed with new methods including microarray and next generation sequencing (NGS) in order to compare their results Methods: Seven patients with BRCA1 mutation, one patient with BRCA2 mutation, and two controls were included. All samples for the microarray method were studied on the GeneChip 3000 Scanner (Affymetrix) system and then analyzed on the Affymetrix GeneChip Resequencing Analysis Software (GSEQ v4.0) system. Four patients from the patient group were selected for next generation sequencing and were analyzed on GS Junior 454 (Roche, Prague, Czech Republic) system. The raw data had been analysed by SeqPilot SeqNext module (v4.0, JSI medical systems, Kippenheim, Germany). Results: Microarray resequencing analysis did not detect the mutations defined by conventional sequencing in patients, but mutations were detected in all of the 4 patients in the next generation sequencing. Conclusion: Our study detected the NGS to be reliable as conventional DNA sequencing for studying BRCA1/BRCA2 gene mutations. However, we suggest to confirm the NGS results with a conventional method because of homopolymer sequences which may cause false positive results.

Subject Keywords

BRCA1, BRCA2, Breast cancer, Microarray, Next generation sequencing

URI

https://hdl.handle.net/11511/52013

Journal

Gazi Medical Journal

DOI

https://doi.org/10.12996/gmj.2018.32

Collections

Graduate School of Informatics, Article

Suggestions

OpenMETU
Core

Application of image enhancement algorithms to improve the visibility and classification of microcalcifications in mammograms Akbay, Cansu; Gençer, Nevzat Güneri; Gençer, Gülay; Department of Biomedical Engineering (2015) Breast cancer is the second leading cause of cancer deaths for women. Mammography is the most effective technology presently available for breast cancer screening, despite the fact that there are still some limitations of the imaging technique, such as insufficient resolution, low local contrast and noise combined with the subtle nature of the usual radiographic findings. One of the most important radiographic findings associated to the existence of breast cancer is the clustered microcalcifications. Especi...
Preparation and characterization of poly(d,l-lactide-co-glycolide) microspheres for controlled release of anticancer drugs Eyövge, Gökçen; Gündüz, Ufuk; Department of Biotechnology (2005) Breast cancer is the most frequent type of cancer seen in woman. Chemotherapy is one of the most important treatments for breast cancer. However, systemic toxicity, drug resistance and unstable kinetics of the drug in the blood are serious problems of chemotherapy. The use of biodegradable polymers for controlled release of anticancer drugs has gained popularity in recent years. Controlled release of anticancer drugs from polymeric carriers has some advantages such as improvement in the efficiency of treatm...
Analyses and modeling of ovarian cancer microarray data Karakelle, Barış S; Purutçuoğlu Gazi, Vilda; Department of Biomedical Engineering (2019) Ovarian cancer is one of the common cancer types among other oncological diseases. The major causes of this cancer can be listed as age, obesity, hormone therapy, material inheritance and contraceptive pills. Due to its generality and importance, many researches have been conducted from distinct labs about this illness and its plausible causes have been intensively investigated either inmicroarray studies, where just part of the related genes are detected, or in thepairwise correlation analyses between the ...
Design for positive breast self-examination experience: an investigation into mobile health apps Karadeniz Küçük, Aylin; Şener Pedgley, Bahar; Department of Industrial Design (2021-5) Breast cancer is one of the most common cancer types among women, responsible for approximately 627,000 deaths globally in 2018. There are various screening methods to detect cancer early, and experts suggest that women should perform breast self-examination (BSE) once a month. Unfortunately, most women fail to do so even if they are aware of the risks and the importance of screening methods. Moreover, developments in technology provide people to manage their own health in their own environments with variou...
Modeling of Breast and Gynecological Cancers Data and Investigating New Biological Findings Ağyüz, Umut; Purutçuoğlu Gazi, Vilda (null; 2018-06-27) The breast and gynecological cancers are two most common fatal cancers’ types in women in the world [1]. In oncological literature, these two cancers types are typically worked together since they are the risk factors of each other if the patient has one of these diseases [2]. In general, the cancers, like the heart diseases, are the systems’ ilnesses in the sense that any malfunctions in the associated transaction pathways cause problems in the activation flow, resulting in tumors. Therefore, the mathemati...

Citation Formats

T. Bahsi, S. G. Ergun, M. A. Ergun, and E. F. Perçin, “Comparison of the Diagnostic Accuracy of Next Generation Sequencing and Microarray Resequencing Methods for Detection of BRCA1 and BRCA2 Gene Mutations,” Gazi Medical Journal, 2018, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/52013.