Browsing by Author "Mocan, Gamze"
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Publication BRCA variations risk assessment in breast cancers using different artificial intelligence models(Mdpi, 2021-11-08) Şentürk, Niyazi; Tuncel, Gülten; Doğan, Berkcan; Aliyeva, Lamiya; Dündar, Mehmet Sait; Özemri Sağ, Şebnem; Mocan, Gamze; Temel, Şehime Gülsün; Dündar, Munis; Ergoren, Mahmut Çerkez; DOĞAN, BERKCAN; ALIYEVA, LAMIYA; ÖZEMRİ SAĞ, ŞEBNEM; TEMEL, ŞEHİME GÜLSÜN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Genetik Anabilim Dalı.; Bursa Uludağ Üniversitesi/Sağlık Bilimleri Enstitüsü/Translasyonel Tıp Anabilim Dalı.; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Histoloji ve Embriyoloji Anabilim Dalı.; 0000-0001-8061-8131; CCG-4609-2022 ; AAH-8355-2021 ; AAD-5249-2020; AAG-8385-2021Artificial intelligence provides modelling on machines by simulating the human brain using learning and decision-making abilities. Early diagnosis is highly effective in reducing mortality in cancer. This study aimed to combine cancer-associated risk factors including genetic variations and design an artificial intelligence system for risk assessment. Data from a total of 268 breast cancer patients have been analysed for 16 different risk factors including genetic variant classifications. In total, 61 BRCA1, 128 BRCA2 and 11 both BRCA1 and BRCA2 genes associated breast cancer patients' data were used to train the system using Mamdani's Fuzzy Inference Method and Feed-Forward Neural Network Method as the model softwares on MATLAB. Sixteen different tests were performed on twelve different subjects who had not been introduced to the system before. The rates for neural network were 99.9% for training success, 99.6% for validation success and 99.7% for test success. Despite neural network's overall success was slightly higher than fuzzy logic accuracy, the results from developed systems were similar (99.9% and 95.5%, respectively). The developed models make predictions from a wider perspective using more risk factors including genetic variation data compared with similar studies in the literature. Overall, this artificial intelligence models present promising results for BRCA variations' risk assessment in breast cancers as well as a unique tool for personalized medicine software.Item Functional coding/non-coding variants in EGFR, ROS1 and ALK genes and their role in liquid biopsy as a personalized therapy(Elsevier Science, 2020-09-18) Ergören, Mahmut Çerkez; Çobanoğulları, Havva; Mocan, Gamze; Temel, Şehime Gülsün; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Histoloji ve Embriyoloji Anabilim Dalı.; 0000-0002-9802-0880; AAG-8385-2021; 6507885442Personalized medicine holds promise to tailor the treatment options for patients' unique genetic make-up, behavioral and environmental background. Liquid biopsy is non-invasive technique and precise diagnosis and treatment approach. Significantly, NGS technologies have revolutionized the genomic medicine by novel identifying SNPs, indel mutations in both coding and non-coding regions and also a promising technology to accelerate the early detection and finding new biomarkers for diagnosis and treatment. The number of the bioinformatics tools have been rapidly increasing with the aim of learning more about the detected mutations either they have a pathogenic role or not. EGFR, ROS1 and ALK genes are members of the RTK family. Until now, mutations within these genes have been associated with many cancers and involved in resistance formation to TKIs. This review article summarized the findings about the mostly investigated variations in EGFR, ROS1 and ALK genes and their potential role in liquid biopsy approach.Publication Identification of a novel de novo COMP gene variant as a likely cause of Pseudoachondroplasia(Lippincott Williams & Wilkins, 2021-08-01) Tuncel, Gülten; Akcan, Neşe; Gül, Şeref; Sağ, Şebnem Ö.; Bundak, Ruveyde; Mocan, Gamze; Temel, Şehime G.; Ergoren, Mahmut C.; ÖZEMRİ SAĞ, ŞEBNEM; TEMEL, ŞEHİME GÜLSÜN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Genetik Anabilim Dalı.; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Histoloji Ve Embriyoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Sağlık Bilimleri Enstitüsü/Translasyonel Tıp Bölümü.; 0000-0002-9802-0880; AAH-8355-2021; AAG-8385-2021Next-generation sequencing technology and advanced sequence analysis techniques are markedly speeding up the identification of gene variants causing rare genetic diseases. Pseudoachondroplasia (PSACH, MIM 177170) is a rare disease inherited in an autosomal dominant manner. It is known that variations in the cartilage oligomeric matrix protein (COMP) gene are associated with the disease. Here, we report a 39-month-old boy with short stature. He gave visible growth and development delayed phenotype after 12 months. Further genetic resequencing analysis was carried out to identified the disease-causing variant. Furthermore, computational approaches were used to characterize the effect of the variant. In this study, we identify and report a novel variation in the COMP gene, c.1420_1422del (p.Asn47del), causing a spontaneous form of PSACH in our patient. Our in silico model indicated that any mutational changes in this region are very susceptible to PASCH phenotype. Overall, this study is the first PSACH case in the Turkish Cypriot population. Moreover, this finding contributes to the concept that the genotype-phenotype correlation in COMP is still unknown and also improves our understanding of this complex disorder.Publication Psychomotor delay in a child with fgfr3 g380r pathogenic mutation causing achondroplasia(Thieme Medical Publication, 2021-05-21) Ergoren, Mahmut C.; Manara, Elena; Paolacci, Stefano; Tulay, Pinar; Bertelli, Matteo; Mocan, Gamze; Eren, Erdal; EREN, ERDAL; Sag, Sebnem O.; ÖZEMRİ SAĞ, ŞEBNEM; Temel, Sehime Gulsun; TEMEL, ŞEHİME GÜLSÜN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Pediatrik Endokrinoloji Anabilim Dalı.; 0000-0001-9593-9325; 0000-0002-1684-1053; 0000-0002-1176-3359; 0000-0002-9552-221X; 0000-0002-9802-0880; AAZ-6885-2021; AAY-1413-2020; GQP-2509-2022; JPK-3909-2023; D-8491-2018Achondroplasia (ACH) is a hereditary disorder of dwarfism that is caused by the aberrant proliferation and differentiation of chondrocyte growth plates. The common findings of macrocephaly and facial anomalies accompany dwarfism in these patients. Fibroblast growth factor receptor 3 ( FGFR3 ) gene mutations are common causes of achondroplasia. The current study presents a case of 2-year-old male presenting with phenotypic characteristics of ACH. The interesting finding of the case is the presence of psychomotor delay that is not very common in these patients. Clinical exome sequencing analyzing 4.813 disease causing genes revealed a de novo c.1138G>A mutation within the FGFR3 gene. In conclusion, the mutation confirms the clinical diagnosis of ACH, and it seems to be causing the psychomotor delay in this patient.Publication The story of a ship journey, malaria, and the HBB gene ivs-ii-745 mutation: Circassian immigration to cyprus(Thieme Medical Publication, 2021-03-16) Ergören, Mahmut C.; Temel, Şehime G.; Mocan, Gamze; Dündar, Munis; Temel, Şehime G.; TEMEL, ŞEHİME GÜLSÜN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Genetik Mühendisliği Anabilim Dalı.; 0000-0001-9593-9325; 0000-0002-9802-0880; 0000-0003-0969-4611; B-3150-2011; D-8491-2018; GQP-2509-2022; AAZ-6885-2021Background During 19th century, the Circassians were secluded from their lands and forced to migrate to Ottoman Empire properties. Approximately 2,346 Circassians were exiled from Istanbul to Cyprus Island. During the deportation journey, many of Circassian were passed away in consequence of malaria and unknown reasons. Overall, 1,351 survivor Circassians managed to reach the island, however, many of them had faced with endemic malaria again in Cyprus. An autosomal recessive hematological disorder thalassemia was the second endemic health condition after malaria, whereas thalassemia carriers show resistance to malaria infections.Materials and Methods A large Cypriot family with 57 members whose grandparents were supposed to be in that ship journey has been investigated in this study. Polymerase chain reaction (PCR)-amplification refractory mutation system (ARMS) analysis technique was used for genotyping the HHB gene.Results The human beta -globin ( HBB ) gene c.316-106C>G (IVS-II-745) (II-745) heterozygous variation have been detected.Conclusion Overall, this study is a very good example for a typical natural selection. In this case, one single gene point mutation did not limit survival in the society; natively, it increased their survival changes to form new colonization and the inheritance of the mutation to the next generations.