Development of bioinformatics analysis algorithms for somatic and germ-line genome sequencing and transcriptome profiling in cancer

Yeni nesil dizileme yöntemi (YND), hassas ve güvenilir bir çalışma yöntemi olması sebebiyle rutin kullanımda yerini almış olup kanserden nadir hastalıklara kadar bütün genetik temelli hastalıklarda değerini ortaya koymaktadır. Ancak hem elde edilen verinin büyüklüğü hem de maliyetleri düşürmek amacıyla yapılan çalışmalar özellikle kansere yönelik somatik çalışmalarda belirli gen bölgeleri ile sınırlıdır. Bu durum kanser gibi karmaşık hastalıkların patogenezinin aydınlatılmasını ve/veya yeni biyobelirteçlerin tespit edilmesini güçleştirmektedir. Tüm genom dizileme gibi kapsamlı bir çalışmadan dahi elde edilen veriler mevcut literatür bilgisinin yetersiz olmasından dolayı yeteri kadar iyi analiz edilememekte ve transkriptom dizileme gibi fonksiyonel testler ile destekleyici uygulamalara ihtiyac duyulmaktadır. Bu tez çalışmasında, Çukurova Üniversitesi Adana Genetik Hastalıklar Tanı ve Tedavi Merkezi (ÇÜ AGENTEM) laboratuvar alt yapısı ile seçilen nadir kanser hastasına ait periferik kan örneğinden germ-line ve FFPE doku ile likit biyopsi materyallerinden somatik tüm genom dizileme ve transkriptom dizileme yapılarak bu verilerin analizlerinin gerçekleştirilmesne yönelik biyoinformatik analiz algoritması geliştirilmiştir.: Next Generation Sequencing (NGS) technologies have constituted a turning point toward clinical routine genetic testing of both cancer and rare disease to deliver reliable and high sensitivity results. However, due to the challenges in management of extensive ease of analyse and cost most of NGS testing, somatic sequencing for cancers mostly limited to specific gene(s) or gene regions. Even though, this targeted approach is useful for routine testing, discovering new biomarkers to understand pathogenesis of cancer. The analysis of the entire genomic DNA sequence called as WGS provides the most comprehensive characterization; WGS still cannot be interpreted in clinical level of precision oncology without the transcriptome profiling yet due to the lack of literature and knowledge

Primary chondrosarcoma of the chest wall: a case report

Göğüs duvarında kondrosarkom tanısı alan bir olgu klinikopatolojik bulgularla sunulmaktadır. 48 yaşındaki kadın hasta göğüs ön duvarında ağrılı kitle şikayetiyle kliniğe başvurdu ve bu alanda 17x14x11 cm boyutlarında kitle saptandı. Kitle total olarak eksize edildi. Toraks duvarında oluşan defekt mersilen mesh ve metil metakrilat sandviç greft ile rekonstrukte edildi. Histolojik inceleme sonucu derece I kondrosarkom tanısı kondu. Göğüs duvarının primer malign tümörleri nadirdir, kondrosarkom göğüs duvarının en sık görülen primer malign tümörüdür.Tedavisinde geniş cerrahi eksizyon uygulanmaktadır.A case with chondrosarcoma of the chest wall is presented with clinicopathological findings. A 48-year-old woman, presenting with a painful anterior chest wall mass measuring 17x14x11 cm in size was admitted to the hospital. Complete surgical resection of the tumor was performed. The resulting defect of the chest wall was restored with mersilene mesh and methyl methacrylate sandwich graft. Histological examination showed grade I chondrosarcoma. Primary cartilaginous tumors of the chest wall are uncommon. Chondrosarcoma is the most common primary malignant tumor of the chest wall. The treatment for this tumor is wide excision

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P < 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P < 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk

IL7R GEN MUTASYON VE POLİMORFİZMLARİNİN AĞIR KOMBİNE İMMUN YETMEZLİKLİ HASTALARDAKİ SIKLIĞI

Öz Ağır kombine immün yetmezlik immün sistem hücrelerinin defektleri ile ilgili olan nadir görülen genetik bir hastalıktır. Bu hastalık T lenfosit, B lenfosit ve Doğal Öldürücü (NK) lenfosit gruplarının birinde veya birkaçında görülebilir. Çalışmamızda Türkiye’nin güneyinde yer alan ağır kombine immün yetmezlikli hastalarda IL7R gen polimorfizmlerinin tanımlanması ve hastaların immünfenotip sonuçları ile birlikte değerlendirilmesi amaçlandı. Çalışmamızda ağır kombine immün yetmezlik tanısı alan 30 hastanın sanger DNA dizi analizi yöntemi ile analizi yapıldı. Hastalardan taze kan örnekleri alınarak akım sitometri yöntemi ile hastalardaki IL7R gen polimorfizmlerinin fenotiplendirilmesi yapıldı. Çalışmanın sonunda ağır kombine immün yetmezlikli hastalardan birinde (%3,3; 1/30) heterozigot p.R140Q (c.419G>A) mutasyonu tespit edilirken, hastaların 26’sında (%86,7; 26/30) de heterozigot ve/veya homozigot IL7R polimorfizmleri (T166I, I138V, T244I ve I356V) saptandı. Ağır immün yetmezlikli hastalarda IL7R gen polimorfizmlerinin sık görülmesi, bu polimorfizm ile hastalık arasında ilişki olduğu görüşünü güçlendirmiştir. Abstract Severe combined immunodeficiencies are a group of rare inherited disorders with profound defects in immune cells. This genetic disorder might have effect on T lymphocytes, B lymphocytes and/or Natural Killer cells (NK). This study aimed at the identifying the polymorphisms in IL7R gene present in severe combined immunodeficies patients who located in southern part of Turkey. A total of 30 patients with severe combined immunodeficiencies were investigated for IL7R polymorphisms using Sanger sequencing and immune phenotyping by flow cytometric analysis. One heterozygote p.R140Q (c.419G>A) mutation was identified in 1 patient (n=1, %3,3) and 86.7% (n=26) of all patients had IL7R polymorphisms (T166I, I138V, T244I and I356V) whether heterozygote and/or homozygote. The frequent occurence of IL7R gene polymorphisms in patients with severe immunodeficiency has strengthened the view that there is a relationship between this polymorphism and disease

Synthesis, characterization, UV-Vis absorption and cholinesterase inhibition properties of bis-indolyl imine ligand systems

A number of bis-indolyl imine helical structures has successfully been synthesized employing Schiff base reaction conditions starting from 4,6-dimethoxy-2,3-diphenylindole with different o-phenyl diamines as pi-spacer bridged. The structures of targeted compounds were identified by FT-IR, mass, H-1 and C-13 NMR spectroscopy along with single crystal X-ray diffraction techniques. The ground state absorption properties of the bis-indolyl compounds were also investigated utilizing UV-Vis absorption spectroscopy. As the biological aspect of the synthesized compounds, the anticholinesterase potency was investigated towards the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes. The highest inhibition was determined in the presence of compound 9 with the values of 89.21 and 96.06, better than standard Galantamine, for AChE and BChE, respectively. (C) 2020 Elsevier B.V. All rights reserved.Research Found of the Gebze Technical University [2019-A-105-37]This work has been supported by Research Found of the Gebze Technical University (Project Number: 2019-A-105-37). We thank to Dr. Michael Dieter Worle for his support in refining compound 10

Dimethoxyindoles based thiosemicarbazones as multi-target agents; synthesis, crystal interactions, biological activity and molecular modeling

Alzheimer's disease (AD) is known as one of the most devastating neurodegenerative disease diagnosed for the old-aged people and cholinesterase inhibitors (ChEI) can be used as an effective palliative treatment for AD. A range of novel monomeric and dimeric indole based thiosemicarbazone derivatives 17–28 was synthesized in order to target cholinesterases (ChE). Biological importance of the targeted compounds 17–28 was investigated by employing the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes along with three different antioxidant property determination assays, namely DPPH free radical scavenging, ABTS cationic radical decolarization, and CUPRAC cupric reducing antioxidant capacity. The compounds 18 and 19 displayed the best inhibitor activity against BChE with IC50 values of 7.42 and 1.95 ?M, respectively. The antioxidant potentials were found to be moderate for DPPH and ABTS assays and the compounds 28 and 18 were the most potent candidates for both antioxidant assays. Cupric reducing capacity was the most promising assay and the compounds 25, 26 and 28 provided better inhibition values than all the standards. Further binding mode and affinity studies performed by molecular docking and molecular dynamics simulations. Accordingly, the compound 19 is the most plausible candidate that can compete with galantamine (GNT), a common pharmaceutics targeting both cholinesterase enzymes. © 2022 Elsevier Inc.The numerical calculations reported in this paper were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). M.S.K. and M.T. acknowledges Abdulkadir Kocak for allowing facilities and helping in computational studies

Germline landscape of BRCAs by 7-site collaborations as a BRCA consortium in Turkey

BRCA1/2 mutations play a significant role in cancer pathogenesis and predisposition particularly in breast, ovarian and prostate cancers. Thus, germline analysis of BRCA1 and BRCA2 is essential for clinical management strategies aiming at the identification of recurrent and novel mutations that could be used as a first screening approach. We analyzed germline variants of BRCA1/2 genes for 2168 individuals who had cancer diagnosis or high risk assessment due to BRCAs related cancers, referred to 10 health care centers distributed across 7 regions covering the Turkish landscape. Overall, 68 and 157 distinct mutations were identified in BRCA1 and BRCA2, respectively. Twenty-two novel variants were reported from both genes while BRCA2 showed higher mutational heterogeneity. We herein report the collective data as BRCA Turkish consortium that confirm the molecular heterogeneity in BRCAs among Turkish population, and also as the first study presenting the both geographical, demographical and gene based landscape of all recurrent and novel mutations which some might be a founder effect in comparison to global databases. This wider perspective leads to the most accurate variant interpretations which pave the way for the more precise and efficient management affecting the clinical and molecular aspects

A Multicenter Study of Genotype Variation/Demographic Patterns in 2475 Individuals Including 1444 Cases With Breast Cancer in Turkey

Objective: Breast cancer (BC) is the most common cancer type in women and may be inherited, mostly in an autosomal dominant pattern. The clinical diagnosis of BC relies on the published diagnostic criteria, and analysis of two genes, BRCA1 and BRCA2, which are strongly associated with BC, are included in these criteria. The aim of this study was to compare BC index cases with non-BC individuals in terms of genotype and diagnostic features to investigate the genotype/demographic information association. Materials and Methods: Mutational analyses for the BRCA1/BRCA2 genes was performed in 2475 individuals between 2013-2022 from collaborative centers across Turkey, of whom 1444 with BC were designated as index cases. Results: Overall, mutations were identified in 17% (421/2475), while the percentage of mutation carriers in cases of BC was similar, 16.6% (239/1444). BRCA1/BRCA2 gene mutations were detected in 17.8% (131/737) of familial cases and 12% (78/549) of sporadic cases. Mutations in BRCA1 were found in 4.9%, whereas 12% were in BRCA2 (p<0.05). Meta-analyses were performed to compare these results with other studies of Mediterranean-region populations. Conclusion: Patients with BRCA2 mutations were significantly more common than those with BRCA1 mutations. In sporadic cases, there was a lower proportion with BRCA1/BRCA2 variants, as expected, and these results were consistent with the data of Mediterranean-region populations. However, the present study, because of the large sample size, revealed more robust findings than previous studies. These findings may be helpful in facilitating the clinical management of BC for both familial and non-familial cases