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R R Jiang, Y J Wang, X D Teng, L Xiao, H Bu, F Ye
Objective: To compare the performance of Miseq and Ion Torrent PGM platforms and library construction method for next-generation sequencing (NGS) technology for formalin-fixed and paraffin-embedded (FFPE) samples. Methods: A total of 204 FFPE cancer samples including 100 non-small cell lung cancers at the First Affiliated Hospital of Zhejiang University, and 104 colorectal cancers at West China Hospital of Sichuan University were retrospectively selected from January 2013 to December 2016. By using the same samples, DNA was extracted, and the same amount of DNA was used for library construction with the same kit, and sequenced on Miseq and Ion Torrent PGM respectively, after passing the quality control...
August 8, 2018: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
Rasha Mohamed Saleh Shoaib, Ayman Hammad, Sohier Yahia, Afaf Elsaid, Camelia Adly Abdel-Malak
Angiotensin II, the major effective molecule of the renin-angiotensin system, plays a vital role in the development of systemic lupus erythematosus (SLE). To study angiotensin II type 1 receptor (AT1R) gene polymorphism at (A1166C) in Egyptian children with SLE and its correlation with serum ACE level and SLE manifestations. AT1R gene polymorphism (A1166C) was done in 123 children with SLE in comparison to 100 healthy controls using polymerase chain reaction-based restriction fragment length polymorphism method (PCR-RFLP) and the tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) to confirm the results of the genotyping...
August 9, 2018: Clinical Rheumatology
Mahdi Mahmoudi, Masoud Garshasbi, Amir Ashraf-Ganjouei, Ali Javinani, Mahdi Vojdanian, Masoumeh Saafi, Nooshin Ahmadzadeh, Ahmadreza Jamshidi
Background: Ankylosing Spondylitis (AS) is a chronic autoinflammatory Spondyloarthropathy (SpA) which is characterized by sacroiliitis, which progresses to the axial skeleton. It seems that non-Human Leukocyte Antigen (HLA) and also HLA-B27 are associated with the susceptibility and pathogenesis of the disease. The recent Ge-nome-Wide Association Studies (GWASs) have reported intergenic rs6759298 to be associated with AS etiology. The aim of this study was investigation of the rs6759298 polymorphism in Iranian AS patients...
July 2018: Avicenna Journal of Medical Biotechnology
Shabnam Abtahi, Fatemeh Izadi Jahromi, Mohammad Hossein Dabbaghmanesh, Mahyar Malekzadeh, Abbas Ghaderi
PURPOSE: Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4 or CD152) is among the immune checkpoint molecules and its abnormal expression in cancer predisposed individuals might make the person more susceptible to tumor initiation and progression. Considering the implication of single-nucleotide polymorphisms (SNPs) in CTLA-4 gene expression and probably protein function, one can assume the involvement of these SNPs in neoplastic diseases. rs5742909 ( - 318C > T) and rs231775 ( + 49 A > G) are among the most commonly studied SNPs and have been considered as genetic factors related to thyroid diseases...
August 4, 2018: Endocrine
Naindeep Kaur, Jagtar Singh, S Reddy
CAD (Coronary Artery Disease) morbidity is becoming an endemic worldwide. Recently, the role of pro- and anti-inflammatory cytokines in the development of atherosclerotic plaques has been explored, but the association of their genetic polymorphisms and CAD has yet not been established. The present study aimed to investigate the association of IL-8-251A/T (rs4073) and IL-10 -592C/A (rs1800872) polymorphisms and the risk of CAD in North Indian population. 1000 subjects (500 angiographically confirmed CAD patients and 500 controls) were genotyped by ARMS-PCR...
August 2, 2018: Biochemical Genetics
Jiashuo Chao, Lina Chai, Xiaolong Yin, Zhongqin Zhou, Suming Xu, Weifeng Zhu, Yan Deng
AIMS: The -94 ATTG insertion/deletion polymorphism (rs28362491) is an important functional polymorphism in the NFKB1 gene. It has been shown that rs28362491 is associated with many diseases. The purpose of this study was to establish a simple and reliable method to detect the ATTG insertion/deletion polymorphism. METHODS: On the basis of the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method, a single-tube tri-primer ARMS-PCR method was developed to detect the ATTG insertion/deletion polymorphism in 93 samples...
July 2018: Genetic Testing and Molecular Biomarkers
Xiangyan Zhang, Lili Wang, Jigang Wang, Han Zhao, Jie Wu, Shuhong Liu, Lu Zhang, Yujun Li, Xiaoming Xing
AIMS: To investigate whether immunohistochemistry (IHC) could be used to screen BRAF mutation status in formalin-fixed paraffin-embedded (FFPE) colorectal carcinoma (CRC) and papillary thyroid carcinoma (PTC) samples. METHODS: Eight surgical resected samples, including 2 CRCs with mutated BRAF V600E, 2 PTCs with mutated BRAF V600E, 2 CRCs with wild-type BRAF and 2 PTCs with wild-type BRAF, were selected to explore the optimized IHC conditions for BRAF V600E (VE1) immunostaining using BenchmarkXT automated immunostainer VENTANA Medical System...
August 2018: Experimental and Molecular Pathology
Kanwaljeet Singh, Sudha Sazawal, Sunita Chhikara, Manoranjan Mahapatra, Renu Saxena
Background: : It is still a matter of debate regarding the association of JAK2V617F mutation with thrombosis in BCR-ABL negative CMPN patients. The role of JAK2V617F mutation in increasing the thrombotic risk in CMPNs is yet unequivocal. Aims: : To clarify the contribution of JAK2V617F mutation in thrombosis in CMPN patients. Settings and Design: This retrospective study was done to evaluate role of JAK2V617F mutation in thrombosis in CMPNs...
July 2018: Indian Journal of Pathology & Microbiology
Mohammad Ehsan Jaripour, Kourosh Hayatigolkhatmi, Vahid Iranmanesh, Farhad Khadivi Zand, Zahra Badiei, Hamid Farhangi, Ali Ghasemi, Abdollah Banihashem, Reza Jafarzadeh Esfehani, Ariane Sadr-Nabavi
Background and Objective: β-thalassemia results from a diverse range of mutations inside the hemoglobin subunit β ( HBB ) gene. In a study of β-thalassemia carriers and some of their at-risk fetuses in the Khorasan province of Iran, we aimed to recognize the most common mutations in the region. We also investigated a possible link between these mutations and some of the relevant hematological indices. Methods: Amplification-refractory mutation system-PCR (ARMS-PCR) was used to detect the typical HBB mutations among 1593 individuals, suspected of having a mutated HBB allele from March/2011 to January/2018...
2018: Mediterranean Journal of Hematology and Infectious Diseases
Liping Liu, Di Shao, Qiuhua Deng, Hailing Tang, Jingjing Wang, Jilong Liu, Fengming Guo, Yongping Lin, Zhiyu Peng, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Background: Molecular profiling of non-small cell lung cancer (NSCLC) is essential for therapeutic decision-making. Pleural effusion obtained by a non-invasive, repeatable procedure may provide an opportunity for molecular profiling and thereby possibly provide information enabling targeted therapy. In this study, we aimed to evaluate the diagnostic performance of pleural effusion as a specimen for molecular analysis. Methods: Thirty patients with paired malignant pleural effusion and thoracic biopsy specimens were included...
May 2018: Journal of Thoracic Disease
Niloofar Naderi, Fariba Ebrahimzadeh, Mohammad Jazebi, Ali Namvar, Mehrdad Hashemi, Azam Bolhassani
OBJECTIVES: Development of neutralizing antibodies against factor VIII is the major complication in hemophilia care which makes replacement therapies ineffective. The reports showed that inflammatory cytokines play an important role in inhibitor production. In the present study, the relationship between inhibitor development and the polymorphisms of two cytokine genes was studied in severe hemophiliac patients from Iran. METHODS: In this case-control study, three polymorphisms of immune regulatory genes [TGF-β (rs1982037) and IL-2 (rs2069762, rs4833248)] were analyzed in 100 Iranian hemophilia A patients divided into 55 inhibitor positive and 45 inhibitor negative patients using Tetra primer ARMS PCR, and DNA sequencing...
July 11, 2018: Hematology (Amsterdam, Netherlands)
Fatemeh Asadi, Reza Mirfakhraie, Farzaneh Mirzajani, Azam Khedri
Background: Studies have revealed a strong association between mutations of CFTR gene and the congenital bilateral absence of the vas deferens (CBAVD), but the role of this gene in other types of male infertility is still unclear. The purpose of the this study was to investigate the frequency of the most common mutations of the CFTR gene (DF508, G542X, N1303K, G551D, and W1282X) in a population of infertile men with nonobstructive azoospermia (NOA) and CBAVD in Iran. Methods: Blood samples were obtained from 50 NOA, 50 CBAVD, and 100 normal males (control)...
July 10, 2018: Iranian Biomedical Journal
Xiqing Li, Zunlan Zhao, Shijiang Yi, Lei Ma, Ming Li, Mingyue Liu, Yaping Zhang, Guangzhi Liu
BACKGROUND: The functions of the protein expressed in the nucleus and cytoplasm were different or opposite. The previous study found that oncogene Klf4 played a role of tumor suppressor in the nasopharyngeal cytoplasm. Cetuximab targeted epidermal growth factor receptor (EGFR) for the treatment of nasopharyngeal carcinoma. METHODS: A cohort of 231 cases of advanced nasopharyngeal carcinoma (7th AJCC III-IVa) samples was assessed by immunohistochemistry (IHC), of which, 63 cases were treated with basic treatment without cetuximab, the basic treatment include chemotherapy and radiotherapy, the regent of the chemotherapy include cisplatin and fluorouracil and 168 cases were treated with cetuximab in addition to the basic treatment...
July 4, 2018: Journal of Translational Medicine
Ebrahim Eskandari, Mohammad Hashemi, Majid Naderi, Gholamreza Bahari, Vahid Safdari, Mohsen Taheri
Background: Telomeres are involved in chromosomal stability, cellular immortality and tumorigenesis. Human telomerase reverse transcriptase (TERT) is essential for the maintenance of telomere DNA length. Recently, a variable tandem-repeats polymorphism, MNS16A, located in the downstream region of the TERT gene, was reported to have an effect on TERT expression and telomerase activity. Previous studies have linked both relative telomere length (RTL) and TERT variants with cancer. Therefore, we evaluated associations between RTL, TERT gene polymorphisms (hTERT, rs2735940 C/T and MNS16A Ins/Del) and risk of childhood acute lymphoblastic leukemia (ALL) in an Iranian population...
June 25, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
Mohammad Javad Mokhtari, Fatemeh Koohpeima, Feyzollah Hashemi-Gorji
This case-control study aimed to investigate the effect of rs11003125 in dental caries. For this purpose, a total number of 404 individuals - from Fars Province in Iran - were studied. The technique of this research was the tetra-primer amplification-refractory mutation system (ARMS)-PCR. Dental caries prevalence among the 404 individuals was assessed by counting the number of decayed, missing, and filled teeth. In this research, individuals were divided into two groups: cases (n = 238) and controls (n = 166), and the peripheral blood samples were used to extract the genomic DNA...
June 14, 2018: Caries Research
Sambuddha Das, Sukanya Purkayastha, Hirakjyoti Roy, Anima Sinha, Yashmin Choudhury
We investigated the effect of polymorphisms in four DNA repair genes, viz. RAD18 Arg302Gln (G>A) (rs373572), XPD Asp312Asn (G>A) (rs1799793), APE1 Asp148Glu (T>G) (rs3136820), and OGG1 Ser326Cys (C>G) (rs1052133) on the risk for type 2 diabetes mellitus (T2DM) and hypertension (HT) in association with smoking, tobacco chewing, and alcohol consumption in a population from Northeast India. The study subjects were comprised of 70 patients suffering from both T2DM and HT and 83 healthy controls. Genotyping was performed using ARMS-PCR for XPD Asp312Asn (G>A) and PCR-CTPP for RAD18 Arg302Gln (G>A), APE1 Asp148Glu (T>G) and OGG1 Ser326Cys (C>G)...
June 9, 2018: Biomolecular Concepts
Simone Cristina Méo Niciura, Giovanna Gabrielle Cruvinel, Caroline Valério Moraes, Flavia Aline Bressani, Wilson Malagó Junior, Magda Vieira Benavides, Ana Carolina Souza de Chagas
Single nucleotide polymorphisms (SNPs) are the main type of variation in genome, enabling them to be associated with traits of economic importance in livestock. Genome-wide association studies (GWAS) have led to the discovery of SNPs associated with desirable traits in sheep. However, in these studies, SNPs are genotyped by high-throughput methods in genome scale, which are expensive and require sophisticated equipment and analysis methods. Therefore, the goal of this study was to develop a reliable, rapid, and inexpensive polymerase chain reaction (PCR)-based method to genotype a medium number of animals for a few candidate SNPs previously associated with desirable phenotypes in sheep by GWAS, using markers associated with gastrointestinal nematode resistance as a model...
August 2018: Molecular Biology Reports
S K Vishwakarma, C Lakkireddy, G Sravani, B V S Sastry, N Raju, S I Ahmed, A A Khan, N Owaisi, A Jaisawal, M A Khan, A A Khan
This study aimed to investigate the genetic basis of ankylosing spondylitis (AS) and polyarthralgia (PA) conditions among Indian subjects through genotyping two immune regulatory genes CD14 (-159C>T) and MIF (-173G>C) and find their association with the expression levels of three circulating inflammatory miRNAs. This investigation may provide early genetic cause of these two forms of arthritis and more optimal biological targets to predict early therapeutic outcomes. A total of 140 patients (AS: 70 and PA: 70) and 156 controls were recruited from Indian population...
August 2018: International Journal of Immunogenetics
Marwa Chaouali, Mouna Ben Azaiez, Aymen Tezeghdenti, Awatef Lagha, Basma Yacoubi-Oueslati, Ezzeddine Ghazouani, Hatem Ben Abdallah, Radhia Kochkar
Autoimmune hepatitis (AIH) is a chronic hepatitis of unknown etiology and several proinflammatory cytokines are implicated in its pathogenesis. The association of TNF-α gene polymorphism with AIH onset is not fully elucidated especially in the Tunisian population. The aim of this study was to determine the association of TNF-α (-308 G > A) polymorphism with AIH susceptibility and with TNF-α expression or clinical manifestations of AIH. A total of 50 AIH patients and 150 controls were included. Evaluation of TNF-α polymorphism was performed by ARMS PCR method...
May 29, 2018: Biochemical Genetics
Shan Yang, Xueting Li, Fei Huang, Yongji Huang, Xinlong Liu, Jiayun Wu, Qinnan Wang, Zuhu Deng, Rukai Chen, Muqing Zhang
The identification of germplasm resources is an important aspect of sugarcane breeding. The aim of this study was to introduce a new method for identifying Saccharum spontaneum and its progeny. First, we cloned and sequenced nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) sequences from 20 Saccharum germplasms. Analysis of these nrDNA-ITS sequences showed a stable mutation at base 89. Primers (FO13, RO13, FI16, and RI16) were then designed for tetra-primer amplification refractory mutation system (ARMS) PCR based on mutations at base 89 of the nrDNA-ITS sequence...
2018: PloS One
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