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Allelic exclusion

Liang Tang, Jianming Li, Meihua Bao, Ju Xiang, Yiwei Chen, Yan Wang
Objective: The estrogen receptor (ER) and the human epidermal growth factor receptor 2 (HER2) each play an important role in female cancers. This study aimed to investigate the genetic association between three common single nucleotide polymorphisms (SNPs) and the risk of ovarian cancer. The SNPs investigated in this study were ESR2 rs1271572 and rs3020450 and HER2 rs1801200. Methods: In this study, databases were electronically searched in a meta-analysis. Databases used were PubMed, Embase, China National Knowledge Infrastructure (CNKI), Wanfang and Cochrane library...
2018: OncoTargets and Therapy
Nazli Bozman, Cemal Gurkan, Huseyin Sevay, Damla Kanliada Demirdov, Filiz Ozbas-Gerceker
BACKGROUND: Southeastern Anatolia is the smallest, yet the most densely populated region among the seven major geographic constituents of Turkey. Situated in the Upper Mesopotamia, Southeastern Anatolia was also the northernmost extension of the Fertile Crescent, which is often considered as the earliest cradle of civilisation. AIM: To investigate the autosomal STR polymorphisms associated with a truly representative population sample pool from Southeastern Anatolia...
March 14, 2018: Annals of Human Biology
Nejla Sellami, Laila Ben Lamine, Amira Turki, Sameh Sarray, Mohammed Jailani, Abrar K Al-Ansari, Mohamed Ghorbel, Touhami Mahjoub, Wassim Y Almawi
BACKGROUND: Vascular endothelial growth factor (VEGF) contributes to type 2 diabetes (T2DM) pathogenesis, and genetic variations in VEGFA gene were suggested to influence VEGF secretion and T2DM pathogenesis. AIM: To evaluate the association of specific VEGFA variants with altered VEGF levels, and with T2DM among Tunisians. SUBJECTS AND METHODS: A retrospective case-control study, performed on 815 T2DM patients, and 805 healthy controls. VEGF levels were measured by ELISA, genotyping of VEGFA variants was done by allelic exclusion method (real-time PCR)...
March 10, 2018: Cytokine
Claudio Toma, Alex D Shaw, Richard J N Allcock, Anna Heath, Kerrie D Pierce, Philip B Mitchell, Peter R Schofield, Janice M Fullerton
Bipolar disorder (BD) is a complex psychiatric condition with high heritability, the genetic architecture of which likely comprises both common variants of small effect and rare variants of higher penetrance, the latter of which are largely unknown. Extended families with high density of illness provide an opportunity to map novel risk genes or consolidate evidence for existing candidates, by identifying genes carrying pathogenic rare variants. We performed whole-exome sequencing (WES) in 15 BD families (117 subjects, of whom 72 were affected), augmented with copy number variant (CNV) microarray data, to examine contributions of multiple classes of rare genetic variants within a familial context...
March 13, 2018: Translational Psychiatry
Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genome-wide association studies (GWASs) have identified multiple intergenic single nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (Hi-C), epigenetic annotation and a series of functional assays...
March 12, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Daniel Shriner, Charles N Rotimi
Five classical designations of sickle haplotypes are made on the basis of the presence or absence of restriction sites and are named after the ethno-linguistic groups or geographic regions from which the individuals with sickle cell anemia originated. Each haplotype is thought to represent an independent occurrence of the sickle mutation rs334 (c.20A>T [p.Glu7Val] in HBB). We investigated the origins of the sickle mutation by using whole-genome-sequence data. We identified 156 carriers from the 1000 Genomes Project, the African Genome Variation Project, and Qatar...
March 7, 2018: American Journal of Human Genetics
Jian Zhang, Zhenghui Li, Xiaoting Mo, Wenhua Ma, Hantao Zhang, Ziqing Lin, Jian Ye
There is currently no large population data-based data set in Kashgar Prefecture Uyghur. The allele frequencies of 18 autosomal short tandem repeat (STR) loci included in the DNATyper™ 19 kit were evaluated in 2600 Uyghur individuals living in Kashgar Prefecture, Northwest China. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) of all 18 autosomal STR loci were 0.99999999999999999998235 and 0.99999998670, respectively. Phylogenetic analyses revealed that the Uyghur population has a closer relationship with the Xinjiang-Kazakh, Inner Mongolia-Mongolian, and other three Uyghur populations...
March 10, 2018: International Journal of Legal Medicine
Ivna V Freire, Cezar A Casotti, Ícaro J S Ribeiro, Jonas R D Silva, Ana A L Barbosa, Rafael Pereira
The angiotensin-converting enzyme insertion/deletion (I/D) gene polymorphism has been widely reported as being associated with hypertension; however, most studies do not consider environmental/behavioral factors. This study aimed to investigate the relationship among angiotensin-converting enzyme insertion/deletion gene polymorphism, environmental/behavioral factors, and hypertension in community-dwelling elderly individuals. All community-dwelling older adults from Aiquara, Bahia, Brazil, were invited to take part in this study...
March 9, 2018: Journal of Clinical Hypertension
Josyf C Mychaleckyj, Uma Nayak, E Ross Colgate, Dadong Zhang, Tommy Carstensen, Shahnawaz Ahmed, Tahmeed Ahmed, Alexander J Mentzer, Masud Alam, Beth D Kirkpatrick, Rashidul Haque, Abu Syed Golam Faruque, William A Petri
BACKGROUND: Breast milk is the sole nutrition source during exclusive breastfeeding, and polyunsaturated fatty acids (FAs) are critical micronutrients in infant physical and cognitive development. There has been no prior genomewide association study of breast milk, hence our objective was to test for genetic association with breast milk FA composition. METHODS: We measured the fractional composition of 26 individual FAs in breast milk samples from three cohorts totalling 1142 Bangladeshi mothers whose infants were genotyped on the Illumina MEGA chip and replicated on a custom Affymetrix 30K SNP array (n=616)...
March 7, 2018: Journal of Medical Genetics
João Paulo Gomes Viana, Marcos Vinícius Bohrer Monteiro Siqueira, Fabiano Lucas Araujo, Carolina Grando, Patricia Sanae Sujii, Ellida de Aguiar Silvestre, Mariana Novello, José Baldin Pinheiro, Marcelo Mattos Cavallari, Pedro H S Brancalion, Ricardo Ribeiro Rodrigues, Anete Pereira de Souza, Julian Catchen, Maria I Zucchi
The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil...
2018: PloS One
Britta Weigelt, Rui Bi, Rahul Kumar, Pedro Blecua, Diana L Mandelker, Felipe C Geyer, Fresia Pareja, Paul A James, Fergus J Couch, Diana M Eccles, Fiona Blows, Paul Pharoah, Anqi Li, Pier Selenica, Raymond S Lim, Gowtham Jayakumaran, Nic Waddell, Ronglai Shen, Larry Norton, Hannah Y Wen, Simon N Powell, Nadeem Riaz, Mark E Robson, Jorge S Reis-Filho, Georgia Chenevix-Trench
Pathogenic germline variants in ataxia-telangiectasia mutated (ATM), a gene that plays a role in DNA damage response and cell cycle checkpoints, confer an increased breast cancer (BC) risk. Here, we investigated the phenotypic characteristics and landscape of somatic genetic alterations in 24 BCs from ATM germline mutation carriers by whole-exome and targeted sequencing. ATM-associated BCs were consistently hormone receptor positive and largely displayed minimal immune infiltrate. Although 79.2% of these tumors exhibited loss of heterozygosity of the ATM wild-type allele, none displayed high activity of mutational signature 3 associated with defective homologous recombination DNA (HRD) repair...
February 28, 2018: Journal of the National Cancer Institute
Atakan Comba, Fatma Demirbaş, Gönül Çaltepe, Esra Eren, Ayhan G Kalayci
BACKGROUND: α-1 Antitrypsin (AAT) deficiency is the most frequently occurring genetic liver disorder. The association among classical α-1 antitrypsin deficiency (AATD), chronic liver disease, and cirrhosis is common in adult patients but rare in children. AIM: To assess the clinical characteristics of children with AATD and to compare symptoms between homozygous and heterozygous children. MATERIALS AND METHODS: The study included 20 children who were found to have mutant Pi alleles...
March 2, 2018: European Journal of Gastroenterology & Hepatology
Atif Adnan, Xiaoni Zhan, Kadirya Kasim, Allah Rakha, Xing Jia Xin
Forensic statistical parameters based on allelic frequencies of commonly used short tandem repeats were estimated for the Han population of Jiangsu province from P.R. China. The 6-dye GlobalFiler™ PCR amplification kit incorporates 21 autosomal STRs, providing reliable DNA typing results with enhanced the power of discrimination. Here, we analyzed the GlobalFiler™ STR loci in 516 unrelated individuals from Jiangsu Han population. A total of 256 alleles were observed ranging between 5 and 35.2 repeat units, and SE33 showed the greatest power of discrimination (34 alleles) in Jiangsu Han population...
March 2, 2018: International Journal of Legal Medicine
Dounin Danielle Zoh, Ludovic Phamien Ahoua Alou, Mahama Toure, Cédric Pennetier, Soromane Camara, Dipomin François Traore, Alphonsine Amanan Koffi, Akré Maurice Adja, Ahoua Yapi, Fabrice Chandre
BACKGROUND: Several studies were carried out in experimental hut station in areas surrounding the city of Bouaké, after the crisis in Côte d'Ivoire. They reported increasing resistance levels to insecticide for malaria transmiting mosquitoes. The present work aims to evaluate the current resistance level of An. gambiae (s.l.) in rural and urban areas in the city of Bouaké. METHODS: Larvae of Anopheles gambiae (s.l.) were collected from five different study sites and reared to adult stages...
March 2, 2018: Parasites & Vectors
Petroula Gerasimou, Vicky Nicolaidou, Nicos Skordis, Michalis Picolos, Demetrios Monos, Paul A Costeas
The contribution of specific HLA Class II alleles in type 1 diabetes is determined by polymorphic amino acid epitopes that direct antigen binding therefore, along with conventional allele frequency analysis, epitope analysis can provide important insights into disease susceptibility. We analyzed the highly heterogeneous Cypriot population for the HLA class II loci of T1DM patients and controls and we report for the first time their allele frequencies. Within our patient cohort we identified a subgroup that did not carry the DRB1*03:01-DQA1*05:01-DQB1*02:01 and DRB1*04:xx-DQA1*03:01-DQB1*03:02 risk haplotypes but a novel recombinant one, DRB1*04:XX-DQA1*03:01-DQB1*02:01 designated DR4-DQ2...
2018: PloS One
Monique Fontaine, Isabelle Kim, Anne-Frédérique Dessein, Karine Mention-Mulliez, Dries Dobbelaere, Claire Douillard, Guilhem Sole, Manuel Schiff, Roland Jaussaud, Caroline Espil-Taris, Audrey Boutron, Wim Wuyts, Cécile Acquaviva, Christine Vianey-Saban, Dominique Roland, Marie Joncquel-Chevalier Curt, Joseph Vamecq
Carnitine palmitoyltransferase type 2 (CPT2) deficiency, a mitochondrial fatty acid oxidation disorder (MFAOD), is a cause of myopathy in its late clinical presentation. As for other MFAODs, its diagnosis may be evocated when blood acylcarnitine profile is abnormal. However, a lack of abnormalities or specificity in this profile is not exclusive of CPT2 deficiency. Our retrospective study reports clinical and biological data in a cohort of 11 patients with circulating acylcarnitine profile unconclusive enough for a specific diagnosis orientation...
February 12, 2018: Molecular Genetics and Metabolism
Hagar Mor-Shaked, Rachel Eiges
Fragile X syndrome (FXS) is one of the most common heritable forms of cognitive impairment. It results from a fragile X mental retardation protein (FMRP) protein deficiency caused by a CGG repeat expansion in the 5'-UTR of the X-linked FMR1 gene. Whereas in most individuals the number of CGGs is steady and ranges between 5 and 44 units, in patients it becomes extensively unstable and expands to a length exceeding 200 repeats (full mutation). Interestingly, this disease is exclusively transmitted by mothers who carry a premutation allele (55-200 CGG repeats)...
2018: Frontiers in Molecular Neuroscience
Mara Colombo, Irene Lòpez-Perolio, Huong D Meeks, Laura Caleca, Michael Parsons, Hongyan Li, Giovanna De Vecchi, Emma Tudini, Claudia Foglia, Patrizia Mondini, Siranoush Manoukian, Raquel Behar, Encarna B Gomez Garcia, Alfons Meindl, Marco Montagna, Dieter Niederacher, Ane Y Schmidt, Liliana Varesco, Barbara Wappenschmidt, Manjeet K Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Kristiina Aittomäki, Irene L Andrulis, Hoda Anton-Culver, Volker Arndt, Matthias W Beckmann, Alicia Beeghly-Fadel, Javier Benitez, Bram Boeckx, Natalia V Bogdanova, Stig E Bojesen, Bernardo Bonanni, Hiltrud Brauch, Hermann Brenner, Barbara Burwinkel, Jenny Chang-Claude, Don M Conroy, Fergus J Couch, Angela Cox, Simon S Cross, Kamila Czene, Peter Devilee, Thilo Dörk, Mikael Eriksson, Peter A Fasching, Jonine Figueroa, Olivia Fletcher, Henrik Flyger, Marike Gabrielson, Montserrat García-Closas, Graham G Giles, Anna González-Neira, Pascal Guénel, Christopher A Haiman, Per Hall, Ute Hamann, Mikael Hartman, Jan Hauke, Antoinette Hollestelle, John L Hopper, Anna Jakubowska, Audrey Jung, Veli-Matti Kosma, Diether Lambrechts, Loic Le Marchand, Annika Lindblom, Jan Lubinski, Arto Mannermaa, Sara Margolin, Hui Miao, Roger L Milne, Susan L Neuhausen, Heli Nevanlinna, Janet E Olson, Paolo Peterlongo, Julian Peto, Katri Pylkäs, Elinor J Sawyer, Marjanka K Schmidt, Rita K Schmutzler, Andreas Schneeweiss, Minouk J Schoemaker, Mee Hoong See, Melissa C Southey, Anthony Swerdlow, Soo H Teo, Amanda E Toland, Ian Tomlinson, Thérèse Truong, Christi J van Asperen, Ans M W van den Ouweland, Lizet van der Kolk, Robert Winqvist, Drakoulis Yannoukakos, Wei Zheng, Alison M Dunning, Douglas F Easton, Alex Henderson, Frans Hogervorst, Louise Izatt, Kenneth Offitt, Lucy E Side, Elizabeth J van Rensburg, Study Embrace, Study Hebon, Lesley McGuffog, Antonis C Antoniou, Georgia Chenevix-Trench, Amanda B Spurdle, David E Goldgar, Miguel de la Hoya, Paolo Radice
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families...
February 20, 2018: Human Mutation
Iris M de Lange, Marco J Koudijs, Ruben van 't Slot, Boudewijn Gunning, Anja C M Sonsma, Lisette J J M van Gemert, Flip Mulder, Ellen C Carbo, Marjan J A van Kempen, Nienke E Verbeek, Isaac J Nijman, Robert F Ernst, Sanne M C Savelberg, Nine V A M Knoers, Eva H Brilstra, Bobby P C Koeleman
OBJECTIVE: Phenotypes caused by de novo SCN1A pathogenic variants are very variable, ranging from severely affected patients with Dravet syndrome to much milder genetic epilepsy febrile seizures plus cases. The most important determinant of disease severity is the type of variant, with variants that cause a complete loss of function of the SCN1A protein (α-subunit of the neuronal sodium channel Nav1.1) being detected almost exclusively in Dravet syndrome patients. However, even within Dravet syndrome disease severity ranges greatly, and consequently other disease modifiers must exist...
February 20, 2018: Epilepsia
David Shahar, John Evans, Mark G L Sayers
BACKGROUND: The literature implies that large enthesophytes are exclusive to genetically predisposed individuals and to Spondyloarthropathies sufferers. Accordingly, the aim of this investigation and report was to assess the involvement of genetic predisposition, inflammatory and/or mechanical influences in the development of large enthesophytes in a sample population of teenagers presenting with large enthesophytes emanating from the external occipital protuberance. METHODS: Analysis was based on four teenage males (13-16 year-old) possessing 14...
February 12, 2018: Clinical Biomechanics
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