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Genetic variation

DarrenM Hutt, Salvatore Loguercio, Alexandre Rosa Campos, William E Balch
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention...
June 17, 2018: Journal of Molecular Biology
Sylvie Oddou-Muratorio, Julie Gauzere, Aurore Bontemps, Jean-François Rey, Etienne K Klein
Inter-individual variation in fecundities has major consequences on population evolutionary potential, through genetic drift and selection. Using two spatially explicit mating models that analyze the genotypes of seeds and seedlings, we investigated the variation of male and female fecundities within and among three European beech (Fagus sylvatica) stands situated along an altitudinal gradient. Female and male individual fecundity distributions were both skewed in this monoecious species, and we found a higher variance in female as compared to male fecundities...
June 20, 2018: Molecular Ecology
Laura Flatau, Markus Reitt, Gunnar Duttge, Christian Lenk, Barbara Zoll, Wolfgang Poser, Alexandra Weber, Urs Heilbronner, Marcella Rietschel, Jana Strohmaier, Rebekka Kesberg, Jonas Nagel, Thomas G Schulze
In clinical practice and in research, there is an ongoing debate on how to return incidental and secondary findings of genetic tests to patients and research participants. Previous investigations have found that most of the people most of the time are in favor of full disclosure of results. Yet, the option to reject disclosure, based on the so-called right not to know, can be valuable especially for some vulnerable subgroups of recipients. In the present study we investigated variations in informational preferences in the context of genetic testing in a large and diverse German sample...
2018: PloS One
Michael B Burns, Emmanuel Montassier, Juan Abrahante, Sambhawa Priya, David E Niccum, Alexander Khoruts, Timothy K Starr, Dan Knights, Ran Blekhman
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues...
June 20, 2018: PLoS Genetics
Katharina Wiedemeyer, Liubov Kyrpychova, Özlem Tanas Işikci, Dominic V Spagnolo, Heinz Kutzner, Arno Rütten, Maria T Fernandez-Figueras, Natalja Denisjuk, Saul Suster, Michal Pavlovsky, Fredrik Petersson, Michal Michal, Joyce Lee, Katrin Kerl, Dmitry V Kazakov
Sebaceous neoplasms with an organoid pattern (rippled, labyrinthine/sinusoidal, carcinoid-like, and petaloid) are rare. Previous studies suggested that the above patterns likely represent variations along a morphological continuum. The objectives of this study were to (1) validate this proposition by studying a large number of cases, (2) determine whether there are specific associations with clinical features, (3) establish their frequency, and (4) determine whether they have any association with Muir-Torre syndrome...
July 2018: American Journal of Dermatopathology
Tslil Gabrieli, Hila Sharim, Gil Nifker, Jonathan Jeffet, Tamar Shahal, Rani Arielly, Michal Levy-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is a distinct product of active DNA demethylation that is linked to gene regulation, development, and disease. In particular, 5-hmC levels dramatically decline in many cancers, potentially serving as an epigenetic biomarker. The noise associated with next-generation 5-hmC sequencing hinders reliable analysis of low 5-hmC containing tissues such as blood and malignant tumors. Additionally, genome-wide 5-hmC profiles generated by short-read sequencing are limited in providing long-range epigenetic information relevant to highly variable genomic regions, such as the 3...
June 20, 2018: ACS Nano
Rachel C McMullan, Martin T Ferris, Timothy A Bell, Vineet D Menachery, Ralph S Baric, Kunjie Hua, Daniel Pomp, Abbie E Smith-Ryan, Fernando Pardo-Manuel de Villena
Exercise results in beneficial health outcomes and protects against a variety of chronic diseases. However, U.S. exercise guidelines recommend identical exercise programs for everyone, despite individual variation in responses to these programs, including paradoxical fat gain. Experimental models of exercise-induced paradoxical outcomes may enable the dissection of underlying physiological mechanisms as well as the evaluation of potential interventions. Whereas several studies have identified individual mice exhibiting paradoxical fat gain following exercise, no systematic effort has been conducted to identify and characterize models of paradoxical response...
June 2018: Physiological Reports
James R Whiting, Isabel S Magalhaes, Abdul R Singkam, Shaun Robertson, Daniele D'Agostino, Janette E Bradley, Andrew D C MacColl
Understanding how wild immune variation covaries with other traits can reveal how costs and trade-offs shape immune evolution in the wild. Divergent life history strategies may increase or alleviate immune costs, helping shape immune variation in a consistent, testable way. Contrasting hypotheses suggest that shorter life histories may alleviate costs by offsetting them against increased mortality; or increase the effect of costs if immune responses are traded off against development or reproduction. We investigated the evolutionary relationship between life history and immune responses within an island radiation of three-spined stickleback, with discrete populations of varying life histories and parasitism...
June 20, 2018: Molecular Ecology
Jianliang Li, Fanfeng Meng, Weihua Li, Yixin Wang, Shuang Chang, Peng Zhao, Zhizhong Cui
Avian leukosis virus subgroup J (ALV-J) has successively infected white feather chickens, layer hens, cultivated yellow chickens, and indigenous chickens; infection rates and tumorigenicity have attracted increasingly extensive attention in China. To clarify the correlation of the epidemiological phenomenon of ALV-J with the evolution of envelope protein gp85, 140 strains of ALV-J isolated from chickens with different genetic backgrounds from 1999 to 2013 were compared. The homology of the gp85 protein and genetic genealogical relationships between 140 strains of ALV-J and the prototype strain HPRS-103, as well as between the same ALV-J strains and 8 American isolates, were analyzed and compared...
June 19, 2018: Poultry Science
P K Piekarski, J M Carpenter, A R Lemmon, E Moriarty Lemmon, B J Sharanowski
The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing → morphologically differentiated castes)...
June 19, 2018: Molecular Biology and Evolution
Jinyoung Byun, Ann G Schwartz, Christine Lusk, Angela S Wenzlaff, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Ming You, Elena Y Kupert, Marshall W Anderson, Younghun Han, Yafang Li, David Qian, Adrienne Stilp, Cathy Laurie, Sarah Nelson, Wenying Zheng, Rayjean J Hung, Valerie Gaborieau, James Mckay, Paul Brennan, Neil E Caporaso, Maria Teresa Landi, Xifeng Wu, John R McLaughlin, Yonathan Brhane, Yohan Bossé, Susan M Pinney, Joan E Bailey-Wilson, Christopher I Amos
To identify genetic variation associated with lung cancer risk, we performed a genome-wide association analysis of 685 lung cancer cases that had a family history of two or more first or second degree relatives compared with 744 controls without lung cancer that were genotyped on an Illumina Human OmniExpressExome-8v1 array. To ensure robust results, we further evaluated these findings using data from six additional studies that were assembled through the Transdisciplinary Research on Cancer of the Lung Consortium comprising 1,993 familial cases and 33,690 controls...
June 19, 2018: Carcinogenesis
Dylan M Williams, Juulia Jylhävä, Nancy L Pedersen, Sara Hägg
Background: Frailty indices (FIs) measure variation in health between aging individuals. Researching FIs in resources with large-scale genetic and phenotypic data will provide insights into the causes and consequences of frailty. Thus, we aimed to develop an FI using UK Biobank data, a cohort study of 500,000 middle-aged and older adults. Methods: An FI was calculated using 49 self-reported questionnaire items on traits covering health, presence of diseases and disabilities, and mental well-being, according to standard protocol...
June 18, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
Keisuke Obase, Greg W Douhan, Yosuke Matsuda, Matthew E Smith
Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 "genotypes" with sequence variation of up to 8...
April 18, 2018: Mycologia
Xu Zhang, Yuzhuo Wang, Tian Tian, Gangqiao Zhou, Guangfu Jin
Genome-wide association studies have identified several germline variants in gastric cancer. Meanwhile, sequencing studies have characterized extensive somatic alterations that arise during gastric carcinogenesis. However, the relationship between the germline variants and somatic alterations is still unclear in gastric cancer. A total of 11 susceptibility loci and 276 driver genes of gastric cancer were determined based on previous studies and publicly available database. An enrichment analysis was made to detect whether driver genes were enriched in susceptibility regions...
June 20, 2018: Cancer Medicine
Irene Jiménez, Mathieu Chicard, Léo Colmet-Daage, Nathalie Clément, Adrien Danzon, Eve Lapouble, Gaelle Pierron, Mylène Bohec, Sylvain Baulande, Dominique Berrebi, Paul Fréneaux, Aurore Coulomb, Louise Galmiche-Rolland, Sabine Sarnacki, Georges Audry, Pascale Philippe-Chomette, Hervé J Brisse, François Doz, Jean Michon, Olivier Delattre, Gudrun Schleiermacher
Circulating tumor DNA (ctDNA) is a powerful tool for the molecular characterization of cancer. The most frequent pediatric kidney tumors (KT) are Wilms' tumors (WT), but other diagnoses may occur. According to the SIOP strategy, in most countries pediatric KT have a presumptive diagnosis of WT if they are clinically and radiologically compatible. The histologic confirmation is established after post-chemotherapy nephrectomy. Thus, there is a risk for a small fraction of patients to receive neoadjuvant chemotherapy that is not adapted to the disease...
June 19, 2018: International Journal of Cancer. Journal International du Cancer
Amélie Pinard, Nathalie Eudes, Julia Mitchell, Fanny Bajolle, Maude Grelet, Joséphine Okoronkwo, Damien Bonnet, Gwenaelle Collod-Béroud, Stéphane Zaffran
Ventricular septal defect (VSD) including outlet VSD of double outlet right ventricle (DORV) and perimembranous VSD are among the most common congenital heart diseases found at birth. HOXB1 encodes a homeodomain transcription factor essential for normal cardiac outflow tract development. The aim of the present study was to investigate the possible genetic effect of sequence variations in HOXB1 on VSD. The coding regions and splice junctions of the HOXB1 gene were sequenced in 57 unrelated VSD patients. As a result, a homozygous c...
June 19, 2018: Molecular Biology Reports
Daniel E Gustavson, Matthew S Panizzon, Jeremy A Elman, Carol E Franz, Asad Beck, Chandra A Reynolds, Kristen C Jacobson, Hong Xian, Rosemary Toomey, Michael J Lyons, William S Kremen
Mounting evidence suggests that measures of phonemic fluency and semantic fluency are differentially associated with other cognitive and health phenotypes, but few studies have examined their shared and unique variance, especially using genetically-informative designs. In this study, 1464 middle-aged twins completed six fluency subtests at up to two time-points (mean age 56 and 62 years). Confirmatory factor analyses supported a two-factor solution: a General Fluency latent factor explained variation in all six subtests and a Semantic-Specific factor accounted for additional variance in semantic subtests...
June 19, 2018: Behavior Genetics
Ignacio Ferrés, Gregorio Iraola
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes...
2018: PeerJ
Ben Trevaskis
Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented...
2018: Frontiers in Plant Science
Wei Liu, Zhidan Xiao, Chao Fan, Nonghui Jiang, Xiangchun Meng, Xu Xiang
Litchi ( Litchi chinensis ) is an important subtropical fruit tree with high commercial value. However, the short and centralized fruit maturation period of litchi cultivars represents a bottleneck for litchi production. Therefore, the development of novel cultivars with extremely early fruit maturation period is critical. Previously, we showed that the genotypes of extremely early-maturing (EEM), early-maturing (EM), and middle-to-late-maturing (MLM) cultivars at a specific locus SNP51 (substitution type C/T) were consistent with their respective genetic background at the whole-genome level; a homozygous C/C genotype at SNP51 systematically differentiated EEM cultivars from others...
2018: Frontiers in Plant Science
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