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https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#1
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29351563/a-consensus-linkage-map-of-lentil-based-on-dart-markers-from-three-ril-mapping-populations
#2
Duygu Ates, Secil Aldemir, Ahmad Alsaleh, Semih Erdogmus, Seda Nemli, Abdullah Kahriman, Hakan Ozkan, Albert Vandenberg, Bahattin Tanyolac
BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39)...
2018: PloS One
https://www.readbyqxmd.com/read/29350394/genetic-variants-in-the-polish-population-of-patients-with-pulmonary-arterial-hypertension-sequencing-of-bmpr2-alk1-and-eng-genes
#3
Barbara Uznańska-Loch, Kamil Wikło, Dominika Kulczycka-Wojdala, Bożena Szymańska, Łukasz Chrzanowski, Karina Wierzbowska-Drabik, Ewa Trzos, Jarosław Damian Kasprzak, Małgorzata Kurpesa
BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with a very serious prognosis. It seems that mutations in genes related to the transforming growth factor-beta signaling pathway are often related to the development of the disease. There was no study in Polish population that would cover this problem. AIM: To screen for genetic mutations in Polish cohort of patients with pulmonary hypertension, especially with idiopathic PAH, treated in a single hospital in Poland...
January 19, 2018: Kardiologia Polska
https://www.readbyqxmd.com/read/29349811/genetic-analysis-of-interleukin-18-gene-polymorphisms-in-alopecia-areata
#4
Sumeyya Deniz Celik, Omer Ates
BACKGROUND: Alopecia areata (AA), which appears as nonscarring hair shedding on any hair-bearing area, is a common organ-specific autoimmune condition. Cytokines have important roles in the development of AA. Interleukin (IL) 18 is a significant proinflammatory cytokine that was found higher in the patients with AA. We aimed to investigate whether the IL-18 (rs187238 and rs1946518) single nucleotide polymorphisms (SNPs) may be associated with AA and/or clinical outcome of patients with AA in Turkish population...
January 18, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29349538/capturing-pair-wise-epistatic-effects-associated-with-three-agronomic-traits-in-barley
#5
Yi Xu, Yajun Wu, Jixiang Wu
Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach...
January 18, 2018: Genetica
https://www.readbyqxmd.com/read/29348692/genome-wide-search-for-higher-order-epistasis-as-modifiers-of-treatment-effects-on-bone-mineral-density-in-childhood-cancer-survivors
#6
Cindy Im, Kirsten K Ness, Sue C Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J Brooke, Melissa M Hudson, Leslie L Robison, Yutaka Yasui, Carmen L Wilson
Single-nucleotide polymorphisms (SNPs) contributing to interactions between regulatory elements that modulate gene transcription may explain some of the uncharacterized variation for complex traits. We explored this hypothesis among 856 adult survivors of pediatric cancer exposed to curative treatments that adversely affect bone mineral density (BMD). To restrict our search to interactions among SNPs in regulatory elements, our analysis considered 75523 SNPs mapped to putative promoter or enhancer regions. In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e...
January 18, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29348129/genomic-cdkn2a-2b-deletions-in-adult-ph-all-are-adverse-despite-allogeneic-stem-cell-transplantation
#7
Heike Pfeifer, Katharina Raum, Sandra Markovic, Verena Nowak, Stephanie Fey, Julia Obländer, Jovita Pressler, Verena Böhm, Monika Brüggemann, Lydia Wunderle, Andreas Hüttmann, Ralph Wäsch, Joachim Beck, Matthias Stelljes, Andreas Viardot, Fabian Lang, Dieter Hoelzer, Wolf-Karsten Hofmann, Hubert Serve, Christel Weiss, Nicola Goekbuget, Oliver G Ottmann, Daniel Nowak
We investigated the role of copy number alterations to refine risk stratification in adult Philadelphia chromosome positive (Ph)+ ALL treated with tyrosine kinase inhibitors (TKI) and allogeneic stem cell transplantation (aSCT). 97 Ph+ ALL patients (median age 41 years, range 18-64 years) within the prospective multicenter GMALL studies 06/99 (n=8) and 07/2003 (n=89) were analysed. All patients received TKI and aSCT in first complete remission (CR1). Copy number analysis was performed with SNP arrays and validated by multiplex ligation-dependent probe amplification (MLPA)...
January 18, 2018: Blood
https://www.readbyqxmd.com/read/29346564/genome-wide-comparison-of-allele-specific-gene-expression-between-african-and-european-populations
#8
Lei Tian, Asifullah Khan, Zhilin Ning, Kai Yuan, Chao Zhang, Haiyi Lou, Yuan Yuan, Shuhua Xu
Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 17 sites in 13 genes showing ASE in both Europeans and Africans, and 19 sites in 18 genes showing population-specific ASE, including both novel and known ASE signals...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346177/no-association-between-foxp2-rs10447760-and-schizophrenia-in-a-replication-study-of-the-chinese-han-population
#9
Jiajun Yin, Ningren Jia, Yansong Liu, Chunhui Jin, Fuquan Zhang, Shui Yu, Jun Wang, Jianmin Yuan
BACKGROUND: Schizophrenia (SCZ) is a severe and heritable psychiatric disorder, and previous studies have shown that regulation of the forkhead-box P2 gene (FOXP2) may play a role in schizophrenia. Moreover, just a few studies have identified a single nucleotide polymorphism (SNP) rs10447760 within the gene that was a risk variant for SCZ in the Chinese Han population. METHODS: To examine whether the variant in the FOXP2 gene contributes toward SCZ susceptibility, we carried out an association analysis of the SNP rs10447760 of the FOXP2 gene in a case-control study (1405 cases, 1137 controls) from China...
January 17, 2018: Psychiatric Genetics
https://www.readbyqxmd.com/read/29345962/role-of-selected-polymorphisms-in-determining-muscle-fiber-composition-in-japanese-men-and-women
#10
Hiroshi Kumagai, Takuro Tobina, Noriko Ichinoseki-Sekine, Ryo Kakigi, Takamasa Tsuzuki, Hirofumi Zempo, Keisuke Shiose, Eiichi Yoshimura, Hideaki Kumahara, Makoto Ayabe, Yasuki Higaki, Ryo Yamada, Hiroyuki Kobayashi, Akira Kiyonaga, Hisashi Naito, Hiroaki Tanaka, Noriyuki Fuku
Genetic polymorphisms and sex differences are suggested to affect muscle fiber composition; however, no study has investigated the effects of genetic polymorphisms on muscle fiber composition with respect to sex differences. Therefore, the present study examined the effects of genetic polymorphisms on muscle fiber composition with respect to sex differences in Japanese population. The present study included 211 healthy Japanese individuals (102 men and 109 women). Muscle biopsies were obtained from the vastus lateralis to determine the proportion of myosin heavy chain isoforms (MHC-I, MHC-IIa, and MHC-IIx)...
January 18, 2018: Journal of Applied Physiology
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#11
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29345073/improving-accuracy-of-genomic-prediction-in-brangus-cattle-by-adding-animals-with-imputed-low-density-snp-genotypes
#12
F B Lopes, X-L Wu, H Li, J Xu, T Perkins, J Genho, R Ferretti, R G Tait, S Bauck, G J M Rosa
Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29344960/association-of-genetic-variation-in-telomere-related-snp-and-telomerase-with-ventricular-arrhythmias-in-ischaemic-cardiomyopathy
#13
Vinit Sawhney, Scott Brouilette, Niall Campbell, Steven Coppen, Victoria Baker, Ross Hunter, Mehul Dhinoja, Atholl Johnston, Mark Earley, Simon Sporton, Ken Suzuki, Richard Schilling
BACKGROUND: Telomeres are known to provide genomic stability and telomere length has been associated with cardiovascular diseases. Moreover, a higher telomerase activity has been shown to be associated with ventricular arrhythmias (VA) in ischaemic cardiomyopathy. Increasing evidence suggests that genetic variation in key telomere genes has an impact on telomerase activity. Each copy of the minor allele of SNP rs12696304, at a locus including TERC (telomerase) has been associated with ∼ 75 bp reduction in mean telomere length likely mediated by an effect on TERC expression...
January 17, 2018: Pacing and Clinical Electrophysiology: PACE
https://www.readbyqxmd.com/read/29344947/genome-wide-population-structure-and-admixture-analysis-reveals-weak-differentiation-among-ugandan-goat-breeds
#14
R B Onzima, M R Upadhyay, R Mukiibi, E Kanis, M A M Groenen, R P M A Crooijmans
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei...
January 17, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29344848/current-status-and-future-possibilities-of-molecular-genetics-techniques-in-brassica-napus
#15
REVIEW
Muhammad Afzal, Salem Safer Alghamdi, Muhammad Habib Ur Rahman, Awais Ahmad, Tahir Farooq, Mukhtar Alam, Imtiaz Ali Khan, Hidayat Ullah, Wajid Nasim, Shah Fahad
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29344113/downregulated-mirna-1269a-variant-rs73239138-decreases-the-susceptibility-to-gastric-cancer-via-targeting-znf70
#16
Wenshuai Li, Huilu Zhang, Pei Min, Jie Zhu, Diannan Xu, Weiru Jiang, Yanyun Ma, Jigang Qiu, Weihong Xu, Jian Chen, Mingqing Zhang, Min Li, Dongqin Yang, Jianping Shi, Jun Zhang, Jie Liu
Although emerging evidence has indicated that single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) are associated with susceptibility to gastric cancer, a limited number of studies have revealed the underlying molecular mechanisms. In the present study, the results suggested that miR-1269a rs73239138 has a role in decreasing the risk of gastric cancer. The level of miR-1269a variant expression was significantly downregulated compared with the wild-type miR-1269a in the gastric cells (Fig. 1). Furthermore, overexpression of miR-1269a inhibited apoptosis of gastric cancer cells...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343869/spatiotemporal-allele-organization-by-allele-specific-crispr-live-cell-imaging-snp-cling
#17
Philipp G Maass, A Rasim Barutcu, David M Shechner, Catherine L Weiner, Marta Melé, John L Rinn
Imaging and chromatin capture techniques have provided important insights into our understanding of nuclear organization. A limitation of these techniques is the inability to resolve allele-specific spatiotemporal properties of genomic loci in living cells. Here, we describe an allele-specific CRISPR live-cell DNA imaging technique (SNP-CLING) to provide the first comprehensive insights into allelic positioning across space and time in mouse embryonic stem cells and fibroblasts. With 3D imaging, we studied alleles on different chromosomes in relation to one another and relative to nuclear substructures such as the nucleolus...
January 8, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29343290/finemav-prioritizing-candidate-genetic-variants-driving-local-adaptations-in-human-populations
#18
Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue, Chris Tyler-Smith
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data...
January 17, 2018: Genome Biology
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#19
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29343214/establishing-a-genetic-link-between-fto-and-vdr-gene-polymorphisms-and-obesity-in-the-emirati-population
#20
Saad Mahmud Khan, Sarah El Hajj Chehadeh, Mehera Abdulrahman, Wael Osman, Habiba Al Safar
BACKGROUND: Obesity is a metabolic disease that is widely prevalent with approximately 600 million people classified as obese worldwide. Its etiology is multifactorial and involves a complex interplay between genes and the environment. Over the past few decades, obesity rates among the Emirati population have been increasing. The aim of this study was to investigate the association of candidate gene single nucleotide polymorphisms (SNPs), namely FTO (rs9939609) and VDR (rs1544410), with obesity in the UAE population...
January 17, 2018: BMC Medical Genetics
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