keyword
MENU ▼
Read by QxMD icon Read
search

Genome wide selection

keyword
https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#1
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29351999/mll1-promotes-il-7-responsiveness-and-survival-during-b-cell-differentiation
#2
Tao Gan, Bin E Li, Bibhu P Mishra, Kenneth L Jones, Patricia Ernst
B lymphocyte differentiation is an exquisitely regulated homeostatic process resulting in continuous production of appropriately selected B cells. Relatively small changes in gene expression can result in deregulation of this process, leading to acute lymphocytic leukemia (ALL), immune deficiency, or autoimmunity. Translocation of MLL1 (KMT2A) often results in a pro-B cell ALL, but little is known about its role in normal B cell differentiation. Using a Rag1-cre mouse knock-in to selectively delete Mll1 in developing lymphocytes, we show that B cell, but not T cell, homeostasis depends on MLL1...
January 19, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29351777/are-minor-alleles-more-likely-to-be-risk-alleles
#3
Takashi Kido, Weronika Sikora-Wohlfeld, Minae Kawashima, Shinichi Kikuchi, Naoyuki Kamatani, Anil Patwardhan, Richard Chen, Marina Sirota, Keiichi Kodama, Dexter Hadley, Atul J Butte
BACKGROUND: Genome-wide association studies (GWASs) have revealed relationships between over 57,000 genetic variants and diseases. However, unlike Mendelian diseases, complex diseases arise from the interplay of multiple genetic and environmental factors. Natural selection has led to a high tendency of risk alleles to be enriched in minor alleles in Mendelian diseases. Therefore, an allele that was previously advantageous or neutral may later become harmful, making it a risk allele. METHODS: Using data in the NHGRI-EBI Catalog and the VARIMED database, we investigated whether (1) GWASs more easily detect risk alleles and (2) facilitate evolutionary insights by comparing risk allele frequencies of different diseases...
January 19, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29348876/genome-wide-transcriptional-profiling-identifies-potential-signatures-in-discriminating-active-tuberculosis-from-latent-infection
#4
Liping Pan, Na Wei, Hongyan Jia, Mengqiu Gao, Xiaoyou Chen, Rongrong Wei, Qi Sun, Shuxiang Gu, Boping Du, Aiying Xing, Zongde Zhang
To better understand the host immune response involved in the progression from latent tuberculosis infection (LTBI) to active tuberculosis (TB) and identify the potential signatures for discriminating TB from LTBI, we performed a genome-wide transcriptional profile of Mycobacterium tuberculosis (M.TB)-specific antigens-stimulated peripheral blood mononuclear cells (PBMCs) from patients with TB, LTBI individuals and healthy controls (HCs). A total of 209 and 234 differentially expressed genes were detected in TB vs...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348143/detecting-polygenic-adaptation-in-admixture-graphs
#5
Fernando Racimo, Jeremy J Berg, Joseph K Pickrell
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred...
January 18, 2018: Genetics
https://www.readbyqxmd.com/read/29347830/an-omic-biomarker-detection-algorithm-trivote-and-its-application-in-methylomic-biomarker-detection
#6
Cheng Xu, Jiamei Liu, Weifeng Yang, Yayun Shu, Zhipeng Wei, Weiwei Zheng, Xin Feng, Fengfeng Zhou
AIM: Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. MATERIALS & METHODS: Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms...
January 19, 2018: Epigenomics
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#7
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346622/a-nosocomial-foodborne-outbreak-of-a-vim-carbapenemase-expressing-citrobacter-freundii
#8
Mathias W Pletz, Antje Wollny, Ute-Heike Dobermann, Jürgen Rödel, Svetlana Neubauer, Claudia Stein, Christian Brandt, Anita Hartung, Alexander Mellmann, Sabine Trommer, Birgit Edel, Vladimir Patchev, Oliwia Makarewicz, Jens Maschmann
Background: A foodborne outbreak of VIM carbapenemase-expressing Citrobacter freundii (CPC) occurred between February and June 2016 at a major university hospital in Germany. Methods: An explosive increase of CPC isolated from rectal swabs of patients during weekly routine screening led to the declaration of an outbreak. A hospital-wide prevalence screening was initiated as well as screening of all patients on admission and before transfer to another ward, and canteen staff, patient rooms, medical and kitchen inventory and food...
January 15, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#9
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/29345071/detecting-selection-signatures-on-the-x-chromosome-of-the-chinese-debao-pony
#10
X-X Liu, J-F Pan, Q-J Zhao, X-H He, Y-B Pu, J-L Han, Y-H Ma, L Jiang
The X chromosome shows a special interaction between demographic factors and genetic variation, and the analysis of X-linked genomic variation can therefore provide insights into the unique effects of demography and selection on the horse genome that cannot be readily detected by autosomal markers. Debao (DB) ponies have experienced intense selective pressure for the development of their small stature (<106 cm at adult height). To identify selective sweeps on the X chromosome of the DB pony, we performed a genome-wide scan of three Chinese horse breeds using an Equine SNP70 BeadChip...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29344347/epigenetic-alterations-in-tramp-mice-epigenome-dna-methylation-profiling-using-medip-seq
#11
Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29343623/identifying-dna-methylation-biomarkers-for-non-endoscopic-detection-of-barrett-s-esophagus
#12
Helen R Moinova, Thomas LaFramboise, James D Lutterbaugh, Apoorva Krishna Chandar, John Dumot, Ashley Faulx, Wendy Brock, Omar De la Cruz Cabrera, Kishore Guda, Jill S Barnholtz-Sloan, Prasad G Iyer, Marcia I Canto, Jean S Wang, Nicholas J Shaheen, Prashanti N Thota, Joseph E Willis, Amitabh Chak, Sanford D Markowitz
We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus...
January 17, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29343308/invited-review-genomic-selection-for-small-ruminants-in-developed-countries-how-applicable-for-the-rest-of-the-world
#13
R Mrode, G M Tarekegn, J M Mwacharo, A Djikeng
Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations...
January 18, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29343290/finemav-prioritizing-candidate-genetic-variants-driving-local-adaptations-in-human-populations
#14
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/29343239/calcium-dependent-protein-kinases-in-cotton-insights-into-early-plant-responses-to-salt-stress
#15
Wei Gao, Fu-Chun Xu, Dan-Dan Guo, Jing-Ruo Zhao, Ji Liu, Ya-Wei Guo, Prashant Kumar Singh, Xiao-Nan Ma, Lu Long, Jose Ramon Botella, Chun-Peng Song
BACKGROUND: Soil salinization is one of the major environmental constraints to plant growth and agricultural production worldwide. Signaling components involving calcium (Ca2+) and the downstream calcium-dependent protein kinases (CPKs) play key roles in the perception and transduction of stress signals. However, the study of CPKs in cotton and their functions in response to salt stress remain unexplored. RESULTS: A total of 98 predicted CPKs were identified from upland cotton (Gossypium hirsutum L...
January 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29342273/hypermethylation-of-eif4e-promoter-is-associated-with-early-onset-of-gastric-cancer
#16
Yuqiu Ge, Qin Wu, Gaoxiang Ma, Wei Shao, Hanting Liu, Qiang Zhang, Junyi Xin, Yao Xue, Mulong Du, Qinghong Zhao, Meilin Wang, Haiyan Chu, Zhengdong Zhang
Although gastric cancer (GC) in young adults (≤ 45 years) accounts for fewer than 10% of newly diagnosed cases, the young patients are more likely to have advanced disease at presentation compared with elderly patients. Previous studies have identified that the DNA methylation of genomes are different during aging. Our study aimed to explore the association between DNA methylation and the onset of GC. We applied Illumina HumanMethylation450 BeadChip to examine methylation expression profiles and compared methylation expression patterns in five early onset GC patients and seven elderly patients...
January 12, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29342241/ipat-intelligent-prediction-and-association-tool-for-genomic-research
#17
Chunpeng James Chen, Zhiwu Zhang
Summary: The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29339415/genome-wide-identification-by-transposon-insertion-sequencing-of-escherichia-coli-k1-genes-essential-for-in-vitro-growth-gastrointestinal-colonizing-capacity-and-survival-in-serum
#18
Alex J McCarthy, Richard A Stabler, Peter W Taylor
Escherichia coli K1 strains are major causative agents of invasive disease of the new born. The age dependency of infection can be reproduced in the neonatal rat. Colonization of the small intestine following oral administration of K1 bacteria leads rapidly to invasion of the blood circulation; bacteria that avoid capture by the mesenteric lymphatic system and evade antibacterial mechanisms in the blood may disseminate to cause organ-specific infections such as meningitis. Some E. coli K1 surface constituents, in particular the polysialic acid capsule, are known to contribute to invasive potential but a comprehensive picture of the factors that determine the fully virulent phenotype has not so far emerged...
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29337486/improving-risk-stratification-among-veterans-diagnosed-with-prostate-cancer-impact-of-the-17-gene-prostate-score-assay
#19
Julie A Lynch, Megan P Rothney, Raoul R Salup, Cesar E Ercole, Sharad C Mathur, David A Duchene, Joseph W Basler, Javier Hernandez, Michael A Liss, Michael P Porter, Jonathan L Wright, Michael C Risk, Mark Garzotto, Olga Efimova, Laurie Barrett, Brygida Berse, Michael J Kemeter, Phillip G Febbo, Atreya Dash
BACKGROUND: Active surveillance (AS) has been widely implemented within Veterans Affairs' medical centers (VAMCs) as a standard of care for low-risk prostate cancer (PCa). Patient characteristics such as age, race, and Agent Orange (AO) exposure may influence advisability of AS in veterans. The 17-gene assay may improve risk stratification and management selection. OBJECTIVES: To compare management strategies for PCa at 6 VAMCs before and after introduction of the Oncotype DX Genomic Prostate Score (GPS) assay...
January 2018: American Journal of Managed Care
https://www.readbyqxmd.com/read/29336373/advances-of-long-noncoding-rnas-mediated-regulation-in-reproduction
#20
REVIEW
Kang-Sheng Liu, Tai-Ping Li, Hua Ton, Xiao-Dong Mao, Ya-Jun Chen
OBJECTIVE: Advances in genomics and molecular biology have led to the discovery of a large group of uncharacterized long noncoding RNAs (lncRNAs). Emerging evidence indicated that many lncRNAs function in multiple biological processes and its dysregulation often causes diseases. Recent studies suggested that almost all regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression mainly on three levels, including epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling...
January 20, 2018: Chinese Medical Journal
keyword
keyword
21601
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"