keyword
MENU ▼
Read by QxMD icon Read
search

Genomic selection

keyword
https://www.readbyqxmd.com/read/28938747/prevalence-of-endocrine-and-genetic-abnormalities-in-boys-evaluated-systematically-for-a-disorder-of-sex-development
#1
R Nixon, V Cerqueira, A Kyriakou, A Lucas-Herald, J McNeilly, M McMillan, A I Purvis, E S Tobias, R McGowan, S F Ahmed
STUDY QUESTION: What is the likelihood of identifying genetic or endocrine abnormalities in a group of boys with 46, XY who present to a specialist clinic with a suspected disorder of sex development (DSD)? SUMMARY ANSWER: An endocrine abnormality of the gonadal axis may be present in a quarter of cases and copy number variants (CNVs) or single gene variants may be present in about half of the cases. WHAT IS KNOWN ALREADY: Evaluation of 46, XY DSD requires a combination of endocrine and genetic tests but the prevalence of these abnormalities in a sufficiently large group of boys presenting to one specialist multidisciplinary service is unclear...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#2
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#3
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938601/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#4
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938564/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#5
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938549/long-non-coding-rnas-may-serve-as-biomarkers-in-breast-cancer-combined-with-primary-lung-cancer
#6
Xianfeng Ding, Yuhan Zhang, Hongjian Yang, Weimin Mao, Bo Chen, Shifeng Yang, Xiaowen Ding, Dehong Zou, Wenju Mo, Xiangming He, Xiping Zhang
Long non-coding RNAs (lncRNAs) have been shown to play important regulatory role in certain type of cancers biology, including breast and lung cancers. However, the lncRNA expression in breast cancer combined with primary lung cancer remains unknown. In this study, databases of the Cancer Genome Atlas (TCGA) and the lncRNA profiler of contained candidate 192 lncRNAs were utilized. 11 lncRNAs were differentially expressed in breast cancer, 9 candidate lncRNAs were differentially expressed in lung cancer. In order to find the aberrant expression of lncRNAs in breast cancer combined with primary lung cancer, seven samples of primary breast cancer and lung cancer were studied for the expression of selected lncRNAs...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938163/tumor-cell-targeted-delivery-of-crispr-cas9-by-aptamer-functionalized-lipopolymer-for-therapeutic-genome-editing-of-vegfa-in-osteosarcoma
#7
Chao Liang, Fangfei Li, Luyao Wang, Zong-Kang Zhang, Chao Wang, Bing He, Jie Li, Zhihao Chen, Atik Badshah Shaikh, Jin Liu, Xiaohao Wu, Songlin Peng, Lei Dang, Baosheng Guo, Xiaojuan He, D W T Au, Cheng Lu, Hailong Zhu, Bao-Ting Zhang, Aiping Lu, Ge Zhang
Osteosarcoma (OS) is a highly aggressive pediatric cancer, characterized by frequent lung metastasis and pathologic bone destruction. Vascular endothelial growth factor A (VEGFA), highly expressed in OS, not only contributes to angiogenesis within the tumor microenvironment via paracrine stimulation of vascular endothelial cells, but also acts as an autocrine survival factor for tumor cell themselves, thus making it a promising therapeutic target for OS. CRISPR/Cas9 is a versatile genome editing technology and holds tremendous promise for cancer treatment...
September 13, 2017: Biomaterials
https://www.readbyqxmd.com/read/28938123/reconstructing-prehistoric-african-population-structure
#8
Pontus Skoglund, Jessica C Thompson, Mary E Prendergast, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Tasneem Salie, Nadin Rohland, Swapan Mallick, Alexander Peltzer, Anja Heinze, Iñigo Olalde, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica I Cerezo-Román, Chrissy Chiumia, Alison Crowther, Elizabeth Gomani-Chindebvu, Agness O Gidna, Katherine M Grillo, I Taneli Helenius, Garrett Hellenthal, Richard Helm, Mark Horton, Saioa López, Audax Z P Mabulla, John Parkington, Ceri Shipton, Mark G Thomas, Ruth Tibesasa, Menno Welling, Vanessa M Hayes, Douglas J Kennett, Raj Ramesar, Matthias Meyer, Svante Pääbo, Nick Patterson, Alan G Morris, Nicole Boivin, Ron Pinhasi, Johannes Krause, David Reich
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28937854/probiotics-from-isolation-to-application
#9
Parisa Shokryazdan, Mohammad Faseleh Jahromi, Juan Boo Liang, Yin Wan Ho
Probiotics have become highly recognized as supplements for humans and animals because of their beneficial effects on health and well-being. The present review aims to provide an overview of different steps through which microbial strains become applicable probiotics in food and/or feed industries. Isolation of potential probiotic strains is the first step. Lactic acid bacteria are the most frequently used microorganisms as probiotics, which can be isolated from human, animal, plant, and environment. The next steps are identification of the isolates and characterization of them based on the main selection criteria for any potential probiotic microorganism, including resistance to gastric acidity and bile salt, adherence to mucus and/or intestinal epithelial cells and cell lines, and antimicrobial and antagonism activity against potentially pathogenic microbes...
September 22, 2017: Journal of the American College of Nutrition
https://www.readbyqxmd.com/read/28936979/advances-of-selectable-marker-genes-in-plastid-genetic-engineering
#10
Yong He, An Luo, Lian-Sheng Mu, Qiang Chen, Yan Zhang, Kai-Wun Yeh, Zhi-Hong Tian
Plastid genetic engineering is a safer, more precise, and more efficient transgene expression system than the nuclear genetic transformation system. It has been widely used in basic research and biotechnology applications as the next-generation transgenic technology in plants. Similar to nuclear genetic transformation, selection markers are needed in plastid genetic engineering to identify 'true' transformants and acquire homoplasmy. Because of the high copy number of plastids, maternal inheritance of the plastid genome, and the long process of homogenization of transplastomic plants, the selection markers for plastid genetic engineering are different from those used in the nuclear transformation system...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28936945/sources-of-fungal-genetic-variation-and-associating-it-with-phenotypic-diversity
#11
John W Taylor, Sara Branco, Cheng Gao, Chris Hann-Soden, Liliam Montoya, Iman Sylvain, Pierre Gladieux
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability...
September 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28936814/-the-role-of-molecular-karyotyping-in-the-genetic-etiology-of-autism
#12
Burcu Özbaran, Bilçağ Akgün, Duygu Kaçamak, Sezen Köse, Ayşenur Kavasoğlu, Hüseyin Onay
OBJECTIVE: The aim of this study was to investigate the deletions and duplications with a molecular karyotyping technique and to elucidate the etiology of autism. METHOD: A total of 31 patients (20 boys and 11 girls) between 4 to 18 years old with normal chromosomal analysis and no Fragile X mutation were diagnosed in the Ege University Child and Adolescent Psychiatry Clinic with autism (according to DSM-IV-TR criteria) and were enrolled in the study. Symptom severity of the patients was evaluated with a Childhood Autism Rating Scale...
2017: Türk Psikiyatri Dergisi, Turkish Journal of Psychiatry
https://www.readbyqxmd.com/read/28936670/agrobacterium-mediated-sorghum-transformation
#13
Emily Wu, Zuo-Yu Zhao
Agrobacterium-mediated plant transformation is commonly used in crop genome modification. An optimized sorghum transformation protocol we developed is described here. Using this protocol, the transformation frequency of sorghum inbred TX430 is over 10% with Agrobacterium strain LBA4404 and 33% with Agrobacterium strain AGL1. Two different selection marker genes, moPAT and PMI, were used in this protocol.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28936114/practical-application-of-genomic-selection-in-a-doubled-haploid-winter-wheat-breeding-program
#14
Jiayin Song, Brett F Carver, Carol Powers, Liuling Yan, Jaroslav Klápště, Yousry A El-Kassaby, Charles Chen
Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28935691/insights-into-ddt-resistance-from-the-drosophila-melanogaster-genetic-reference-panel
#15
Joshua M Schmidt, Paul Battlay, Rebecca S Gledhill-Smith, Robert T Good, Chris Lumb, Alexandre Fournier-Level, Charles Robin
Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in Drosophila melanogaster, however only the Cyp6g1 locus has previously been shown to be relevant to field populations...
September 21, 2017: Genetics
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#16
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28934964/comprehensive-benchmarking-and-ensemble-approaches-for-metagenomic-classifiers
#17
Alexa B R McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J Prill, Elizabeth Hénaff, Noah Alexander, Samuel S Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R Colwell, Gail L Rosen, Christopher E Mason
BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934948/multi-breed-genomic-prediction-using-bayes-r-with-sequence-data-and-dropping-variants-with-a-small-effect
#18
Irene van den Berg, Phil J Bowman, Iona M MacLeod, Ben J Hayes, Tingting Wang, Sunduimijid Bolormaa, Mike E Goddard
BACKGROUND: The increasing availability of whole-genome sequence data is expected to increase the accuracy of genomic prediction. However, results from simulation studies and analysis of real data do not always show an increase in accuracy from sequence data compared to high-density (HD) single nucleotide polymorphism (SNP) chip genotypes. In addition, the sheer number of variants makes analysis of all variants and accurate estimation of all effects computationally challenging. Our objective was to find a strategy to approximate the analysis of whole-sequence data with a Bayesian variable selection model...
September 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28934946/genome-wide-snp-data-unveils-the-globalization-of-domesticated-pigs
#19
Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P M A Crooijmans, Natalia Zinovieva, Lawrence B Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A M Groenen, Lusheng Huang, Hendrik-Jan Megens
BACKGROUND: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection...
September 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28934931/mitochondrial-genomes-of-african-pangolins-and-insights-into-evolutionary-patterns-and-phylogeny-of-the-family-manidae
#20
Zelda du Toit, Morné du Plessis, Desiré L Dalton, Raymond Jansen, J Paul Grobler, Antoinette Kotzé
BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P...
September 21, 2017: BMC Genomics
keyword
keyword
9513
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"