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https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#1
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
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/28938685/a-case-control-study-of-the-association-between-the-egfr-gene-and-glioma-risk-in-a-chinese-han-population
#3
Mengdan Yan, Jingjie Li, Na He, Xugang Shi, Shuli Du, Bin Li, Tianbo Jin
The Epidermal Growth Factor Receptor gene has been reported to be involved in the progression of gliomas which is one of the deadliest primary brain tumors in humans. To determine potential association between EGFR and glioma risk, we performed a case-control study with 394 glioma patients and 298 cancer-free controls in which captured a total of 8 tag single nucleotide polymorphisms of EGFR gene from Xi'an, China. SPSS 19.0 statistical packages, χ(2) test, genetic model analysis and SHEsis software platform were analyzed s the variants in EGFR gene associations with glioma risk...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938673/quantitative-assessment-of-lncrna-hotair-polymorphisms-and-cancer-risk-in-chinese-population-a-meta-analysis-based-on-26-810-subjects
#4
Xu Liu, Qiongyu Duan, Jian Zhang
As a well-known long non-coding RNA, HOTAIR has been demonstrated to be involved in carcinogenesis and progression of various human cancers. Previous studies have investigated the potential association between HOTAIR polymorphisms and cancer risk in Chinese population. However, the results remain conflicting. Therefore, for the first time, we conducted a meta-analysis to derive a more precise estimation of these associations for Chinese. PubMed, Embase, CNKI and Wanfang databases were systematically searched...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938654/methylenetetrahydrofolate-reductase-c677t-polymorphism-and-the-risks-of-polycystic-ovary-syndrome-an-updated-meta-analysis-of-14-studies
#5
Lihong Wang, Wenting Xu, Caihong Wang, Mengyu Tang, Yujia Zhou
Some studies have reported an association between the Methylenetetrahydrofolate reductase (MTHFR) C667T genetic variant and risk of polycystic ovary syndrome (PCOS), although the results remain controversial. A systematic search was conducted on PubMed, Web of Science, EMBASE, Ovid, Chinese National Knowledge Databases and WanFang databases with relevant keywords. Fourteen studies of sixteen distinct populations involving 1478 PCOS cases and used to conduct a meta-analysis. The T allele was not significantly associated with increased risk of PCOS [OR: 1...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938645/sex-specific-association-of-sh2b3-and-smarca4-polymorphisms-with-coronary-artery-disease-susceptibility
#6
Yuqiang Ji, Yanbin Song, Qingwen Wang, Pengcheng Xu, Zhao Zhao, Xia Li, Nan Wang, Tianbo Jin, Chao Chen
To determine whether sex differences affect the association between genetic polymorphisms and coronary artery disease (CAD) in the Chinese Han population, we conducted a study comparing the frequency of SH2B3 and SMARCA4 variants in 456 CAD patients (291 men, 165 women) and 685 age-matched controls (385 men, 300 women). Ten single nucleotide polymorphisms (SNPs) in SH2B3 and SMARCA4 were genotyped using MassARRAY technology. Allelic and genotypic models and haplotype frequencies were compared between groups...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938640/association-of-two-obesity-related-gene-polymorphisms-lepg2548a-rs7799039-and-leprq223r-rs1137101-with-the-risk-of-breast-cancer
#7
Hui Luan, Hong Zhang, Ying Li, Ping Wang, Lifei Cao, Honglan Ma, Qing Cui, Gang Tian
Many studies have been performed to investigate the correlation of leptin (LEP) and leptin receptor (LEPR) polymorphisms with breast cancer (BC) risk, however the results are inconclusive. To obtain a more precise estimation, we conducted this meta-analysis. We searched PubMed, EMBASE, and Web of Science databases to identify qualified studies. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the association. Eight eligible studies (2,124 cases and 5,476 controls) for LEP G2548A (rs7799039) polymorphism, and thirteen studies (5,282 cases and 6,140 controls) for LEPR Q223R (rs1137101) polymorphism were included in our study...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938607/hgfl-mediated-ron-signaling-supports-breast-cancer-stem-cell-phenotypes-via-activation-of-non-canonical-%C3%AE-catenin-signaling
#8
Sasha J Ruiz-Torres, Nancy M Benight, Rebekah A Karns, Elyse E Lower, Jun-Lin Guan, Susan E Waltz
Breast cancer stem cells (BCSCs), which drive tumor progression, recurrence, and metastasis, are considered a major challenge for breast cancer treatments, thus the discovery of novel pathways regulating BCSC maintenance remains essential to develop new strategies to effectively target this population and combat disease mortality. The HGFL-RON signaling is overexpressed in human breast cancers and is associated with increased breast cancer progression, metastasis, and poor prognosis. Here, we report that overexpression of RON/MST1R and HGFL/MST1 in cell lines and primary tumors increases BCSC self-renewal, numbers, and tumorigenic potential after syngeneic transplantation...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938557/the-p-g534e-variant-of-habp2-is-not-associated-with-sporadic-papillary-thyroid-carcinoma-in-a-polish-population
#9
Artur Kowalik, Danuta Gąsior-Perczak, Martyna Gromek, Monika Siołek, Agnieszka Walczyk, Iwona Pałyga, Małgorzata Chłopek, Janusz Kopczyński, Ryszard Mężyk, Aldona Kowalska, Stanisław Góźdź
Thyroid cancer is one of the most frequently diagnosed cancers of the endocrine system. There are no known genetic risk factors for non-medullary thyroid cancer, other than a small number of hereditary syndromes; however, approximately 5% of non-medullary thyroid cancer, designated familial non-medullary thyroid cancer, exhibits heritability. The p.G534E (c.1601G>A) variant of HABP2 was recently reported as a risk factor for familial non-medullary thyroid cancer, including papillary thyroid carcinoma. We analyzed the incidence of the c...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938451/antibody-mediated-targeting-of-the-fgfr1c-isoform-increases-glucose-uptake-in-white-and-brown-adipose-tissue-in-male-mice
#10
Jo E Lewis, Ricardo J Samms, Scott Cooper, Jeni C Luckett, Alan C Perkins, James D Dunbar, Dennis P Smith, Paul J Emmerson, Andrew C Adams, Francis J P Ebling, Kostas Tsintzas
The increased prevalence of obesity and its cardiometabolic implications demonstrates the imperative to identify novel therapeutic targets able to effect meaningful metabolic changes in this population. Antibody-mediated targeting of fibroblast growth factor receptor 1c isoform (FGFR1c) has been shown to ameliorate hyperglycaemia and protect from diet- and genetically-induced obesity in rodents and non-human primates. However, it is currently unknown which tissue(s) contribute to this glucose lowering effect...
August 16, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938159/lunatic-fringe-and-p53-cooperatively-suppress-mesenchymal-stem-like-breast-cancer
#11
Wen-Cheng Chung, Shubing Zhang, Lavanya Challagundla, Yunyun Zhou, Keli Xu
Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology...
September 19, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28938152/comparison-of-manual-and-automated-ampliseq%C3%A2-workflows-in-the-typing-of-a-somali-population-with-the-precision-id-identity-panel
#12
Suzanne van der Heijden, Susanne Juel de Oliveira, Marie-Louise Kampmann, Claus Børsting, Niels Morling
The Precision ID Identity Panel was used to type 109 Somali individuals in order to obtain allele frequencies for the Somali population. These frequencies were used to establish a Somali HID-SNP database, which will be used for the biostatistic calculations in family and immigration cases. Genotypes obtained with the Precision ID Identity Panel were found to be almost in complete concordance with genotypes obtained with the SNPforID PCR-SBE-CE assay. In seven SNP loci, silent alleles were identified, of which most were previously described in the literature...
September 14, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28938133/genetic-polymorphisms-for-19-x-str-loci-of-sichuan-han-ethnicity-and-its-comparison-with-chinese-populations
#13
Guanglin He, Ye Li, Xing Zou, Mengge Wang, Pengyu Chen, Miao Liao, Jin Wu
X-chromosomal short tandem repeats (X-STRs) can be serviced as a complementary tool in forensic deficiency cases and other complicated kinship identification. To investigate the genetic variation of the western Chinese Han population, genetic polymorphisms of 19 X-STR loci (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074 and DXS10135) included in the AGCU X19 PCR amplification kit were obtained from 201 Chinese Han individuals (108 females and 93 males) residing in Sichuan province, western China...
September 15, 2017: Legal Medicine
https://www.readbyqxmd.com/read/28938023/exploration-of-genetic-architecture-through-sib-ship-reconstruction-in-advanced-breeding-population-of-eucalyptus-nitens
#14
Jaroslav Klápště, Mari Suontama, Emily Telfer, Natalie Graham, Charlie Low, Toby Stovold, Russel McKinley, Heidi Dungey
Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population...
2017: PloS One
https://www.readbyqxmd.com/read/28937887/characteristics-and-associated-comorbidities-of-pediatric-dental-patients-treated-under-general-anesthesia
#15
Alexandra Delfiner, Aaron Myers, Christie Lumsden, Steve Chussid, Richard Yoon
OBJECTIVE: To describe characteristics and identify common comorbidities of children receiving dental treatment under general anesthesia at Children's Hospital of New York-Presbyterian. STUDY DESIGN: Electronic medical records of all children that received dental treatment under general anesthesia through the Division of Pediatric Dentistry from 2012-2014 were reviewed. Data describing patient characteristics (age, sex, race/ethnicity, insurance carrier, and American Society of Anesthesiologists physical status classification system), medical history, and justification for treatment were collected...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28937819/should-i-change-or-should-i-go-phenotypic-plasticity-and-matching-habitat-choice-in-the-adaptation-to-environmental-heterogeneity
#16
Pim Edelaar, Roger Jovani, Ivan Gomez-Mestre
It can be challenging for organisms to achieve a good match between their phenotypic characteristics and environmental requirements that vary in space and time. The evolution of adaptive phenotypes can result from genetic differentiation at the population level. Individuals, however, could also change their phenotype (adaptive plasticity) or select an environment because it matches with their phenotype (matching habitat choice). It is poorly known under which conditions these different solutions to environmental heterogeneity evolve and whether they operate together...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937818/divorce-in-an-island-bird-population-causes-consequences-and-lack-of-inheritance
#17
Nathaniel T Wheelwright, Céline Teplitsky
Divorce (mate switching) is widely considered an adaptive strategy that female birds use to improve their reproductive success. However, in few species are the causes and consequences of divorce well understood, and the genetic basis and inheritance of divorce have never been explored. In Savannah sparrows (Passerculus sandwichensis) breeding on Kent Island, New Brunswick, Canada, 47.0% of pairs in which both partners survived to the following breeding season ended in divorce. Secondary females, which received less parental assistance than primary females, tended to divorce when breeding success was low or when paired with small males...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937817/sanctions-partner-recognition-and-variation-in-mutualism
#18
Jeremy B Yoder, Peter Tiffin
Mutualistic interactions can be stabilized against invasion by noncooperative individuals by putting such "cheaters" at a selective disadvantage. Selection against cheaters should eliminate genetic variation in partner quality-yet such variation is often found in natural populations. One explanation for this paradox is that mutualism outcomes are determined not only by responses to partner performance but also by partner signals. Here, we build a model of coevolution in a symbiotic mutualism, in which hosts' ability to sanction noncooperative symbionts and recognition of symbiont signals are determined by separate loci, as are symbionts' cooperation and expression of signals...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937812/predator-perspective-drives-geographic-variation-in-frequency-dependent-polymorphism
#19
Iris A Holmes, Maggie R Grundler, Alison R Davis Rabosky
Color polymorphism in natural populations can manifest as a striking patchwork of phenotypes in space, with neighboring populations characterized by dramatic differences in morph composition. These geographic mosaics can be challenging to explain in the absence of localized selection because they are unlikely to result from simple isolation-by-distance or clinal variation in selective regimes. To identify processes that can lead to the formation of geographic mosaics, we developed a simulation-based model to explore the influence of predator perspective, selection, migration, and genetic linkage of color loci on allele frequencies in polymorphic populations over space and time...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937811/maladaptive-plasticity-masks-the-effects-of-natural-selection-in-the-red-shouldered-soapberry-bug
#20
Meredith L Cenzer
Natural selection can produce local adaptation, but local adaptation can be masked by maladaptive plasticity. Maladaptive plasticity may arise as a result of gene flow producing novel gene combinations that have not been exposed to selection. In the 1980s, populations of the red-shouldered soapberry bug (Jadera haematoloma) were locally adapted to feed on the seeds of a native host plant and an introduced host plant; by 2014, local differentiation in beak length had been lost, likely as a consequence of increased gene flow...
October 2017: American Naturalist
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