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population genome

Ilana E Green, Shareena A Rahman, Debra L Owens, Michèle M Sale, Lillian J Currie, Keith L Keene, Bradford B Worrall, Andrew M Southerland
BACKGROUND AND PURPOSE: The majority of published data in cervical artery dissection (CeAD), a common cause of stroke in young adults, derive from populations of European ancestry (EA), including a recent genome-wide study identifying an association with the rs9349379 polymorphism of the PHACTR1 gene. Little is known about CeAD in individuals of African ancestry (AA) despite robust epidemiological data showing increased risk of stroke at younger ages. We hypothesize that AA patients with CeAD have different epidemiology and clinical profiles compared to those of EA, and a different genetic architecture related to rs9349379 of the PHACTR1 gene...
December 5, 2018: Cerebrovascular Diseases
Lex Flagel, Yaniv Brandvain, Daniel R Schrider
Population-scale genomic datasets have given researchers incredible amounts of information from which to infer evolutionary histories. Concomitant with this flood of data, theoretical and methodological advances have sought to extract information from genomic sequences to infer demographic events such as population size changes and gene flow among closely related populations/species, construct recombination maps, and uncover loci underlying recent adaptation. To date most methods make use of only one or a few summaries of the input sequences and therefore ignore potentially useful information encoded in the data...
December 4, 2018: Molecular Biology and Evolution
Salvatore Mastrangelo, Filippo Biscarini, Marco Tolone, Barbara Auzino, Marco Ragatzu, Andrea Spaterna, Roberta Ciampolini
The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain uncharacterized. Braque Français type Pyrénées (BRA) is a dog breed originating from a very old type of gun-dog used for pointing the location of game birds to hunters...
2018: PloS One
Rabin Kadariya, Michito Shimozuru, Jesús E Maldonado, Mohamed Abdallah Mohamed Moustafa, Mariko Sashika, Toshio Tsubota
Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies...
2018: PloS One
Gaurav Thareja, Sweety Mathew, Lisa S Mathew, Yasmin Ali Mohamoud, Karsten Suhre, Joel A Malek
Understanding the genetic diversity in a crop population is key to its targeted breeding for desired traits, such as higher yields, better fruit quality and resistance to disease and changing climates. Date fruits represent a major crop in the Middle East and are key to achieving future food independence in arid countries like Qatar. We previously determined the genome of the date palm Phoenix dactylifera and showed that date palm trees world-wide divide into two distinct subpopulations of Eastern and Western origins...
2018: PloS One
Farid Rajabli, Briseida E Feliciano, Katrina Celis, Kara L Hamilton-Nelson, Patrice L Whitehead, Larry D Adams, Parker L Bussies, Clara P Manrique, Alejandra Rodriguez, Vanessa Rodriguez, Takiyah Starks, Grace E Byfield, Carolina B Sierra Lopez, Jacob L McCauley, Heriberto Acosta, Angel Chinea, Brian W Kunkle, Christiane Reitz, Lindsay A Farrer, Gerard D Schellenberg, Badri N Vardarajan, Jeffery M Vance, Michael L Cuccaro, Eden R Martin, Jonathan L Haines, Goldie S Byrd, Gary W Beecham, Margaret A Pericak-Vance
The ApoE ε4 allele is the most significant genetic risk factor for late-onset Alzheimer disease. The risk conferred by ε4, however, differs across populations, with populations of African ancestry showing lower ε4 risk compared to those of European or Asian ancestry. The cause of this heterogeneity in risk effect is currently unknown; it may be due to environmental or cultural factors correlated with ancestry, or it may be due to genetic variation local to the ApoE region that differs among populations. Exploring these hypotheses may lead to novel, population-specific therapeutics and risk predictions...
December 2018: PLoS Genetics
Harold C Slavkin
In anticipation of a major transformation in healthcare, this review provides highlights that anticipate the near future for oral public health (and beyond). Personalized or precision healthcare reflects the expectation that advances in genomics, imaging, and other domains will extend our risk assessment, diagnostic, and prognostic capabilities, and enables more effective prevention and therapeutic options for all Americans. Meanwhile, the current healthcare system does not meet cost, access, or quality criteria for all Americans...
December 5, 2018: Journal of Public Health Dentistry
Cecilia Chao, Lakshmi Akileswaran, Jessica N Cooke Bailey, Mark Willcox, Russell Van Gelder, Carol Lakkis, Fiona Stapleton, Kathryn Richdale
Purpose: The purpose of this study was to explore differences in genotype, ocular surface microbiome, tear inflammatory markers, and environmental and behavioral exposures in soft contact lens (SCL) wearers with and without a history of corneal infiltrative events (CIEs). Methods: Nine SCL wearers with a recent CIE and nine age-, sex-, and SCL material- and modality-matched controls were enrolled. The Contact Lens Risk Survey, slit-lamp examination data, basal tears, conjunctival microbial cultures, and peripheral blood samples were collected...
December 3, 2018: Investigative Ophthalmology & Visual Science
Jennifer Pugh, Sikandar G Khan, Deborah Tamura, Alisa M Goldstein, Maria Teresa Landi, John J DiGiovanna, Kenneth H Kraemer
Importance: Wide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations. Objective: To correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease. Design, Setting, and Participants: Xeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP...
December 5, 2018: JAMA Dermatology
Annarita Marrano, Pedro J Martínez-García, Luca Bianco, Gina M Sideli, Erica A Di Pierro, Charles A Leslie, Kristian A Stevens, Marc W Crepeau, Michela Troggio, Charles H Langley, David B Neale
Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9...
November 22, 2018: Plant Biotechnology Journal
Amir Tajbakhsh, Fahimeh Afzal Javan, Mahdi Rivandi, Atefeh Moezzi, Soheila Abedini, Mahla Asghari, Zahra Farjami, Hosein Soltanian, Fatemeh Homaei Shandiz, Mohammad Mahdi Kooshyar, Alireza Pasdar
Genome-wide association studies normally focus on low penetrance and moderate to high-frequency single nucleotide polymorphisms (SNPs), which lead to genetic susceptibility to breast cancer. In this regard, the T allele of rs3803662 has been associated with breast cancer risk and with lower expression level of TOX3. We aimed to assess the risk of breast cancer associated with this polymorphism in an Iranian population. Using Tetra Primer ARMS PCR, rs3803662 was analyzed in a total of 943 individuals (430 cases and 513 healthy controls form North East of Iran)...
December 4, 2018: Molecular Biology Reports
Natalia M Gonzales, Jungkyun Seo, Ana I Hernandez Cordero, Celine L St Pierre, Jennifer S Gregory, Margaret G Distler, Mark Abney, Stefan Canzar, Arimantas Lionikas, Abraham A Palmer
The LG/J x SM/J advanced intercross line of mice (LG x SM AIL) is a multigenerational outbred population. High minor allele frequencies, a simple genetic background, and the fully sequenced LG and SM genomes make it a powerful population for genome-wide association studies. Here we use 1,063 AIL mice to identify 126 significant associations for 50 traits relevant to human health and disease. We also identify thousands of cis- and trans-eQTLs in the hippocampus, striatum, and prefrontal cortex of ~200 mice. We replicate an association between locomotor activity and Csmd1, which we identified in an earlier generation of this AIL, and show that Csmd1 mutant mice recapitulate the locomotor phenotype...
December 4, 2018: Nature Communications
Pierre Zalloua, Catherine J Collins, Anna Gosling, Simone Andrea Biagini, Benjamí Costa, Olga Kardailsky, Lorenzo Nigro, Wissam Khalil, Francesc Calafell, Elizabeth Matisoo-Smith
Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza...
December 4, 2018: Scientific Reports
Daniel Golparian, Valentina Donà, Leonor Sánchez-Busó, Sunniva Foerster, Simon Harris, Andrea Endimiani, Nicola Low, Magnus Unemo
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day...
December 4, 2018: Scientific Reports
Mao-Lun Weng, Claude Becker, Julia Hildebrandt, Matthew T Rutter, Ruth G Shaw, Detlef Weigel, Charles B Fenster
Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A...
December 4, 2018: Genetics
Ehsan Ullah, Raghvendra Mall, Mostafa M Abbas, Khalid Kunji, Alejandro Q Nato, Halima Bensmail, Ellen M Wijsman, Mohamad Saad
Genotype imputation is widely used in genome-wide association studies to boost variant density, allowing increased power in association testing. Many studies currently include pedigree data due to increasing interest in rare variants coupled with the availability of appropriate analysis tools. The performance of population-based (subjects are unrelated) imputation methods is well established. However, the performance of family- and population-based imputation methods on family data has been subject to much less scrutiny...
December 4, 2018: Genome Research
Binliang Liu, Tao An, Meiying Li, Zongbi Yi, Chunxiao Li, Xiaoying Sun, Xiuwen Guan, Lixi Li, Yanfeng Wang, Yuhui Zhang, Binghe Xu, Fei Ma, Yixin Zeng
BACKGROUND: An increasing number of cancer patients die of cardiovascular diseases. The cardiotoxicity of chemotherapy is particularly important in triple-negative breast cancer (TNBC) with limited therapeutic options. Cardiac autophagy is an important mechanism of cardiotoxicity. This research was aimed to investigate the cardiotoxicity of chemotherapy in TNBC, screen the susceptible population, and determine the relationship between cardiotoxicity and autophagy-related polymorphisms...
December 4, 2018: Cancer communications
Helena Štorchová, James D Stone, Daniel B Sloan, Oushadee A J Abeyawardana, Karel Müller, Jana Walterová, Marie Pažoutová
BACKGROUND: Silene vulgaris (bladder campion) is a gynodioecious species existing as two genders - male-sterile females and hermaphrodites. Cytoplasmic male sterility (CMS) is generally encoded by mitochondrial genes, which interact with nuclear fertility restorer genes. Mitochondrial genomes of this species vary in DNA sequence, gene order and gene content. Multiple CMS genes are expected to exist in S. vulgaris, but little is known about their molecular identity. RESULTS: We assembled the complete mitochondrial genome from the haplotype KRA of S...
December 4, 2018: BMC Genomics
Florian Herry, Frédéric Hérault, David Picard Druet, Amandine Varenne, Thierry Burlot, Pascale Le Roy, Sophie Allais
BACKGROUND: The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix® Axiom® HD genotyping array) for chicken has enabled the implementation of genomic selection in layer and broiler breeding, but the genotyping costs remain high for a routine use on a large number of selection candidates. It has thus been deemed interesting to develop a low density genotyping chip that would induce lower costs...
December 4, 2018: BMC Genetics
Takanori Yoshida, Yoshiaki Tarutani, Tetsuji Kakutani, Akira Kawabe
Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing...
December 3, 2018: Genes
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