Genomes and Genes
Summary: Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
Publications101 found, 100 shown here
- Moretti T, Just R, Kehl S, Willis L, Buckleton J, Bright J, et al. Internal validation of STRmixâ„¢ for the interpretation of single source and mixed DNA profiles. Forensic Sci Int Genet. 2017;29:126-144 pubmed publisher..This comprehensive evaluation provides a model in accordance with SWGDAM recommendations for internal validation of a probabilistic genotyping system for DNA evidence interpretation. ..
- Zaidi S, Hameed A, Ali N, Umair M, Alam M, Rana M, et al. A measles outbreak in Sindh, Pakistan caused by a genotype B3 virus. Arch Virol. 2017;162:3603-3610 pubmed publisher..This is the first report on the phylogenetic analysis of measles B3 genotype strains from Pakistan and highlights the need for strengthening the surveillance systems and improving immunization coverage across the country. ..
- Persad P, Heid I, Weeks D, Baird P, de Jong E, Haines J, et al. Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1. Invest Ophthalmol Vis Sci. 2017;58:4027-4038 pubmed publisher..0020, OR = 2.17, 95% CI = 1.34-3.60). These results show that joint tests of main effects and gene-gene interaction reveal associations at some novel loci that were missed when considering main effects alone. ..
- Doukali H, Ben Salah G, Ben Rhouma B, Hajjaji M, Jaouadi A, Belguith Mahfouth N, et al. Cytogenetic monitoring of hospital staff exposed to ionizing radiation: optimize protocol considering DNA repair genes variability. Int J Radiat Biol. 2017;93:1283-1288 pubmed publisher..Paradoxically, these variants are not associated with the severity of damages, according to used assays, in the studied cohort of Tunisian population, unlike other studies. ..
- Zhou Y, Simpson S, Charlesworth J, van der Mei I, Lucas R, Ponsonby A, et al. Variation within MBP gene predicts disease course in multiple sclerosis. Brain Behav. 2017;7:e00670 pubmed publisher..Our results provide novel insights into the role of genetic variation within the MBP gene predicting MS clinical course, both directly and by interaction with known environmental MS risk factors. ..
- Hurtado A, Alonso E, Aspiritxaga I, López Etxaniz I, Ocabo B, Barandika J, et al. Environmental sampling coupled with real-time PCR and genotyping to investigate the source of a Q fever outbreak in a work setting. Epidemiol Infect. 2017;145:1834-1842 pubmed publisher..These results confirmed the link between the goat farm and the outbreak and allowed the identification of the source of infection. The circumstances and possible vehicles for the bacteria entering the factory are discussed...
- Opiro R, Saarman N, Echodu R, Opiyo E, Dion K, Halyard A, et al. Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control. PLoS Negl Trop Dis. 2017;11:e0005485 pubmed publisher..Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control...
- HoltkÃ¶tter H, Beyer V, Schwender K, Glaub A, Johann K, SchÃ¼renkamp M, et al. Independent validation of body fluid-specific CpG markers and construction of a robust multiplex assay. Forensic Sci Int Genet. 2017;29:261-268 pubmed publisher..The main advantage of using DNA methylation assays over alternative tests is that it can be applied at a later time point in the investigative process since testing is possible even after DNA analysis. ..
- Qin N, Wang C, Lu Q, Huang T, Zhu M, Wang L, et al. A cis-eQTL genetic variant of the cancer-testis gene CCDC116 is associated with risk of multiple cancers. Hum Genet. 2017;136:987-997 pubmed publisher..Moreover, our findings suggest that low abundance expression of CT genes in normal tissues may also contribute to tumorigenesis, providing a new mechanism of CT genes in the development of cancer. ..
- Xu J, Boström A, Saeed M, Dubey R, Waeber G, Vollenweider P, et al. A genetic variant in the catechol-O-methyl transferase (COMT) gene is related to age-dependent differences in the therapeutic effect of calcium-channel blockers. Medicine (Baltimore). 2017;96:e7029 pubmed publisher..08 mm Hg, P?=?.0005).These results underline the important role of estrogens and catecholamines in hypertension and the importance of genotype dependent, age-related adjustments of calcium-channel blocker treatment. ..
- Ray N, Li T, Lin Z, Protack T, van Ham P, Hwang C, et al. The Second-Generation Maturation Inhibitor GSK3532795 Maintains Potent Activity Toward HIV Protease Inhibitor-Resistant Clinical Isolates. J Acquir Immune Defic Syndr. 2017;75:52-60 pubmed publisher..This finding supports continued development of GSK3532795 in treatment-experienced patients with or without previous PI therapy. ..
- Li Y, Li C, Yang Y, Shi L, Tao W, Liu S, et al. The association of six single nucleotide polymorphisms and their haplotypes in CDH13 with T2DM in a Han Chinese population. Medicine (Baltimore). 2017;96:e7063 pubmed publisher..These results highlight the need to study the functional effects of these CDH13 gene variants in relation to the risk of developing T2DM. ..
- Reinartz S, Distl O. Breeding experiments and genome-wide association analysis elucidate two genetically different forms of non-syndromic congenital cleft lip and jaw in Vorderwald × Montbéliarde cattle. Anim Genet. 2017;48:523-530 pubmed publisher..095, BTA4) and 6/346 (0.017, BTA29) homozygous mutant genotypes. Further studies should elucidate the responsible mutations underlying the different types of CLJ in Vorderwald × Montbéliarde cattle. ..
- Bokore F, Cuthbert R, Knox R, Randhawa H, Hiebert C, DePauw R, et al. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes. Theor Appl Genet. 2017;130:2617-2635 pubmed publisher..Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada. ..
- Morishige D, Klein P, Hilley J, Sahraeian S, Sharma A, Mullet J. Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome. BMC Genomics. 2013;14:448 pubmed publisher..DG in combination with whole genome resequencing is dramatically accelerating all aspects of genetic analysis of sorghum, an important genetic reference for C4 grass species. ..
- Fan Y, Song Y. PyHLA: tests for the association between HLA alleles and diseases. BMC Bioinformatics. 2017;18:90 pubmed publisher..PyHLA is implemented in Python. PyHLA is a free, open source software distributed under the GPLv2 license. The source code, tutorial, and examples are available at https://github.com/felixfan/PyHLA. ..
- SchÃ¶fl G, Lang K, Quenzel P, BÃ¶hme I, Sauter J, Hofmann J, et al. 2.7 million samples genotyped for HLA by next generation sequencing: lessons learned. BMC Genomics. 2017;18:161 pubmed publisher..The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows. ..
- de Pokomandy A, Kaufman E, De Castro C, Mayrand M, Burchell A, Klein M, et al. The EVVA Cohort Study: Anal and Cervical Type-Specific Human Papillomavirus Prevalence, Persistence, and Cytologic Findings in Women Living With HIV. J Infect Dis. 2017;216:447-456 pubmed publisher..High-resolution anoscopy was indicated in more than one third of results. As anal cancer is potentially preventable, these important findings need to be considered when selecting the best approach for anal cancer screening programs. ..
- Hall E, Nahorski M, Murray L, Shaheen R, Perkins E, Dissanayake K, et al. PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins. Am J Hum Genet. 2017;100:706-724 pubmed publisher..Through characterization of this neurological intracellular trafficking disorder, we establish the importance of ubiquitin-mediated endolysosomal trafficking at the synapse. ..
- Zhang S, Xiao Q, Shi Z, Yu G, Ma X, Chen H, et al. Caspase polymorphisms and prognosis of hepatocellular carcinoma. PLoS ONE. 2017;12:e0176802 pubmed publisher..012 and 0.010, respectively). In conclusion, the CASP9 rs4645981 polymorphism, CASP3 and CASP9 haplotypes may be useful prognosis markers for HCC patients with surgical resection of tumor. ..
- Lee N, Cao B, Ke C, Lu H, Hu Y, Tam C, et al. IFITM3, TLR3, and CD55 Gene SNPs and Cumulative Genetic Risks for Severe Outcomes in Chinese Patients With H7N9/H1N1pdm09 Influenza. J Infect Dis. 2017;216:97-104 pubmed publisher..TLR4 was nonpolymorphic. Host genetic factors may influence clinical outcomes of avian and pandemic influenza infections. Such findings have important implications on disease burden and patient care in at-risk populations. ..
- Hampras S, Rollison D, Giuliano A, McKay Chopin S, Minoni L, Sereday K, et al. Prevalence and Concordance of Cutaneous Beta Human Papillomavirus Infection at Mucosal and Cutaneous Sites. J Infect Dis. 2017;216:92-96 pubmed publisher..Cutaneous beta human papillomavirus (HPV) infection across cutaneous and mucosal tissues within individuals has not been examined...
- Megawati D, Masyeni S, Yohan B, Lestarini A, Hayati R, Meutiawati F, et al. Dengue in Bali: Clinical characteristics and genetic diversity of circulating dengue viruses. PLoS Negl Trop Dis. 2017;11:e0005483 pubmed publisher..Our data highlights the role of this tourist destination as a potential source of dengue transmission in the region. ..
- Meyers A, Meinders M, Hamer S. Widespread Trypanosoma cruzi infection in government working dogs along the Texas-Mexico border: Discordant serology, parasite genotyping and associated vectors. PLoS Negl Trop Dis. 2017;11:e0005819 pubmed publisher..Working dogs are highly trained in security functions and potential loss of duty from the clinical outcomes of infection could affect the work force and have broad consequences. ..
- Uebe S, Ehrlicher M, Ekici A, Behrens F, Böhm B, Homuth G, et al. Genome-wide association and targeted analysis of copy number variants with psoriatic arthritis in German patients. BMC Med Genet. 2017;18:92 pubmed publisher..CNVs are thus good candidate disease variants, while the methods to detect them should be applied cautiously and reproduced by an independent method. ..
- Deng J, Hu J, Tan H, Su G, Cao Q, Huang X, et al. Association of a PDCD1 Polymorphism With Sympathetic Ophthalmia in Han Chinese. Invest Ophthalmol Vis Sci. 2017;58:4218-4222 pubmed publisher..56). This study shows that only PDCD1/rs2227981 contributes to the genetic susceptibility of SO, and that the other 23 susceptibility loci of VKH disease are probably not involved in the pathogenesis of this disease. ..
- Purfield D, McParland S, Wall E, Berry D. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS ONE. 2017;12:e0176780 pubmed publisher..Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production. ..
- Edea Z, Hong J, Jung J, Kim D, Kim Y, Kim E, et al. Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip. Anim Genet. 2017;48:473-477 pubmed publisherThe development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs...
- Schepers R, Markus C. The interaction between 5-HTTLPR genotype and ruminative thinking on BMI. Br J Nutr. 2017;118:629-637 pubmed publisher..These results suggest that cognitive rumination may be a critical moderator of the association between 5-HTTLPR and body mass...
- Quaranta S, Thomas F. Pharmacogenetics of anti-cancer drugs: State of the art and implementation - recommendations of the French National Network of Pharmacogenetics. Therapie. 2017;72:205-215 pubmed publisher..Other applications, for which the level of evidence is still discussed, will be evoked in the final section of this review. ..
- Novák K, Pikousová J, Czerneková V, Mátlová V. Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform. Anim Biotechnol. 2017;28:228-236 pubmed publisher..PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a ..
- Figueredo Lago J, Armas Cayarga A, González González Y, Collazo Mesa T. A simple, fast and inexpensive method for mutation scanning of CFTR gene. BMC Med Genet. 2017;18:58 pubmed publisher..As the method is fast, inexpensive and highly reliable, it is advisable for scanning CFTR gene mutations in newborns, patients with a clinical suspicion of CF as well as in the preconception carrier screening. ..
- Stelzl E, Haas B, Bauer B, Zhang S, Fiss E, Hillman G, et al. First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing. PLoS ONE. 2017;12:e0181273 pubmed publisher..The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment. ..
- Tang F, Ma L, Tam P, Pang C, Tham C, Chen L. Genetic Association of the PARL-ABCC5-HTR3D-HTR3C Locus With Primary Angle-Closure Glaucoma in Chinese. Invest Ophthalmol Vis Sci. 2017;58:4384â€“4389 pubmed publisher..We identified no tagging SNP responsible for the association of the whole region. Further deep sequencing analysis of this region should be warranted to uncover whether there is still disease associated variant in this region. ..
- Miño C, de Souza E, Moralez Silva E, Valdes T, Cortiço Corrêa Rodrigues V, Del Lama S. Use of noninvasive 'bug-eggs' to enable comparative inferences on genetic mating system with and without parental information: A study in a cattle egret colony. PLoS ONE. 2017;12:e0183153 pubmed publisher..We expand knowledge on the reproductive tactics of colonial waterbirds, contributing novel data on the genetic mating system of the cattle egret, valuable for the design of management strategies for this invasive bird. ..
- Tettey R, Ayeh Kumi P, Tettey P, Adjei G, Asmah R, Dodoo D. Severity of malaria in relation to a complement receptor 1 polymorphism: a case-control study. Pathog Glob Health. 2015;109:247-52 pubmed publisher..Further studies with large sample size in other malaria endemic regions in Africa are warranted to confirm these findings. ..
- Kachwamba Y, Mohammed A, Lukupulo H, Urio L, Majigo M, Mosha F, et al. Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania. BMC Infect Dis. 2017;17:157 pubmed publisher..We conclude that genetically related V. cholerae cluster in outbreaks, and distinct strains circulate simultaneously. ..
- Bedere N, Bovenhuis H. Characterizing a region on BTA11 affecting ?-lactoglobulin content of milk using high-density genotyping and haplotype grouping. BMC Genet. 2017;18:17 pubmed publisher..These findings can be used for selection of cows with higher cheese yield, which is desirable for the dairy industry. ..
- Abanda N, Djieugoué J, Lim E, Pefura Yone E, Mbacham W, Vernet G, et al. Diagnostic accuracy and usefulness of the Genotype MTBDRplus assay in diagnosing multidrug-resistant tuberculosis in Cameroon? a cross-sectional study. BMC Infect Dis. 2017;17:379 pubmed publisher..For routine MDR-TB diagnosis, this assay could be used for Mycobacterium tuberculosis cultures containing contaminants, to complement culture-based drug susceptibility testing or to determine drug resistant mutations. ..
- Pisanu C, Preisig M, Castelao E, Glaus J, Pistis G, Squassina A, et al. A genetic risk score is differentially associated with migraine with and without aura. Hum Genet. 2017;136:999-1008 pubmed publisher..We show that a GRS combining multiple genetic risk variants is associated with MWOA but not MWA, suggesting a different genetic susceptibility background underlying the two forms of migraine. ..
- Giri A, Edwards T, Hartmann K, Torstenson E, Wellons M, Schreiner P, et al. African genetic ancestry interacts with body mass index to modify risk for uterine fibroids. PLoS Genet. 2017;13:e1006871 pubmed publisher..Findings from our study provide an example of how modifiable and non-modifiable factors may interact to influence fibroid risk and suggest a biological role for BMI in fibroid etiology. ..
- Xu M, Xu M, Han L, Yuan C, Mei Y, Zhang H, et al. Role for Functional SOD2 Polymorphism in Pulmonary Arterial Hypertension in a Chinese Population. Int J Environ Res Public Health. 2017;14: pubmed publisher..There is significant association between SOD rs4880 polymorphism and the PAH susceptibility, and this polymorphism influenced PAH susceptibility by altering the expression of SOD2. ..
- Yadav D, Arora R, Jain A. Classification and conservation priority of five Deccani sheep ecotypes of Maharashtra, India. PLoS ONE. 2017;12:e0184691 pubmed publisher..The findings gave highest conservation priority to Lonand and least to Solapuri ecotype. ..
- Suzuki T, Hasebe A. A provisional complete genome-based genotyping system for rotavirus species C from terrestrial mammals. J Gen Virol. 2017;98:2647-2662 pubmed publisher..The system established in this study deepens our understanding of RVC evolution and facilitates the discovery of genetic events (gene reassortment and interspecies transmission) among RVCs...
- Thurber C, Ma J, Higgins R, Brown P. Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production. Genome Biol. 2013;14:R68 pubmed publisher..Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel. ..
- Li L, Fang Z, Zhou J, Chen H, Hu Z, Gao L, et al. An accurate and efficient method for large-scale SSR genotyping and applications. Nucleic Acids Res. 2017;45:e88 pubmed publisher..While the work we present focused on rice, AmpSeq-SSR can be readily extended to animals and micro-organisms. ..
- Wu H, Jia X, Zhao H, Huang Y, Liu C, Huang Z, et al. Identification of SEPP1 polymorphisms is not a genetic risk factor for preeclampsia in Chinese Han women: A clinical trial and experimental study. Medicine (Baltimore). 2017;96:e7249 pubmed publisher..Our data indicate that the 2 genetic variants of rs7579 and rs230813 in SEPP1 may not play a role in the pathogenesis of PE in Chinese Han Women. ..
- Jena K, Hechanova S, Verdeprado H, Prahalada G, Kim S. Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis. Theor Appl Genet. 2017;130:2345-2360 pubmed publisher..These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries. ..
- Ziems L, Franckowiak J, Platz G, Mace E, Park R, Singh D, et al. Investigating successive Australian barley breeding populations for stable resistance to leaf rust. Theor Appl Genet. 2017;130:2463-2477 pubmed publisher..This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments. ..
- Trifonov V, Pasqualucci L, Tiacci E, Falini B, Rabadan R. SAVI: a statistical algorithm for variant frequency identification. BMC Syst Biol. 2013;7 Suppl 2:S2 pubmed publisher..Analyzing sequencing data through estimating allele frequencies using empirical Bayes methods is a powerful complement to the ever-increasing throughput of the sequencing technologies. ..
- Baker B, Poonja S, Mesrobian M, Lai A, Hwang S. Notes from the field: use of genotyping to disprove a presumed outbreak of Mycobacterium tuberculosis - Los Angeles County, 2013-2014. MMWR Morb Mortal Wkly Rep. 2014;63:907-8 pubmed
- Marini N, Bevilacqua C, Büttow M, Raseira M, Bonow S. Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements. Genet Mol Res. 2017;16: pubmed publisher..This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results. ..
- Xiong X, Li S, Cai Y, Chen F. Targeted sequencing in FGF/FGFR genes and association analysis of variants for mandibular prognathism. Medicine (Baltimore). 2017;96:e7240 pubmed publisher..Future studies with larger sample sizes and more comprehensive genome coverage, and also in other population are required to replicate these findings. ..
- Dietrich P, Johnson I, Alli S, Dragatsis I. Elimination of huntingtin in the adult mouse leads to progressive behavioral deficits, bilateral thalamic calcification, and altered brain iron homeostasis. PLoS Genet. 2017;13:e1006846 pubmed publisher..Here we show that elimination of Htt expression in the adult mouse results in behavioral deficits, progressive neuropathological changes including bilateral thalamic calcification, and altered brain iron homeostasis. ..
- Musolf A, Simpson C, Moiz B, Long K, Portas L, Murgia F, et al. Caucasian Families Exhibit Significant Linkage of Myopia to Chromosome 11p. Invest Ophthalmol Vis Sci. 2017;58:3547-3554 pubmed publisher..We further plan targeted sequencing on 11p for our most highly linked families to more clearly understand the source of the linkage in this region. ..
- Leo P, Madeleine M, Wang S, Schwartz S, Newell F, Pettersson Kymmer U, et al. Defining the genetic susceptibility to cervical neoplasia-A genome-wide association study. PLoS Genet. 2017;13:e1006866 pubmed publisher..6% risk, of developing cervical neoplasia. Future studies should examine genetic risk prediction in assessing the risk of cervical neoplasia further, in combination with other screening methods. ..
- Bui T, Hoa N, Yen J, Schafleitner R. PCR-based assays for validation of single nucleotide polymorphism markers in rice and mungbean. Hereditas. 2017;154:3 pubmed publisher..CEL-I genotyping performed better in terms of genotyping accuracy and costs than tetra markers. The method is highly useful for validating SNPs in small to medium size germplasm panels. ..
- Ndiaye Y, Diedhiou C, Bei A, Dieye B, Mbaye A, Mze N, et al. High resolution melting: a useful field-deployable method to measure dhfr and dhps drug resistance in both highly and lowly endemic Plasmodium populations. Malar J. 2017;16:153 pubmed publisher..A high prevalence of samples harbouring mutant DHFR alleles was observed in both population using both genotyping techniques. HRM was better able to detect mixed alleles compared to PCR/RFLP for DHFR codon 51 in Tanzania; and only ..
- Moghaddar N, Swan A, van der Werf J. Genomic prediction from observed and imputed high-density ovine genotypes. Genet Sel Evol. 2017;49:40 pubmed publisher..2%) was observed for animals that were genetically lowly related to the reference set while it ranged from 0.0 to 5.0% for across-breed prediction. On average, no significant advantage was observed with BayesR compared to GBLUP. ..
- Abeku T, Helinski M, Kirby M, Ssekitooleko J, Bass C, Kyomuhangi I, et al. Insecticide resistance patterns in Uganda and the effect of indoor residual spraying with bendiocarb on kdr L1014S frequencies in Anopheles gambiae s.s. Malar J. 2017;16:156 pubmed publisher..This study suggests that using a carbamate insecticide for IRS in areas with high levels of pyrethroid resistance may reduce kdr frequencies in An. gambiae s.s. ..
- Zhang X, Xie J, Zhu S, Chen Y, Wang L, Xu B. Next-generation sequencing identifies pathogenic and modifier mutations in a consanguineous Chinese family with hypertrophic cardiomyopathy. Medicine (Baltimore). 2017;96:e7010 pubmed publisher..Our results suggest that CACNB2 is a possible candidate genetic modifier of MYBPC3-associated familial HCM, but more genetic evidence and functional experiments are needed to confirm. ..
- Oki E, Norde M, Carioca A, Souza J, Castro I, Marchioni D, et al. Polymorphisms of the TNF-? gene interact with plasma fatty acids on inflammatory biomarker profile: a population-based, cross-sectional study in São Paulo, Brazil. Br J Nutr. 2017;117:1663-1673 pubmed publisher..Our study contributes to knowledge on TNF-? SNP and their association with inflammatory biomarker levels, plasma FA and the interaction among them, of particular interest for the Brazilian population. ..
- Liu X, Li J, Yang Z. Genetic diversity and structure of core collection of winter mushroom (Flammulina velutipes) developed by genomic SSR markers. Hereditas. 2018;155:3 pubmed publisher..In addition, the wild strains in the core collection possess favorable agronomic characters and produce unique bioactive compounds, adding value to the platform. More attention should be paid to wild strains in further strain breeding. ..
- Jeanmougin M, Noirel J, Coulonges C, Zagury J. HLA-check: evaluating HLA data from SNP information. BMC Bioinformatics. 2017;18:334 pubmed publisher..Overall, HLA-check was able to identify a limited number of implausible HLA typings (less than 10%) in a population, and these samples can then either be removed or be retyped by NGS for HLA association analysis. ..
- Khella M, Hamdy N, Amin A, El Mesallamy H. The (FTO) gene polymorphism is associated with metabolic syndrome risk in Egyptian females: a case- control study. BMC Med Genet. 2017;18:101 pubmed publisher..The association of this genetic polymorphism with ALT levels needs to be studied in other populations with larger sample size. ..
- Gandhi N, Brust J, Moodley P, Weissman D, Heo M, Ning Y, et al. Minimal diversity of drug-resistant Mycobacterium tuberculosis strains, South Africa. Emerg Infect Dis. 2014;20:426-33 pubmed publisher..We conclude that, although Beijing strain was common among drug-susceptible TB, other strains predominated among MDR TB and XDR TB cases. Drug-resistance was a stronger predictor of survival than strain type. ..
- Casaril A, de Oliveira L, Alonso D, de Oliveira E, Gomes Barrios S, de Oliveira Moura Infran J, et al. Standardization of DNA extraction from sand flies: Application to genotyping by next generation sequencing. Exp Parasitol. 2017;177:66-72 pubmed publisher..This is the first study on the standardization of methods for the extraction of DNA from sand flies for application to next-generation sequencing, which is a promising tool for entomological and molecular studies of sand flies. ..
- Faux P, Druet T. A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels. Genet Sel Evol. 2017;49:46 pubmed publisher..This strategy results in very few mismatches with the phase obtained by Mendelian segregation rules. Finally, we propose a strategy to further improve phasing accuracy based on haplotype clusters obtained with genotyping data. ..
- Wang Y, Cao X, Zhao Y, Fei J, Hu X, Li N. Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens. PLoS ONE. 2017;12:e0179073 pubmed publisher..The approach that we developed in chickens, which is high-quality, high-density, cost-effective (300 K, $30/sample), and time-saving (within 48 h), will have broad applications in animal breeding programs. ..
- Garrine M, Mandomando I, Vubil D, Nhampossa T, Acácio S, Li S, et al. Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLoS Negl Trop Dis. 2017;11:e0005671 pubmed publisher..Our data raises important questions related to where these isolates persist and how identical isolates can be collected years apart despite our understanding of high change rate of MLVA loci and the V. cholerae molecular clock. ..
- Qu J, Lu S, Lu Z, Xu P, Xiang D, Qu Q. Pharmacogenetic and case-control study on potassium channel related gene variants and genetic generalized epilepsy. Medicine (Baltimore). 2017;96:e7321 pubmed publisher..Further multicenter, multiethnic, and large sample size pharmacogenetic and case-control studies are warranted to confirm our negative results. ..
- Snelling W, Kuehn L, Keel B, Thallman R, Bennett G. Linkage disequilibrium among commonly genotyped SNP variants detected from bull sequence. Anim Genet. 2017;48:516-522 pubmed publisher..Genotypes used for this study are available from https://www.animalgenome.org/repository/pub/;USDA2017.0519/. ..
- Mohamad Ishak N, Nong Q, Matsuura T, Kato Y, Watanabe H. Co-option of the bZIP transcription factor Vrille as the activator of Doublesex1 in environmental sex determination of the crustacean Daphnia magna. PLoS Genet. 2017;13:e1006953 pubmed publisher..These results indicate that Vri was co-opted as a transcriptional activator of Dsx1 in environmental sex determination of D. magna. The data suggests the remarkably plastic nature of gene regulatory network in sex determination...
- Crompton M, Purnell T, Tyrer H, Parker A, Ball G, Hardisty Hughes R, et al. A mutation in Nischarin causes otitis media via LIMK1 and NF-ÎºB pathways. PLoS Genet. 2017;13:e1006969 pubmed publisher..Our analysis implicates PAK1 and RAC1, and downstream signalling in LIMK1 and NF-ÎºB pathways in the development of chronic OM. ..
- Takagi S, Naito M, Kawai S, Okada R, Nagata C, Hosono S, et al. Macronutrient intakes and serum oestrogen, and interaction with polymorphisms in CYP19A1 and HSD17B1 genes: a cross-sectional study in postmenopausal Japanese women. Br J Nutr. 2017;118:463-472 pubmed publisher..Macronutrient intakes were associated with serum E2 level, and these associations may be modified by HSD17B1 polymorphism in postmenopausal women...