Genomes and Genes
Experts and Doctors on genetic variation in United States
Locale: United States
Topic: genetic variation
- van Waasbergen L, Balkwill D, Crocker F, Bjornstad B, Miller R. Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences. Appl Environ Microbiol. 2000;66:3454-63 pubmed..Thus, this work suggests that within sedimentary deep-subsurface environments, permeability of the deposits plays a major role in determining the genetic structure of resident bacterial populations. ..
- Canver M, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern E, et al. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017;49:625-634 pubmed publisher..Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions. ..
- Converse P, Kuchta S, Hauswaldt J, Roosenburg W. Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin). PLoS ONE. 2017;12:e0181898 pubmed publisher..In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities. ..
- Pless E, Gloria Soria A, Evans B, Kramer V, Bolling B, Tabachnick W, et al. Multiple introductions of the dengue vector, Aedes aegypti, into California. PLoS Negl Trop Dis. 2017;11:e0005718 pubmed publisher..This work has implications for mosquito surveillance and vector control activities not only in California but also in other regions where the distribution of this invasive mosquito is expanding. ..
- Zhang Y, Li S, Abyzov A, Gerstein M. Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput Biol. 2017;13:e1005567 pubmed publisher..We anticipate our approach and analytical methodology to have application in a more clinical context, where exome sequencing data is abundant and the discovery of retroduplications can potentially improve the accuracy of SNP calling. ..
- Claytor S, Subramaniam K, Landrau Giovannetti N, Chinchar V, Gray M, Miller D, et al. Ranavirus phylogenomics: Signatures of recombination and inversions among bullfrog ranaculture isolates. Virology. 2017;511:330-343 pubmed publisher..Our study underscores the role international trade in farmed bullfrogs may have played in the global dissemination of highly pathogenic ranaviruses. ..
- Bolnick D, Stutz W. Frequency dependence limits divergent evolution by favouring rare immigrants over residents. Nature. 2017;546:285-288 pubmed publisher..Our results suggest a more nuanced view in which negative frequency dependence alters the fate of migrants to promote or constrain evolutionary divergence between populations. ..
- Pashos E, Park Y, Wang X, Raghavan A, Yang W, Abbey D, et al. Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. Cell Stem Cell. 2017;20:558-570.e10 pubmed publisher..These findings endorse an iPSC-based experimental framework to discover functional variants and genes contributing to complex human traits. ..
- Weber J, Gibson R, Sácká L, Strunin D, Hodek J, Weberova J, et al. Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals. AIDS Res Ther. 2017;14:15 pubmed publisher..e., high CD4+ cell counts with detectable plasma HIV-1 RNA load), reduced viral replicative fitness seems to be linked to slow disease progression in these antiretroviral-naïve individuals. ..
- Landrian I, McFarland K, Liu J, Mulligan C, Rasmussen A, Ashizawa T. Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions. PLoS ONE. 2017;12:e0175958 pubmed publisher..In addition, analysis of the interruption alleles across these families support a parsimonious single origin of the mutation with a shared distant ancestor. ..
- Roman T, Cannon M, Vadlamudi S, Buchkovich M, Wolford B, Welch R, et al. A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus. Diabetes. 2017;66:2521-2530 pubmed publisher..Together, these data suggest that rs11708067-A risk allele contributes to type 2 diabetes by disrupting an islet enhancer, which results in reduced ADCY5 expression and impaired insulin secretion. ..
- Liu H, Liu Z, Wang Y, Stinchcombe T, Owzar K, Han Y, et al. Functional variants in DCAF4 associated with lung cancer risk in European populations. Carcinogenesis. 2017;38:541-551 pubmed publisher..Taken together, our results suggest that rs12587742 is associated with an increased lung cancer risk, possibly by up-regulating mRNA expression and decreasing methylation status of DCAF4. ..
- Lee H, Smith S, Yoon Y. The short variant of the mitochondrial dynamin OPA1 maintains mitochondrial energetics and cristae structure. J Biol Chem. 2017;292:7115-7130 pubmed publisher..Our results demonstrate that, contrary to conventional notion, S-OPA1 is fully competent for maintaining mitochondrial energetics and cristae structure. ..
- Sun R, Hu Z, Sottoriva A, Graham T, Harpak A, Ma Z, et al. Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nat Genet. 2017;49:1015-1024 pubmed publisher..Our findings have broad implications for how human tumors progress, how they accumulate intratumoral heterogeneity, and ultimately how they may be more effectively treated...
- Chi H, Taik P, Foley E, Racicot A, Gray H, Guzzetta K, et al. High genetic diversities between isolates of the fish parasite Cryptocaryon irritans (Ciliophora) suggest multiple cryptic species. Mol Phylogenet Evol. 2017;112:47-52 pubmed publisher..Taken together, the C. irritans species may consists of many subspecies and/or syngens. Further work is needed to determine if there is reproductive isolation between the groups we have defined. ..
- Varshney R, Shi C, Thudi M, Mariac C, Wallace J, Qi P, et al. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol. 2017;35:969-976 pubmed publisher..We believe that these resources should empower researchers and breeders to improve this important staple crop. ..
- Billings L, Jablonski K, Warner A, Cheng Y, McAteer J, Tipton L, et al. Variation in Maturity-Onset Diabetes of the Young Genes Influence Response to Interventions for Diabetes Prevention. J Clin Endocrinol Metab. 2017;102:2678-2689 pubmed publisher..Variation in genes that cause maturity-onset diabetes of the young (MODY) has been associated with diabetes incidence and glycemic traits...
- Kittichai V, Koepfli C, Nguitragool W, Sattabongkot J, Cui L. Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission. PLoS Negl Trop Dis. 2017;11:e0005930 pubmed publisher..Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country...
- Campbell L, Alexander A. Landscape Genetics of Aedes mcintoshi (Diptera: Culicidae), an Important Vector of Rift Valley Fever Virus in Northeastern Kenya. J Med Entomol. 2017;54:1258-1265 pubmed publisher..Further understanding of the genetic structure of Ae. mcintoshi could provide useful information regarding the potential for RVFV to spread across East African landscapes. ..
- Hick P, Subramaniam K, Thompson P, Waltzek T, Becker J, Whittington R. Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV). Virology. 2017;511:320-329 pubmed publisher..There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish. ..
- Krupp D, Barnard R, Duffourd Y, Evans S, Mulqueen R, Bernier R, et al. Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder. Am J Hum Genet. 2017;101:369-390 pubmed publisher..We estimate that PMMs potentially contribute risk to 3%-4% of simplex ASD case subjects and future studies of PMMs in ASD and related disorders are warranted. ..
- Wheeler E, Leong A, Liu C, Hivert M, Strawbridge R, Podmore C, et al. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Med. 2017;14:e1002383 pubmed publisher..Screening with direct glucose measurements, or genetically-informed HbA1c diagnostic thresholds in people with G6PD deficiency, may be required to avoid missed or delayed diagnoses. ..
- Mantooth K, Hadziabdic D, Boggess S, Windham M, Miller S, Cai G, et al. Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America. PLoS ONE. 2017;12:e0180345 pubmed publisher..These primers may be useful for investigating the genetic diversity and population structure of these Discula species. ..
- Horner A, Hoffman E, Tye M, Hether T, Savage A. Cryptic chytridiomycosis linked to climate and genetic variation in amphibian populations of the southeastern United States. PLoS ONE. 2017;12:e0175843 pubmed publisher..Incorporating both genetic and environmental information into conservation plans for amphibians is necessary for the development of more effective management strategies to mitigate the impact of emerging infectious diseases. ..
- Orquera Tornakian G, Garrido P, Kronmiller B, Hunger R, Tyler B, Garzón C, et al. Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici. J Microbiol Methods. 2017;139:113-122 pubmed publisher..andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species. ..
- Afshar M, Luk K, Do R, Dufresne L, Owens D, Harris T, et al. Association of Triglyceride-Related Genetic Variants With Mitral Annular Calcification. J Am Coll Cardiol. 2017;69:2941-2948 pubmed publisher..Whether reducing triglyceride levels can lower the incidence of clinically significant mitral valve disease requires further study. ..
- Willsey A, Fernandez T, Yu D, King R, Dietrich A, Xing J, et al. De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron. 2017;94:486-499.e9 pubmed publisher..Overall, we estimate that de novo damaging variants in approximately 400 genes contribute risk in 12% of clinical cases. VIDEO ABSTRACT. ..
- Bouchet S, Olatoye M, Marla S, Perumal R, Tesso T, Yu J, et al. Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population. Genetics. 2017;206:573-585 pubmed publisher..i> association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits. ..
- Willoughby J, Ivy J, Lacy R, Doyle J, DeWoody J. Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PLoS ONE. 2017;12:e0175996 pubmed publisher..Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild. ..
- Eberle R, Maxwell L, Nicholson S, Black D, Jones Engel L. Genome sequence variation among isolates of monkey B virus (Macacine alphaherpesvirus 1) from captive macaques. Virology. 2017;508:26-35 pubmed publisher..Sequence variation between BV isolates from different macaque species (different BV genotypes) was much greater and was spread across the entire genome, confirming the existence of different genotypes of BV in different macaque species. ..
- Faria N, Quick J, Claro I, Theze J, de Jesus J, Giovanetti M, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. 2017;546:406-410 pubmed publisher..The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus...
- McClung J, McCord T, Ryan T, Schmidt C, Green T, Southerland K, et al. BAG3 (Bcl-2-Associated Athanogene-3) Coding Variant in Mice Determines Susceptibility to Ischemic Limb Muscle Myopathy by Directing Autophagy. Circulation. 2017;136:281-296 pubmed publisher..These results highlight a pathway that preserves tissue survival and muscle function in the setting of ischemia. ..
- Wood A, Jonsson A, Jackson A, Wang N, van Leewen N, Palmer N, et al. A Genome-Wide Association Study of IVGTT-Based Measures of First-Phase Insulin Secretion Refines the Underlying Physiology of Type 2 Diabetes Variants. Diabetes. 2017;66:2296-2309 pubmed publisher..In summary, our study provides further insight into the mechanisms by which common genetic variation influences type 2 diabetes risk and glycemic traits. ..
- Shi Q, Liu H, Han P, Li C, Wang Y, Wu W, et al. Genetic Variants in WNT2B and BTRC Predict Melanoma Survival. J Invest Dermatol. 2017;137:1749-1756 pubmed publisher..41-2.81, P = 8.10 × 10-5) and 0.61 (0.46-0.80, 3.12×10-4), respectively. Collectively, these variants in the Wnt pathway genes may be biomarkers for outcomes of patients with CM, if validated by larger studies. ..
- Bohling J, Mastro L, Adams J, Gese E, Owen S, Waits L. Panmixia and Limited Interspecific Introgression in Coyotes (Canis latrans) from West Virginia and Virginia, USA. J Hered. 2017;108:608-617 pubmed publisher..Coyotes appear to display a panmictic population structure despite high habitat heterogeneity and heavy human influence in the spatial environment, underscoring the adaptability of the species...
- Jeffrey B, Rose S, Gilbert K, Lewis M, Bermudez L. Comparative analysis of the genomes of clinical isolates of Mycobacterium avium subsp. hominissuis regarding virulence-related genes. J Med Microbiol. 2017;66:1063-1075 pubmed publisher..The bacteria belonging to this complex have variable virulence, depending on the strain considered, and therefore a representative of the most common clinical phenotype was analysed...
- Teotónio H, Estes S, Phillips P, Baer C. Experimental Evolution with Caenorhabditis Nematodes. Genetics. 2017;206:691-716 pubmed publisher..We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative. ..
- Kemp B, Judd K, Monroe C, Eerkens J, Hilldorfer L, Cordray C, et al. Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest. PLoS ONE. 2017;12:e0178882 pubmed publisher..These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations. ..
- Brown H, Thompson R, Murphy G, Peters D, La Rue B, King J, et al. Development and validation of a novel multiplexed DNA analysis system, InnoTyperÂ® 21. Forensic Sci Int Genet. 2017;29:80-99 pubmed publisher..This study has demonstrated that the bi-allelic INNULs in the InnoTyper 21 system provide a sensitivity of detection and a power of discrimination that makes them useful for human identification of extremely degraded samples. ..
- McCreight J, Schneider S, Wilburn D, Swanson W. Evolution of microRNA in primates. PLoS ONE. 2017;12:e0176596 pubmed publisher..Many of these non-conserved miRNA appear to regulate neuronal processes, illustrating the importance of investigating miRNA to learn more about human evolution. ..
- Balazik M, Farrae D, Darden T, Garman G. Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia. PLoS ONE. 2017;12:e0179661 pubmed publisher..S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history. ..
- Panopoulos A, Smith E, ARIAS A, Shepard P, Hishida Y, Modesto V, et al. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. Cell Stem Cell. 2017;20:505-517.e6 pubmed publisher..Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming. ..