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https://www.readbyqxmd.com/read/28102151/pleiotropic-genetic-effects-influencing-sleep-and-neurological-disorders
#1
REVIEW
Olivia J Veatch, Brendan T Keenan, Philip R Gehrman, Beth A Malow, Allan I Pack
Research evidence increasingly points to the large impact of sleep disturbances on public health. Many aspects of sleep are heritable and genes influencing traits such as timing, EEG characteristics, sleep duration, and response to sleep loss have been identified. Notably, large-scale genome-wide analyses have implicated numerous genes with small effects on sleep timing. Additionally, there has been considerable progress in the identification of genes influencing risk for some neurological sleep disorders. For restless legs syndrome, implicated variants are typically in genes associated with neuronal development...
February 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28102150/ultra-rare-genetic-variation-in-common-epilepsies-a-case-control-sequencing-study
#2
(no author information available yet)
BACKGROUND: Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. METHODS: We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy...
February 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28102005/blind-prediction-of-deleterious-amino-acid-variations-with-snps-go
#3
Emidio Capriotti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
: SNPs&GO is a machine learning method for predicting the association of single amino acid variations (SAVs) to disease, considering protein functional annotation. The method is a binary classifier that implements a Support Vector Machine algorithm to discriminate between disease-related and neutral SAVs. SNPs&GO combines information from protein sequence with functional annotation encoded by Gene Ontology terms. Tested in sequence mode on more than 38,000 SAVs from the SwissVar dataset, our method reached 81% overall accuracy and an area under the receiving operating characteristic curve (AUC) of 0...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101908/recurrent-rearrangements-of-human-amylase-genes-create-multiple-independent-cnv-series
#4
Nzar A A Shwan, Sandra Louzada, Fengtang Yang, John A L Armour
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of copy number variation (CNV) has only been defined in detail very recently. In this work we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A and AMY2B...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101462/identification-and-molecular-characterization-of-genes-coding-pharmaceutically-important-enzymes-from-halo-thermo-tolerant-bacillus
#5
Azam Safary, Rezvan Moniri, Maryam Hamzeh-Mivehroud, Siavoush Dastmalchi
Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp...
December 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28101224/impact-of-chromosome-17q-deletion-in-the-primary-lesion-of-colorectal-cancer-on-liver-metastasis
#6
Masaya Kawai, Hiromitsu Komiyama, Masaki Hosoya, Haruna Okubo, Tomoaki Fujii, Norihiko Yokoyama, Chiyo Sato, Takae Ueyama, Atsushi Okuzawa, Michitoshi Goto, Yutaka Kojima, Makoto Takahashi, Kiichi Sugimoto, Shun Ishiyama, Shinya Munakata, Dai Ogura, Shin-Ichiro Niwa, Yuichi Tomiki, Takumi Ochiai, Kazuhiro Sakamoto
Colorectal cancer is a prevalent malignancy worldwide, and investigations are required to elucidate the underlying carcinogenic mechanisms. Amongst these mechanisms, de novo carcinogenesis and the adenoma to carcinoma sequence, are the most understood. Metastasis of colorectal cancer to the liver often results in fatality, therefore, it is important for any associated risk factors to be identified. Regarding the treatment of the disease, it is important to manage not only the primary colorectal tumor, but also the liver metastases...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100915/whole-exome-sequencing-study-reveals-common-copy-number-variants-in-protocadherin-genes-associated-with-childhood-obesity-in-koreans
#7
S Moon, M Y Hwang, H B Jang, S Han, Y J Kim, J-Y Hwang, H-J Lee, S I Park, J Song, B-J Kim
Recently, the prevalence of childhood obesity has significantly increased in industrialized countries, including Korea, and now controlling obesity is becoming an economic burden. However, knowledge of the risk factors associated with obesity is still limited. In this study, we aimed to discover additional obesity-associated loci in children. To achieve this, we conducted an exome-wide association analysis of copy number variation (CNV) using whole-exome sequencing (WES) data from a total of 102 cases and 86 controls...
January 19, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28100912/cryptic-splice-activation-but-not-exon-skipping-is-observed-in-minigene-assays-of-dystrophin-c-9361-1g-a-mutation-identified-by-ngs
#8
Emma Tabe Eko Niba, Atsushi Nishida, Van Khanh Tran, Dung Chi Vu, Masaaki Matsumoto, Hiroyuki Awano, Tomoko Lee, Yasuhiro Takeshima, Hisahide Nishio, Masafumi Matsuo
Next-generation sequencing (NGS) discloses nucleotide changes in the genome. Mutations at splicing regulatory elements are expected to cause splicing errors, such as exon skipping, cryptic splice site activation, partial exon loss or intron retention. In dystrophinopathy patients, prediction of splicing outcomes is essential to determine the phenotype: either severe Duchenne or mild Becker muscular dystrophy, based on the reading frame rule. In a Vietnamese patient, NGS identified a c.9361+1G>A mutation in the dystrophin gene and an additional DNA variation of A>G at +117 bases in intron 64...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100911/variants-on-chromosome-4q21-near-pkd2-and-siblings-are-associated-with-dental-caries
#9
Scott Eckert, Eleanor Feingold, Margaret Cooper, Michael M Vanyukov, Brion S Maher, Rebecca L Slayton, Marcia C Willing, Steven E Reis, Daniel W McNeil, Richard J Crout, Robert J Weyant, Steven M Levy, Alexandre R Vieira, Mary L Marazita, John R Shaffer
A recent genome-wide association study (GWAS) for dental caries nominated the chromosomal region 4q21 near ABCG2, PKD2 and the SIBLING (small integrin-binding ligand N-linked glycoprotein) gene family. In this investigation, we followed up and fine-mapped this region using a tag-SNP (single-nucleotide polymorphism) approach in 13 age- and race-stratified samples from 6 independent studies (N=4089). Participants were assessed for dental caries via intraoral examination and 49 tag-SNPs were genotyped capturing much of the variation in the 4q21 locus...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100788/genomic-infectious-disease-epidemiology-in-partially-sampled-and-ongoing-outbreaks
#10
Xavier Didelot, Christophe Fraser, Jennifer Gardy, Caroline Colijn
Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100590/inferring-individual-inbreeding-and-demographic-history-from-segments-of-identity-by-descent-in-ficedula-flycatcher-genome-sequences
#11
Marty Kardos, Anna Qvarnström, Hans Ellegren
Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287 Ficedula flycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28100189/an-snp-based-saturated-genetic-map-and-qtl-analysis-of-fruit-related-traits-in-zucchini-using-genotyping-by-sequencing
#12
Javier Montero-Pau, José Blanca, Cristina Esteras, Eva Ma Martínez-Pérez, Pedro Gómez, Antonio J Monforte, Joaquín Cañizares, Belén Picó
BACKGROUND: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100185/an-improved-genome-assembly-uncovers-prolific-tandem-repeats-in-atlantic-cod
#13
Ole K Tørresen, Bastiaan Star, Sissel Jentoft, William B Reinar, Harald Grove, Jason R Miller, Brian P Walenz, James Knight, Jenny M Ekholm, Paul Peluso, Rolf B Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S Jakobsen, Alexander J Nederbragt
BACKGROUND: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100184/cnvs-into-the-wild-screening-the-genomes-of-conifer-trees-picea-spp-reveals-fewer-gene-copy-number-variations-in-hybrids-and-links-to-adaptation
#14
Julien Prunier, Sébastien Caron, John MacKay
BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#15
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28100171/genome-wide-standing-variation-facilitates-long-term-response-to-bidirectional-selection-for-antibody-response-in-chickens
#16
Mette Lillie, Zheya Sheng, Christa F Honaker, Ben J Dorshorst, Christopher M Ashwell, Paul B Siegel, Örjan Carlborg
BACKGROUND: Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. RESULTS: We observed wide genome involvement in response to this selection regime...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100040/induced-pluripotent-stem-cell-research-in-the-era-of-precision-medicine
#17
Takashi Hamazaki, Nihal El Rouby, Natalie C Fredette, Katherine E Santostefano, Naohiro Terada
Recent advances in DNA sequencing technologies are revealing how human genetic variations associate with differential health risks, disease susceptibilities and drug responses. Such information is now expected to help evaluate individual health risks, design personalized health plans and treat patients with precision. It is still challenging, however, to understand how such genetic variations cause the phenotypic alterations in pathobiologies and treatment response. Human induced pluripotent stem cell (iPSC) technologies are emerging as a promising strategy to fill the knowledge gaps between genetic association studies and underlying molecular mechanisms...
January 18, 2017: Stem Cells
https://www.readbyqxmd.com/read/28100011/association-mapping-of-morphological-traits-in-wild-and-captive-zebra-finches-reliable-within-but-not-between-populations
#18
Ulrich Knief, Holger Schielzeth, Niclas Backström, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C Griffith, Hans Ellegren, Bart Kempenaers, Wolfgang Forstmeier
Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099990/statistical-significance-for-hierarchical-clustering
#19
Patrick K Kimes, Yufeng Liu, David Neil Hayes, James Stephen Marron
Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high-dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other fields for their ability to simultaneously uncover multiple layers of clustering structure. A critical and challenging question in cluster analysis is whether the identified clusters represent important underlying structure or are artifacts of natural sampling variation...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099784/investigating-the-extent-of-parallelism-in-morphological-and-genomic-divergence-among-lake-trout-ecotypes-in-lake-superior
#20
Alysse Perreault-Payette, Andrew M Muir, Frederick Goetz, Charles Perrier, Eric Normandeau, Pascal Sirois, Louis Bernatchez
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology...
January 18, 2017: Molecular Ecology
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