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https://www.readbyqxmd.com/read/28938721/the-draft-genome-sequence-of-a-desert-tree-populus-pruinosa
#1
Wenlu Yang, Kun Wang, Jian Zhang, Jianchao Ma, Jianquan Liu, Tao Ma
Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation compared to its sister species, P. euphratica. Here we present a draft genome sequence for P. pruinosa and examine genomic variations between the 2 species. A total of 60 Gb of clean reads from whole-genome sequencing of a P. pruinosa individual were generated using the Illumina HiSeq2000 platform. The assembled genome is 479.3 Mb in length, with an N50 contig size of 14.0 kb and a scaffold size of 698...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#2
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/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#3
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937979/molecular-genomic-characterization-of-tick-and-human-derived-severe-fever-with-thrombocytopenia-syndrome-virus-isolates-from-south-korea
#4
Seok-Min Yun, Su-Jin Park, Sun-Whan Park, WooYoung Choi, Hye Won Jeong, Young-Ki Choi, Won-Ja Lee
BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral disease caused by the SFTS virus (SFTSV) from Bunyaviridae that is endemic in East Asia. However, the genetic and evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited. METHODOLOGY/PRINCIPAL FINDINGS: In this study we identify, for the first time, the genome sequence of a tick (Haemaphysalis longicornis)-derived Korean SFTSV strain (designated as KAGWT) and compare this virus with recent human SFTSV isolates to identify the genetic variations and relationships among SFTSV strains...
September 22, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28936945/sources-of-fungal-genetic-variation-and-associating-it-with-phenotypic-diversity
#5
John W Taylor, Sara Branco, Cheng Gao, Chris Hann-Soden, Liliam Montoya, Iman Sylvain, Pierre Gladieux
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability...
September 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28936814/-the-role-of-molecular-karyotyping-in-the-genetic-etiology-of-autism
#6
Burcu Özbaran, Bilçağ Akgün, Duygu Kaçamak, Sezen Köse, Ayşenur Kavasoğlu, Hüseyin Onay
OBJECTIVE: The aim of this study was to investigate the deletions and duplications with a molecular karyotyping technique and to elucidate the etiology of autism. METHOD: A total of 31 patients (20 boys and 11 girls) between 4 to 18 years old with normal chromosomal analysis and no Fragile X mutation were diagnosed in the Ege University Child and Adolescent Psychiatry Clinic with autism (according to DSM-IV-TR criteria) and were enrolled in the study. Symptom severity of the patients was evaluated with a Childhood Autism Rating Scale...
2017: Türk Psikiyatri Dergisi, Turkish Journal of Psychiatry
https://www.readbyqxmd.com/read/28936219/a-high-density-genetic-map-derived-from-rad-sequencing-and-its-application-in-qtl-analysis-of-yield-related-traits-in-vigna-unguiculata
#7
Lei Pan, Nian Wang, Zhihua Wu, Rui Guo, Xiaolu Yu, Yu Zheng, Qiuju Xia, Songtao Gui, Chanyou Chen
Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28935855/establishing-multiple-omics-baselines-for-three-southeast-asian-populations-in-the-singapore-integrative-omics-study
#8
Woei-Yuh Saw, Erwin Tantoso, Husna Begum, Lihan Zhou, Ruiyang Zou, Cheng He, Sze Ling Chan, Linda Wei-Lin Tan, Lai-Ping Wong, Wenting Xu, Don Kyin Nwe Moong, Yenly Lim, Bowen Li, Nisha Esakimuthu Pillai, Trevor A Peterson, Tomasz Bielawny, Peter J Meikle, Piyushkumar A Mundra, Wei-Yen Lim, Ma Luo, Kee-Seng Chia, Rick Twee-Hee Ong, Liam R Brunham, Chiea-Chuen Khor, Heng Phon Too, Richie Soong, Markus R Wenk, Peter Little, Yik-Ying Teo
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28934976/desman-a-new-tool-for-de-novo-extraction-of-strains-from-metagenomes
#9
Christopher Quince, Tom O Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E Darling, Gavin Collins, A Murat Eren
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934931/mitochondrial-genomes-of-african-pangolins-and-insights-into-evolutionary-patterns-and-phylogeny-of-the-family-manidae
#10
Zelda du Toit, Morné du Plessis, Desiré L Dalton, Raymond Jansen, J Paul Grobler, Antoinette Kotzé
BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934591/combining-traditional-mutagenesis-with-new-high-throughput-sequencing-and-genome-editing-to-reveal-hidden-variation-in-polyploid-wheat
#11
Cristobal Uauy, Brande B H Wulff, Jorge Dubcovsky
Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28934590/the-relationship-between-the-human-genome-and-microbiome-comes-into-view
#12
Julia K Goodrich, Emily R Davenport, Andrew G Clark, Ruth E Ley
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28934436/insights-into-onchocerca-volvulus-population-biology-through-multilocus-immunophenotyping
#13
Carmelle T Norice-Tra, José Ribeiro, Sasisekhar Bennuru, Michael P Fay, Rahul Tyagi, Makedonka Mitreva, Thomas B Nutman
We have developed a serologically based immunophenotyping approach to study Onchocerca volvulus (Ov) population diversity. Using genomic sequence data and polymerase chain reaction-based genotyping, we identified nonsynonymous single-nucleotide polymorphisms (SNPs) in the genes of 16 major immunogenic Ov proteins: Ov-CHI-1/Ov-CHI-2, Ov16, Ov-FAR-1, Ov-CPI-1, Ov-B20, Ov-ASP-1, Ov-TMY-1, OvSOD1, OvGST1, Ov-CAL-1, M3/M4, Ov-RAL-1, Ov-RAL-2, Ov-ALT-1, Ov-FBA-1, and Ov-B8. We assessed the immunoreactivity of onchocerciasis patient sera (n = 152) from the Americas, West Africa, Central Africa, and East Africa against peptides derived from 10 of these proteins containing SNPs...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934397/a-modifier-of-huntington-s-disease-onset-at-the-mlh1-locus
#14
Jong-Min Lee, Michael J Chao, Denise Harold, Kawther Abu Elneel, Tammy Gillis, Peter Holmans, Lesley Jones, Michael Orth, Richard H Myers, Seung Kwak, Vanessa C Wheeler, Marcy E MacDonald, James F Gusella
Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in HTT. Many clinical characteristics of HD such as age at motor onset are determined largely by the size of HTT CAG repeat. However, emerging evidence strongly supports a role for other genetic factors in modifying the disease pathogenesis driven by mutant huntingtin. A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome 3...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934307/amplification-of-the-egfr-gene-can-be-maintained-and-modulated-by-variation-of-egf-concentrations-in-in-vitro-models-of-glioblastoma-multiforme
#15
Doreen William, Poroshista Mokri, Nora Lamp, Michael Linnebacher, Carl Friedrich Classen, Andreas Erbersdobler, Björn Schneider
Glioblastoma multiforme (GBM) is the most common and lethal brain tumor in adults. It is known that amplification of the epidermal growth factor receptor gene (EGFR) occurs in approximately 40% of GBM, leading to enhanced activation of the EGFR signaling pathway and promoting tumor growth. Although GBM mutations are stably maintained in GBM in vitro models, rapid loss of EGFR gene amplification is a common observation during cell culture. To maintain EGFR amplification in vitro, heterotopic GBM xenografts with elevated EGFR copy number were cultured under varying serum conditions and EGF concentrations...
2017: PloS One
https://www.readbyqxmd.com/read/28931914/high-resolution-analysis-of-rare-copy-number-variants-in-patients-with-autism-spectrum-disorder-from-taiwan
#16
Chia-Hsiang Chen, Hsin-I Chen, Wei-Hsien Chien, Ling-Hui Li, Yu-Yu Wu, Yen-Nan Chiu, Wen-Che Tsai, Susan Shur-Fen Gau
Rare genomic copy number variations (CNVs) (frequency <1%) contribute a part to the genetic underpinnings of autism spectrum disorders (ASD). The study aimed to understand the scope of rare CNV in Taiwanese patients with ASD. We conducted a genome-wide CNV screening of 335 ASD patients (299 males, 36 females) from Taiwan using Affymetrix Genome-Wide Human SNP Array 6.0 and compared the incidence of rare CNV with that of 1093 control subjects (525 males, 568 females). We found a significantly increased global burden of rare CNVs in the ASD group compared to the controls as a whole or when the rare CNVs were classified by the size and types of CNV...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931750/adrenal-gipr-expression-and-chromosome-19q13-microduplications-in-gip-dependent-cushing-s-syndrome
#17
Anne-Lise Lecoq, Constantine A Stratakis, Say Viengchareun, Ronan Chaligné, Lucie Tosca, Vianney Deméocq, Mirella Hage, Annabel Berthon, Fabio R Faucz, Patrick Hanna, Hadrien-Gaël Boyer, Nicolas Servant, Sylvie Salenave, Gérard Tachdjian, Clovis Adam, Vanessa Benhamo, Eric Clauser, Anne Guiochon-Mantel, Jacques Young, Marc Lombès, Isabelle Bourdeau, Dominique Maiter, Antoine Tabarin, Jérôme Bertherat, Hervé Lefebvre, Wouter de Herder, Estelle Louiset, André Lacroix, Philippe Chanson, Jérôme Bouligand, Peter Kamenický
GIP-dependent Cushing's syndrome is caused by ectopic expression of glucose-dependent insulinotropic polypeptide receptor (GIPR) in cortisol-producing adrenal adenomas or in bilateral macronodular adrenal hyperplasias. Molecular mechanisms leading to ectopic GIPR expression in adrenal tissue are not known. Here we performed molecular analyses on adrenocortical adenomas and bilateral macronodular adrenal hyperplasias obtained from 14 patients with GIP-dependent adrenal Cushing's syndrome and one patient with GIP-dependent aldosteronism...
September 21, 2017: JCI Insight
https://www.readbyqxmd.com/read/28931740/single-sperm-sequencing-reveals-the-accelerated-mitochondrial-mutation-rate-in-male-daphnia-pulex-crustacea-cladocera
#18
Sen Xu, Kenny Van Tran, Swatantra Neupane, Marelize Snyman, Trung Viet Huynh, Way Sung
Mutation rate in the nuclear genome differs between sexes, with males contributing more mutations than females to their offspring. The male-biased mutation rates in the nuclear genome is most likely to be driven by a higher number of cell divisions in spermatogenesis than in oogenesis, generating more opportunities for DNA replication errors. However, it remains unknown whether male-biased mutation rates are present in mitochondrial DNA (mtDNA). Although mtDNA is maternally inherited and male mtDNA mutation typically does not contribute to genetic variation in offspring, male mtDNA mutations are critical for male reproductive health...
September 27, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28931559/variation-in-position-effect-variegation-within-a-natural-population
#19
Keegan J P Kelsey, Andrew G Clark
Changes in chromatin state may drive changes in gene expression, and it is of growing interest to understand the population genetic forces that drive differences in chromatin state. Here, we use the phenomenon of position effect variegation (PEV), a well-studied proxy for chromatin state, to survey variation in PEV among a naturally derived population. Further, we explore the genetic architecture of natural variation in factors that modify PEV. While previous mutation screens have identified over 150 suppressors and enhancers of PEV, it remains unknown to what extent allelic variation in these modifiers mediate inter-individual variation in PEV...
September 20, 2017: Genetics
https://www.readbyqxmd.com/read/28931550/variation-in-akt-protein-kinases-in-human-populations
#20
Peter Rotwein
The three AKT kinases are related proteins that are essential for normal growth and metabolic regulation, and are implicated as key signaling mediators in many physiological and patho-physiological processes. Each AKT is activated by common biochemical signals that act downstream of growth factor and hormone receptors via phosphatidylinositol-3 kinase, and each controls several downstream pathways. The importance of AKT actions in human physiology is strengthened by the rarity of modifying mutations in their genes, and by the devastating impact caused by these mutations on growth and development, and in disorders such as cancer...
September 20, 2017: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology
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