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Wei Liu, Changhong Liu, Feng Chen, Jianbo Yang, Lei Zheng
Discrimination of genetically modified organisms is increasingly demanded by legislation and consumers worldwide. The feasibility of a non-destructive discrimination of glyphosate-resistant and conventional soybean seeds and their hybrid descendants was examined by terahertz time-domain spectroscopy system combined with chemometrics. Principal component analysis (PCA), least squares-support vector machines (LS-SVM) and PCA-back propagation neural network (PCA-BPNN) models with the first and second derivative and standard normal variate (SNV) transformation pre-treatments were applied to classify soybean seeds based on genotype...
October 26, 2016: Scientific Reports
Shuai Wang, James B Meigs, Josée Dupuis
In recent years, improved genotyping and sequencing technologies have enabled the discovery of new loci associated with various diseases or traits. For instance, by testing the association with each single-nucleotide variant (SNV) separately, genome-wide association studies (GWAS) have achieved tremendous success in identifying SNVs associated with specific traits. However, little is known about the common genetic basis of multiple traits owing to lack of efficient methods. With the use of extended quasi-likelihood, a Wald test has been proposed to perform a bivariate analysis of a continuous and a binary trait in unrelated samples...
October 26, 2016: European Journal of Human Genetics: EJHG
Juliane Krüger, Christian Ehm, Dieter Lentz
Catalytic hydrodefluorination of perfluoroallylbenzene with Cp2TiH in THF is unselective and yields a variety of previously unknown compounds, predominantly activated in the allylic position. Several different mechanisms have been examined in detail using solvent corrected (THF) DFT(M06-2X) calculations for the archetypal perfluorinated olefin perfluoropropene and perfluoroallylbenzene: (a) single electron transfer, (b) hydrometallation/fluoride elimination, (c) σ-bond metathesis (allylic or vinylic), and (d) nucleophilic vinylic substitution (SNV, w/o Ti-F contacts in the TS)...
October 25, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Yan Guo, Jie Wu, Shilin Zhao, Fei Ye, Yinghao Su, Travis Clark, Quanhu Sheng, Brian Lehmann, Xiao-Ou Shu, Qiuyin Cai
Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N = 16). We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates...
2016: International Journal of Genomics
Amanda McGuire, Kaitlyn Miedema, Joseph R Fauver, Amber Rico, Tawfik Aboellail, Sandra L Quackenbush, Ann Hawkinson, Tony Schountz
Rodent-borne hantaviruses can cause two human diseases with many pathological similarities: hantavirus cardiopulmonary syndrome (HCPS) in the western hemisphere and hemorrhagic fever with renal syndrome in the eastern hemisphere. Each virus is hosted by specific reservoir species without conspicuous disease. HCPS-causing hantaviruses require animal biosafety level-4 (ABSL-4) containment, which substantially limits experimental research of interactions between the viruses and their reservoir hosts. Maporal virus (MAPV) is a South American hantavirus not known to cause disease in humans, thus it can be manipulated under ABSL-3 conditions...
October 18, 2016: Viruses
Mayuko Furuta, Masaki Ueno, Akihiro Fujimoto, Shinya Hayami, Satoru Yasukawa, Fumiyoshi Kojima, Koji Arihiro, Yoshiiku Kawakami, Christopher P Wardell, Yuichi Shiraishi, Hiroko Tanaka, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Naoki Tokunaga, Keith A Boroevich, Tetsuo Abe, Hiroshi Aikata, Hideki Ohdan, Kunihito Goto, Michiaki Kubo, Tatsuhiko Tsunoda, Satoru Miyano, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa
BACKGROUND & AIMS: Liver cancer has a high risk of multi-centric (MC) occurrence due to a strong carcinogenic background in the liver, in addition to a high risk of intrahepatic metastasis (IM). There are large characteristic differences between IM and MC with regards to their development and clinical outcome, but discriminating between IM and MC is usually non-trivial with respect to clinical or pathological aspects. METHODS: In this study, we performed whole-genome and RNA sequencing analyses of 49 liver nodules and two extra-hepatic metastatic tumors from 23 patients to investigate for any potential to discriminate between IM and MC at the molecular level...
October 11, 2016: Journal of Hepatology
Daniel R Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey, David Haussler
BACKGROUND: The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed that genomes are highly plastic, and that whole regions can be moved, removed or duplicated in bulk. These structural variants (SV) have been shown to have significant impact on phenotype, but their study has been held back by the combinatorial complexity of the underlying models...
September 29, 2016: BMC Bioinformatics
Stefan Taudien, Ludwig Lausser, Evangelos J Giamarellos-Bourboulis, Christoph Sponholz, Franziska Schöneweck, Marius Felder, Lyn-Rouven Schirra, Florian Schmid, Charalambos Gogos, Susann Groth, Britt-Sabina Petersen, Andre Franke, Wolfgang Lieb, Klaus Huse, Peter F Zipfel, Oliver Kurzai, Barbara Moepps, Peter Gierschik, Michael Bauer, André Scherag, Hans A Kestler, Matthias Platzer
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups...
September 14, 2016: EBioMedicine
Terri-Lee Kammies, Marena Manley, Pieter A Gouws, Paul J Williams
The potential for near-infrared (NIR) hyperspectral imaging and multivariate data analysis to be used as a rapid non-destructive tool for detection and differentiation of bacteria was investigated. NIR hyperspectral images were collected of Bacillus cereus, Escherichia coli, Salmonella enteritidis, Staphylococcus aureus and Staphylococcus epidermidis grown on agar for 20 h at 37 °C. Principal component analysis (PCA) was applied to mean-centred data. Standard normal variate (SNV) correction and the Savitzky-Golay technique was applied (2nd derivative, 3rd-order polynomial; 25 point smoothing) to wavelengths in the range of 1103 to 2471 nm...
November 2016: Applied Microbiology and Biotechnology
Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata, Fuli Yu
BACKGROUND: The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies...
2016: BMC Bioinformatics
Niko Popitsch, Anna Schuh, Jenny C Taylor
MOTIVATION: The increasing adoption of clinical whole-genome resequencing (WGS) demands for highly-accurate and reproducible variant calling (VC) methods. The observed discordance between state-of-the-art VC pipelines, however, indicates that the current practice still suffers from non-negligible numbers of false positive and negative SNV and INDEL calls that were shown to be enriched among discordant calls but also in genomic regions with low sequence complexity. RESULTS: Here, we describe our method ReliableGenome (RG) for partitioning genomes into high and low concordance regions with respect to a set of surveyed VC pipelines...
September 7, 2016: Bioinformatics
Steve Laurie, Marcos Fernandez-Callejo, Santiago Marco-Sola, Jean-Remi Trotta, Jordi Camps, Alejandro Chacón, Antonio Espinosa, Marta Gut, Ivo Gut, Simon Heath, Sergi Beltran
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample...
September 8, 2016: Human Mutation
Benjamin Gaastra, Aleksey Shatunov, Sara Pulit, Ashley R Jones, William Sproviero, Alexandra Gillett, Zhongbo Chen, Janine Kirby, Isabella Fogh, John F Powell, P Nigel Leigh, Karen E Morrison, Pamela J Shaw, Christopher E Shaw, Leonard H van den Berg, Jan H Veldink, Cathryn M Lewis, Ammar Al-Chalabi
Our objective was to identify whether rare genetic variation in amyotrophic lateral sclerosis (ALS) candidate survival genes modifies ALS survival. Candidate genes were selected based on evidence for modifying ALS survival. Each tail of the extreme 1.5% of survival was selected from the UK MND DNA Bank and all samples available underwent whole genome sequencing. A replication set from the Netherlands was used for validation. Sequences of candidate survival genes were extracted and variants passing quality control with a minor allele frequency ≤0...
September 1, 2016: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, Anelia Horvath
We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting)...
August 30, 2016: Nucleic Acids Research
Swneke D Bailey, Kinjal Desai, Ken J Kron, Parisa Mazrooei, Nicholas A Sinnott-Armstrong, Aislinn E Treloar, Mark Dowar, Kelsie L Thu, David W Cescon, Jennifer Silvester, S Y Cindy Yang, Xue Wu, Rossanna C Pezo, Benjamin Haibe-Kains, Tak W Mak, Philippe L Bedard, Trevor J Pugh, Richard C Sallari, Mathieu Lupien
Sustained expression of the estrogen receptor-α (ESR1) drives two-thirds of breast cancer and defines the ESR1-positive subtype. ESR1 engages enhancers upon estrogen stimulation to establish an oncogenic expression program. Somatic copy number alterations involving the ESR1 gene occur in approximately 1% of ESR1-positive breast cancers, suggesting that other mechanisms underlie the persistent expression of ESR1. We report significant enrichment of somatic mutations within the set of regulatory elements (SRE) regulating ESR1 in 7% of ESR1-positive breast cancers...
October 2016: Nature Genetics
Benjamin N Bimber, Michael J Raboin, John Letaw, Kimberly A Nevonen, Jennifer E Spindel, Susan R McCouch, Rita Cervera-Juanes, Eliot Spindel, Lucia Carbone, Betsy Ferguson, Amanda Vinson
BACKGROUND: Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still in its infancy. Whole-genome sequence (WGS) data in large pedigreed macaque colonies could provide substantial experimental power for genetic discovery, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for 30X WGS, followed by low-cost genotyping-by-sequencing (GBS) at 30X on the remaining macaques in order to generate sparse genotype data at high accuracy...
2016: BMC Genomics
Z H Li, Y Z Wang, J Liu, M Zhu, J B Du, J Yuan, W H Chen, Z D Zhang, Z B Hu, T C Wu, H B Shen
OBJECTIVE: To explore the association between DNA damage-related genetic variants and lung cancer susceptibility in a Han Chinese population. METHODS: This case-control study enrolled patients from the Cancer Hospital of Jiangsu Province and Jiangsu Province Hospital from 2003 to 2009. Controls were randomly selected from individuals who visited the same hospital or a community-based health examination program during the same time period. A 5 ml venous blood sample was obtained from each participant and epidemiological information was collected on a standard questionnaire...
August 6, 2016: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
Douglas M Ruderfer, Tymor Hamamsy, Monkol Lek, Konrad J Karczewski, David Kavanagh, Kaitlin E Samocha, Mark J Daly, Daniel G MacArthur, Menachem Fromer, Shaun M Purcell
Copy number variation (CNV) affecting protein-coding genes contributes substantially to human diversity and disease. Here we characterized the rates and properties of rare genic CNVs (<0.5% frequency) in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium (ExAC) database. On average, individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one rare genic CNV. For every gene, we empirically estimated an index of relative intolerance to CNVs that demonstrated moderate correlation with measures of genic constraint based on single-nucleotide variation (SNV) and was independently correlated with measures of evolutionary conservation...
October 2016: Nature Genetics
Can Kockan, Faraz Hach, Iman Sarrafi, Robert H Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W Wyatt, Stanislav V Volik, Kim N Chi, Colin C Collins, S Cenk Sahinalp
MOTIVATION: Successful development and application of precision oncology approaches require robust elucidation of the genomic landscape of a patient's cancer and, ideally, the ability to monitor therapy-induced genomic changes in the tumour in an inexpensive and minimally invasive manner. Thanks to recent advances in sequencing technologies, "liquid biopsy", the sampling of patient's bodily fluids such as blood and urine, is considered as one of the most promising approaches to achieve this goal...
August 16, 2016: Bioinformatics
Seungeun Yeo, Colin A Hodgkinson, Zhifeng Zhou, Jeesun Jung, Ming Leung, Qiaoping Yuan, David Goldman
BACKGROUND: Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes...
2016: BMC Genomics
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