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BMC Medical Genomics

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https://www.readbyqxmd.com/read/27884142/dna-methylation-patterns-associated-with-oxidative-stress-in-an-ageing-population
#1
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27871291/-a-rising-tide-lifts-all-boats-establishing-a-multidisciplinary-genomic-tumor-board-for-breast-cancer-patients-with-advanced-disease
#2
Michelle L McGowan, Roselle S Ponsaran, Paula Silverman, Lyndsay N Harris, Patricia A Marshall
BACKGROUND: Research suggests that multidisciplinary genomic tumor boards (MGTB) can inform cancer patient care, though little is known about factors influencing how MGTBs interpret genomic test results, make recommendations, and perceive the utility of this approach. This study's objective was to observe, describe, and assess the establishment of the Breast Multidisciplinary Genomic Tumor Board, the first MGTB focused on interpreting genomic test results for breast cancer patients with advanced disease...
November 21, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27846842/a-meta-analysis-of-public-microarray-data-identifies-gene-regulatory-pathways-deregulated-in-peripheral-blood-mononuclear-cells-from-individuals-with-systemic-lupus-erythematosus-compared-to-those-without
#3
Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
BACKGROUND: Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus have been extensively investigated using a variety of -omics approaches, including genome-wide association studies, candidate gene studies and microarray experiments of differential gene expression in lupus samples compared to controls. METHODS: This study analyses a combination of existing microarray data sets to identify differentially regulated genetic pathways that are dysregulated in human peripheral blood mononuclear cells from SLE patients compared to unaffected controls...
November 15, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27756306/adaptation-of-a-ras-pathway-activation-signature-from-ff-to-ffpe-tissues-in-colorectal-cancer
#4
Bernard Omolo, Mingli Yang, Fang Yin Lo, Michael J Schell, Sharon Austin, Kellie Howard, Anup Madan, Timothy J Yeatman
BACKGROUND: The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60 % of patients with a wild type KRAS fail to respond to EGFRi combination therapies, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues...
October 19, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27756300/pitfalls-of-improperly-procured-adjacent-non-neoplastic-tissue-for-somatic-mutation-analysis-using-next-generation-sequencing
#5
Lei Wei, Antonios Papanicolau-Sengos, Song Liu, Jianmin Wang, Jeffrey M Conroy, Sean T Glenn, Elizabeth Brese, Qiang Hu, Kiersten Marie Miles, Blake Burgher, Maochun Qin, Karen Head, Angela R Omilian, Wiam Bshara, John Krolewski, Donald L Trump, Candace S Johnson, Carl D Morrison
BACKGROUND: The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent to the excised neoplasm is often used for this purpose as it is simultaneously collected and generally contains the same tissue type as the neoplasm. Following NGS analysis, we and others have frequently observed low-level somatic mutations in these non-neoplastic tissues, which may impose additional challenges to somatic mutation detection as it complicates germline variant filtering...
October 19, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27733153/protecting-genomic-data-analytics-in-the-cloud-state-of-the-art-and-opportunities
#6
Haixu Tang, Xiaoqian Jiang, Xiaofeng Wang, Shuang Wang, Heidi Sofia, Dov Fox, Kristin Lauter, Bradley Malin, Amalio Telenti, Li Xiong, Lucila Ohno-Machado
The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies...
October 13, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27716216/the-anatomy-to-genomics-atg-start-genetics-medical-school-initiative-incorporating-exome-sequencing-data-from-cadavers-used-for-anatomy-instruction-into-the-first-year-curriculum
#7
Glenn S Gerhard, Qunyan Jin, Barbara V Paynton, Steven N Popoff
BACKGROUND: The increasing use of next generation DNA sequencing in clinical medicine is exposing the need for more genetics education in physician training. We piloted an initiative to determine the feasibility of incorporating exome sequencing data generated from DNA obtained from cadavers used for teaching Anatomy into a first year medical student integrated block-style course. METHODS: We optimized the procedure to obtain DNA for exome sequencing by comparing the quality and quantity of DNA isolated from several tissues by two different extraction methods...
October 6, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27716407/an-adaptive-detection-method-for-fetal-chromosomal-aneuploidy-using-cell-free-dna-from-447-korean-women
#8
Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Minae An, Jungsu Ha, Kyusang Lee, Byung Chul Kim, Hailing Zheng, Xinqiang Zhu, Hongliang Chen, Jong Bhak
BACKGROUND: Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predictions which occur while performing NIPT still exist in pregnant women at high risk for fetal aneuploidy. We performed the largest-scale clinical NIPT study in Korea to date to assess the risk of false negatives and false positives using next-generation sequencing. METHODS: A total of 447 pregnant women at high risk for fetal aneuploidy were enrolled at 12 hospitals in Korea...
October 3, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27634286/genome-wide-positioning-of-bivalent-mononucleosomes
#9
Subhojit Sen, Kirsten F Block, Alice Pasini, Stephen B Baylin, Hariharan Easwaran
BACKGROUND: Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes. RESULTS: Here, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes...
September 15, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27624058/immunoseq-the-identification-of-functionally-relevant-variants-through-targeted-capture-and-sequencing-of-active-regulatory-regions-in-human-immune-cells
#10
Andréanne Morin, Tony Kwan, Bing Ge, Louis Letourneau, Maria Ban, Karolina Tandre, Maxime Caron, Johanna K Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann-Christine Syvanen, Lars Ronnblom, Stephen J Sawcer, Mark G Lathrop, Tomi Pastinen
BACKGROUND: The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - "Immunoseq"...
September 13, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27568008/explorations-to-improve-the-completeness-of-exome-sequencing
#11
Chen Du, Barbara N Pusey, Christopher J Adams, C Christopher Lau, William P Bone, William A Gahl, Thomas C Markello, David R Adams
BACKGROUND: Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis...
August 27, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27259591/breast-cancer-subtype-predictors-revisited-from-consensus-to-concordance
#12
Herman Mj Sontrop, Marcel Jt Reinders, Perry D Moerland
BACKGROUND: At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-stage approach consisting of clustering and subtype predictor construction based on the cluster labels of individual cases. SSPs have been criticized because their subtype assignments for the same samples were only moderately concordant (Cohen's κ<0.6). METHODS: We propose a semi-supervised approach where for five datasets, consensus sets were constructed consisting of those samples that were concordantly subtyped by a number of different predictors...
June 3, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27052975/saliva-dna-quality-and-genotyping-efficiency-in-a-predominantly-elderly-population
#13
Harini V Gudiseva, Mark Hansen, Linda Gutierrez, David W Collins, Jie He, Lana D Verkuil, Ian D Danford, Anna Sagaser, Anita S Bowman, Rebecca Salowe, Prithvi S Sankar, Eydie Miller-Ellis, Amanda Lehman, Joan M O'Brien
BACKGROUND: The question of whether DNA obtained from saliva is an acceptable alternative to DNA from blood is a topic of considerable interest for large genetics studies. We compared the yields, quality and performance of DNAs from saliva and blood from a mostly elderly study population. METHODS: Two thousand nine hundred ten DNAs from primarily elderly subjects (mean age ± standard deviation (SD): 65 ± 12 years), collected for the Primary Open-Angle African-American Glaucoma Genetics (POAAGG) study, were evaluated by fluorometry and/or spectroscopy...
April 7, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/26729011/the-ignite-network-a-model-for-genomic-medicine-implementation-and-research
#14
Kristin Wiisanen Weitzel, Madeline Alexander, Barbara A Bernhardt, Neil Calman, David J Carey, Larisa H Cavallari, Julie R Field, Diane Hauser, Heather A Junkins, Phillip A Levin, Kenneth Levy, Ebony B Madden, Teri A Manolio, Jacqueline Odgis, Lori A Orlando, Reed Pyeritz, R Ryanne Wu, Alan R Shuldiner, Erwin P Bottinger, Joshua C Denny, Paul R Dexter, David A Flockhart, Carol R Horowitz, Julie A Johnson, Stephen E Kimmel, Mia A Levy, Toni I Pollin, Geoffrey S Ginsburg
BACKGROUND: Patients, clinicians, researchers and payers are seeking to understand the value of using genomic information (as reflected by genotyping, sequencing, family history or other data) to inform clinical decision-making. However, challenges exist to widespread clinical implementation of genomic medicine, a prerequisite for developing evidence of its real-world utility. METHODS: To address these challenges, the National Institutes of Health-funded IGNITE (Implementing GeNomics In pracTicE; www...
January 5, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27609023/a-19-gene-expression-signature-as-a-predictor-of-survival-in-colorectal-cancer
#15
Nurul Ainin Abdul Aziz, Norfilza M Mokhtar, Roslan Harun, Md Manir Hossain Mollah, Isa Mohamed Rose, Ismail Sagap, Azmi Mohd Tamil, Wan Zurinah Wan Ngah, Rahman Jamal
BACKGROUND: Histopathological assessment has a low potential to predict clinical outcome in patients with the same stage of colorectal cancer. More specific and sensitive biomarkers to determine patients' survival are needed. We aimed to determine gene expression signatures as reliable prognostic marker that could predict survival of colorectal cancer patients with Dukes' B and C. METHODS: We examined microarray gene expression profiles of 78 archived tissues of patients with Dukes' B and C using the Illumina DASL assay...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27586379/known-unknowns-building%C3%A2-an-ethics-of-uncertainty-into-genomic-medicine
#16
Ainsley J Newson, Samantha J Leonard, Alison Hall, Clara L Gaff
BACKGROUND: Genomic testing has reached the point where, technically at least, it can be cheaper to undertake panel-, exome- or whole genome testing than it is to sequence a single gene. An attribute of these approaches is that information gleaned will often have uncertain significance. In addition to the challenges this presents for pre-test counseling and informed consent, a further consideration emerges over how - ethically - we should conceive of and respond to this uncertainty. To date, the ethical aspects of uncertainty in genomics have remained under-explored...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27561550/within-pair-differences-of-dna-methylation-levels-between-monozygotic-twins-are-different-between-male-and-female-pairs
#17
Mikio Watanabe, Chika Honda, Yoshinori Iwatani, Shiro Yorifuji, Hiroyasu Iso, Kei Kamide, Jun Hatazawa, Shinji Kihara, Norio Sakai, Hiroko Watanabe, Kiyoko Makimoto, Mikio Watanabe, Chika Honda, Yoshinori Iwatani
BACKGROUND: DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related individual differences in the sensitivity to methylation rigorously, we performed a systematic analysis of DNA methylation in monozygotic twins, an optimal model to evaluate them because the genetic backgrounds are the same. RESULTS: We examined 30 male and 43 female older monozygotic twin pairs recruited from the registry established by the Center for Twin Research, Osaka University...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27542606/reliable-gene-expression-profiling-of-formalin-fixed-paraffin-embedded-breast-cancer-tissue-ffpe-using-cdna-mediated-annealing-extension-selection-and-ligation-whole-genome-dasl-wg-assay
#18
Mahesh Iddawela, Oscar M Rueda, Marcus Klarqvist, Stefan Graf, Helena M Earl, Carlos Caldas
BACKGROUND: The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27538512/reproducible-detection-of-disease-associated-markers-from-gene-expression-data
#19
Katsuhiro Omae, Osamu Komori, Shinto Eguchi
BACKGROUND: Detection of disease-associated markers plays a crucial role in gene screening for biological studies. Two-sample test statistics, such as the t-statistic, are widely used to rank genes based on gene expression data. However, the resultant gene ranking is often not reproducible among different data sets. Such irreproducibility may be caused by disease heterogeneity. RESULTS: When we divided data into two subsets, we found that the signs of the two t-statistics were often reversed...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27535823/fast-comparison-of-genomic-and-meta-genomic-reads-with-alignment-free-measures-based-on-quality-values
#20
Matteo Comin, Michele Schimd
BACKGROUND: Sequencing technologies are generating enormous amounts of read data, however assembly of genomes and metagenomes remain among the most challenging tasks. In this paper we study the comparison of genomes and metagenomes only based on read data, using word counts statistics called alignment-free thus not requiring reference genomes or assemblies. Quality scores produced by sequencing platforms are fundamental for various analyses, moreover future-generation sequencing platforms, will produce longer reads but with error rate around 15 %...
2016: BMC Medical Genomics
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