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BMC Medical Genomics

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https://www.readbyqxmd.com/read/28081699/erratum-to-experiences-and-attitudes-of-residents-regarding-a-community-based-genome-cohort-study-in-japan-a-population-based-cross-sectional-study
#1
Keiko Miyamoto, Miho Iwakuma, Takeo Nakayama
No abstract text is available yet for this article.
January 12, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28077143/pregnant-women-carrying-microcephaly-foetuses-and-zika-virus-contain-potentially-pathogenic-microbes-and-parasites-in-their-amniotic-fluid
#2
Diogo Antonio Tschoeke, Louisi Souza de Oliveira, Luciana Leomil, Amilcar Tanuri, Fabiano Lopes Thompson
BACKGROUND: Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new microcephaly cases in Brazil. Inside the uterus, the foetus is surrounded by the Amniotic Fluid, a proximal fluid that contains foetal and maternal cells as well as microorganisms and where Zika Virus was already found. CASE PRESENTATION: A previous study reported the presence of the Zika Virus in the amniotic fluid (collected in the 28th gestational week) of two pregnant women carrying microcephaly foetuses in Brazil...
January 11, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28069037/health-and-genetic-ancestry-testing-time-to-bridge-the-gap
#3
Andrew Smart, Deborah A Bolnick, Richard Tutton
BACKGROUND: It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health risks associated with particular ancestral lineages. Because some of the proposed associations have received little attention from oversight agencies and professional genetic associations, scientific developments are currently outpacing governance regimes for consumer genetic testing...
January 9, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28056976/a-novel-approach-to-genome-wide-association-analysis-identifies-genetic-associations-with-primary-biliary-cholangitis-and-primary-sclerosing-cholangitis-in-polish-patients
#4
Agnieszka Paziewska, Andrzej Habior, Agnieszka Rogowska, Włodzimierz Zych, Krzysztof Goryca, Jakub Karczmarski, Michalina Dabrowska, Filip Ambrozkiewicz, Bozena Walewska-Zielecka, Marek Krawczyk, Halina Cichoz-Lach, Piotr Milkiewicz, Agnieszka Kowalik, Krzysztof Mucha, Joanna Raczynska, Joanna Musialik, Grzegorz Boryczka, Michal Wasilewicz, Irena Ciecko-Michalska, Malgorzata Ferenc, Maria Janiak, Alina Kanikowska, Rafal Stankiewicz, Marek Hartleb, Tomasz Mach, Marian Grzymislawski, Joanna Raszeja-Wyszomirska, Ewa Wunsch, Tomasz Bobinski, Michal Mikula, Jerzy Ostrowski
BACKGROUND: Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic architecture of PBC and PSC within the Polish population. METHODS: Subjects were 443 women with PBC, 120 patients with PSC, and 934 healthy controls recruited from Gastroenterology Departments in various Polish hospitals. Allelotyping employed a pooled-DNA sample-based genome-wide association study (GWAS) approach, using Illumina Human Omni2...
January 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28057009/erratum-to-conserved-recurrent-gene-mutations-correlate-with-pathway-deregulation-and-clinical-outcomes-of-lung-adenocarcinoma-in-never-smokers
#5
Zhifu Sun, Liang Wang, Bruce W Eckloff, Bo Deng, Yi Wang, Jason A Wampfler, JinSung Jang, Eric D Wieben, Jin Jen, Ming You, Ping Yang
No abstract text is available yet for this article.
January 5, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/27955658/genetic-study-of-congenital-bile-duct-dilatation-identifies-de-novo-and-inherited-variants-in-functionally-related-genes
#6
John K L Wong, Desmond Campbell, Ngoc Diem Ngo, Fanny Yeung, Guo Cheng, Clara S M Tang, Patrick H Y Chung, Ngoc Son Tran, Man-Ting So, Stacey S Cherny, Pak C Sham, Paul K Tam, Maria-Mercè Garcia-Barcelo
BACKGROUND: Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic study has ever been conducted. METHODS: We aim to identify genetic risk factors by a "trio-based" exome-sequencing approach, whereby 31 CDD probands and their unaffected parents were exome-sequenced. Seven-hundred controls from the local population were used to detect gene-sets significantly enriched with rare variants in CDD patients...
December 12, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27884142/dna-methylation-patterns-associated-with-oxidative-stress-in-an-ageing-population
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
LETTER
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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/26979972/experiences-and-attitudes-of-residents-regarding-a-community-based-genome-cohort-study-in-japan-a-population-based-cross-sectional-study
#20
Keiko Miyamoto, Miho Iwakuma, Takeo Nakayama
BACKGROUND: Because of the rapid development in genomics, more research findings have emerged. However, the association between society and research results remains controversial. This article examines the experiences and attitudes of residents regarding a community-based genomic cohort study. METHODS: This study was conducted as a part of the health survey of the City Health Promotion section. At the conclusion of the first stage of the project, a self-administered questionnaire was mailed to a random sample of 2,500 residents in 2012...
March 15, 2016: BMC Medical Genomics
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