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Genome Medicine

Lin Zhou, Fangqing Zhao
Unraveling functional noncoding variants associated with complex diseases is still a great challenge. We present a novel algorithm, Prioritization And Functional Assessment (PAFA), that prioritizes and assesses the functionality of genetic variants by introducing population differentiation measures and recalibrating training variants. Comprehensive evaluations demonstrate that PAFA exhibits much higher sensitivity and specificity in prioritizing noncoding risk variants than existing methods. PAFA achieves improved performance in distinguishing both common and rare recurrent variants from non-recurrent variants by integrating multiple annotations and metrics...
July 11, 2018: Genome Medicine
Annie N Cowell, Hugo O Valdivia, Danett K Bishop, Elizabeth A Winzeler
BACKGROUND: Plasmodium vivax poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69 P. vivax whole genome sequences obtained from subjects residing in three different villages along the Peruvian Amazon. This included 23 paired P. vivax samples from subjects who experienced recurrent P. vivax parasitemia following observed treatment with chloroquine and primaquine...
July 4, 2018: Genome Medicine
Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
BACKGROUND: A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data...
June 29, 2018: Genome Medicine
Laura M Winchester, John Powell, Simon Lovestone, Alejo J Nevado-Holgado
BACKGROUND: Studies have shown that low haemoglobin and anaemia are associated with poor cognition, and anaemia is known to be associated with Alzheimer's disease (AD), but the mechanism of this risk is unknown. Here, we first seek to confirm the association between cognition and anaemia and secondly, in order to further understand the mechanism of this association, to estimate the direction of causation using Mendelian randomisation. METHODS: Two independent cohorts were used in this analysis: AddNeuroMed, a longitudinal study of 738 subjects including AD and age-matched controls with blood cell measures, cognitive assessments and gene expression data from blood; and UK Biobank, a study of 502,649 healthy participants, aged 40-69 years with cognitive test measures and blood cell indices at baseline...
June 28, 2018: Genome Medicine
Ksenia S Anufrieva, Victoria О Shender, Georgij P Arapidi, Marat S Pavlyukov, Michail I Shakhparonov, Polina V Shnaider, Ivan O Butenko, Maria A Lagarkova, Vadim M Govorun
BACKGROUND: Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear. METHODS: To evaluate the effect of chemotherapy on slicing regulation, we performed meta-analyses of previously published transcriptomic, proteomic, phosphoproteomic, and secretome datasets. Our findings were verified by LC-MS/MS, western blotting, immunofluorescence, and FACS analyses of multiple cancer cell lines treated with cisplatin and pladienolide B...
June 27, 2018: Genome Medicine
Tommy T Lam, Oliver G Pybus
Avian influenza A viruses (AIVs) pose a threat to global health because of their sporadic zoonotic transmission and potential to cause pandemics. Genomic surveillance of AIVs has become a powerful, cost-effective approach for studying virus transmission, evolution, and dissemination, and has the potential to inform outbreak control efforts and policies.
June 27, 2018: Genome Medicine
Angela Mo, Urko M Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad, Greg Gibson
BACKGROUND: The genetic and immunological factors that contribute to differences in susceptibility and progression between sub-types of inflammatory and autoimmune diseases continue to be elucidated. Inflammatory bowel disease and juvenile idiopathic arthritis are both clinically heterogeneous and known to be due in part to abnormal regulation of gene activity in diverse immune cell types. Comparative genomic analysis of these conditions is expected to reveal differences in underlying genetic mechanisms of disease...
June 27, 2018: Genome Medicine
Alan D T Barrett
There is an urgent need to develop vaccines against emerging diseases, including those caused by pathogens that are currently unknown to cause human disease, termed 'disease X'. Here, Zika virus infection is considered as an example of disease X. The speed of Zika vaccine development provides optimism for our ability to prepare vaccines against unknown pathogens.
June 26, 2018: Genome Medicine
Erika Bongen, Francesco Vallania, Paul J Utz, Purvesh Khatri
BACKGROUND: Influenza infects tens of millions of people every year in the USA. Other than notable risk groups, such as children and the elderly, it is difficult to predict what subpopulations are at higher risk of infection. Viral challenge studies, where healthy human volunteers are inoculated with live influenza virus, provide a unique opportunity to study infection susceptibility. Biomarkers predicting influenza susceptibility would be useful for identifying risk groups and designing vaccines...
June 14, 2018: Genome Medicine
Zeran Li, Jorge L Del-Aguila, Umber Dube, John Budde, Rita Martinez, Kathleen Black, Qingli Xiao, Nigel J Cairns, Joseph D Dougherty, Jin-Moo Lee, John C Morris, Randall J Bateman, Celeste M Karch, Carlos Cruchaga, Oscar Harari
BACKGROUND: Alzheimer's disease (AD) is characterized by neuronal loss and astrocytosis in the cerebral cortex. However, the specific effects that pathological mutations and coding variants associated with AD have on the cellular composition of the brain are often ignored. METHODS: We developed and optimized a cell-type-specific expression reference panel and employed digital deconvolution methods to determine brain cellular distribution in three independent transcriptomic studies...
June 8, 2018: Genome Medicine
Mamoru Kato, Hiromi Nakamura, Momoko Nagai, Takashi Kubo, Asmaa Elzawahry, Yasushi Totoki, Yuko Tanabe, Eisaku Furukawa, Joe Miyamoto, Hiromi Sakamoto, Shingo Matsumoto, Kuniko Sunami, Yasuhito Arai, Yutaka Suzuki, Teruhiko Yoshida, Katsuya Tsuchihara, Kenji Tamura, Noboru Yamamoto, Hitoshi Ichikawa, Takashi Kohno, Tatsuhiro Shibata
Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples...
June 7, 2018: Genome Medicine
Elena Piñeiro-Yáñez, Miguel Reboiro-Jato, Gonzalo Gómez-López, Javier Perales-Patón, Kevin Troulé, José Manuel Rodríguez, Héctor Tejero, Takeshi Shimamura, Pedro Pablo López-Casas, Julián Carretero, Alfonso Valencia, Manuel Hidalgo, Daniel Glez-Peña, Fátima Al-Shahrour
BACKGROUND: Large-sequencing cancer genome projects have shown that tumors have thousands of molecular alterations and their frequency is highly heterogeneous. In such scenarios, physicians and oncologists routinely face lists of cancer genomic alterations where only a minority of them are relevant biomarkers to drive clinical decision-making. For this reason, the medical community agrees on the urgent need of methodologies to establish the relevance of tumor alterations, assisting in genomic profile interpretation, and, more importantly, to prioritize those that could be clinically actionable for cancer therapy...
May 31, 2018: Genome Medicine
Jinming Cheng, Dongkai Wei, Yuan Ji, Lingli Chen, Liguang Yang, Guang Li, Leilei Wu, Ting Hou, Lu Xie, Guohui Ding, Hong Li, Yixue Li
BACKGROUND: Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis and diagnosis. METHODS: Using the TCGA HCC dataset, we classified HCC patients into different methylation subtypes, identified differentially methylated and expressed genes, and analyzed cis- and trans-regulation of DNA methylation and gene expression...
May 30, 2018: Genome Medicine
Chunjie Liu, Ruixue Cao, Yuejuan Xu, Tingting Li, Fen Li, Sun Chen, Rang Xu, Kun Sun
BACKGROUND: Heterotaxy (Htx) syndrome comprises a class of congenital disorders resulting from malformations in left-right body patterning. Approximately 90% of patients with heterotaxy have serious congenital heart diseases; as a result, the survival rate and outcomes of Htx patients are not satisfactory. However, the underlying etiology and mechanisms in the majority of Htx cases remain unknown. The aim of this study was to investigate the function of rare copy number variants (CNVs) in the pathogenesis of Htx...
May 30, 2018: Genome Medicine
Vinod Kumar, Frank L van de Veerdonk, Mihai G Netea
Understanding the complex and highly dynamic interactions between fungi and host cells in a tissue-specific manner is crucial to facilitate the development of new therapeutic approaches to infections. Here, we discuss recent studies that are revealing the mechanisms underlying this context-dependent interplay.
May 25, 2018: Genome Medicine
Stephan Beck
Stephan Beck discusses recent developments in sharing personal genomes as part of the Personal Genome Project in the UK and globally, and how these efforts are advancing research.
May 24, 2018: Genome Medicine
Genevieve Stein-O'Brien, Luciane T Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V Favorov, Ludmila V Danilova, Joseph A Califano, Evgeny Izumchenko, Daria A Gaykalova, Christine H Chung, Elana J Fertig
BACKGROUND: Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients' treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors...
May 23, 2018: Genome Medicine
Rajan Jain, Andrey Poleshko, Jonathan A Epstein
The heart is one of the least regenerative organs in the human body; adult cardiac myocytes divide at extremely low frequency. Therefore, meaningful induction of cardiac regeneration requires in-depth understanding of myocyte cell-cycle control. Recent insights into how myocytes can be coaxed into duplicating in vivo might inform emerging therapeutics.
May 18, 2018: Genome Medicine
Pawel F Przytycki, Mona Singh
Due to an error introduced during copyediting of this article [1], reference [8] incorrectly reads.
May 10, 2018: Genome Medicine
Praneeth Reddy Devulapally, Jörg Bürger, Thorsten Mielke, Zoltán Konthur, Hans Lehrach, Marie-Laure Yaspo, Jörn Glökler, Hans-Jörg Warnatz
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization...
April 27, 2018: Genome Medicine
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