Text-mining clinically relevant cancer biomarkers for curation into the CIViC database.

abstract：:Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic barriers, and exposure to nosocomial (hospital-acquired) pathogens. Consequently, cancer-related infections are u...

journal_title：Genome medicine

authors： Taur Y,Pamer EG

更新日期：2016-04-18 00:00:00

abstract：BACKGROUND:Expression quantitative trait loci (eQTL) analysis is a powerful method to detect correlations between gene expression and genomic variants and is widely used to interpret the biological mechanism underlying identified genome wide association studies (GWAS) risk loci. Numerous eQTL studies have been performe...

journal_title：Genome medicine

authors： Blauwendraat C,Francescatto M,Gibbs JR,Jansen IE,Simón-Sánchez J,Hernandez DG,Dillman AA,Singleton AB,Cookson MR,Rizzu P,Heutink P

更新日期：2016-06-10 00:00:00

abstract：:Systems biology has matured considerably as a discipline over the last decade, yet some of the key challenges separating current research efforts in systems biology and clinically useful results are only now becoming apparent. As these gaps are better defined, the new discipline of systems medicine is emerging as a tr...

journal_title：Genome medicine

authors： Clermont G,Auffray C,Moreau Y,Rocke DM,Dalevi D,Dubhashi D,Marshall DR,Raasch P,Dehne F,Provero P,Tegner J,Aronow BJ,Langston MA,Benson M

更新日期：2009-09-29 00:00:00

abstract：BACKGROUND:Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. METHODS:We comprehensively m...

journal_title：Genome medicine

authors： Liu S,Harmston N,Glaser TL,Wong Y,Zhong Z,Madan B,Virshup DM,Petretto E

更新日期：2020-10-22 00:00:00

abstract：BACKGROUND:The HHIP gene, encoding Hedgehog interacting protein, has been implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS), and our subsequent studies identified a functional upstream genetic variant that decreased HHIP transcription. However, little is known about ho...

journal_title：Genome medicine

authors： Lao T,Glass K,Qiu W,Polverino F,Gupta K,Morrow J,Mancini JD,Vuong L,Perrella MA,Hersh CP,Owen CA,Quackenbush J,Yuan GC,Silverman EK,Zhou X

更新日期：2015-02-14 00:00:00

abstract：:Pancreatic cancer is a highly lethal tumor type for which there are few viable therapeutic options. It is also caused by the accumulation of mutations in a variety of genes. These genetic alterations can be grouped into those that accumulate during pancreatic intraepithelial neoplasia (precursor lesions) and thus are ...

journal_title：Genome medicine

authors： Makohon-Moore A,Brosnan JA,Iacobuzio-Donahue CA

更新日期：2013-03-28 00:00:00

abstract：:The role of ezetimibe in lowering plasma cholesterol has been established; however, controversy remains about its clinical benefit. A recent study utilizes naturally occurring genetic variation within the NPC1-like 1 gene (NPC1L1) to demonstrate the potential for pharmacologic inhibition of the protein to reduce the r...

journal_title：Genome medicine

authors： Corbin LJ,Timpson NJ

更新日期：2015-01-28 00:00:00

abstract：BACKGROUND:Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several differe...

journal_title：Genome medicine

authors： Heiden SE,Hübner NO,Bohnert JA,Heidecke CD,Kramer A,Balau V,Gierer W,Schaefer S,Eckmanns T,Gatermann S,Eger E,Guenther S,Becker K,Schaufler K

更新日期：2020-12-09 00:00:00

abstract：:Aberrant DNA methylation, in particular promoter hypermethylation and transcriptional silencing of tumor suppressor genes, has an important role in the development of many human cancers, including renal cell carcinoma (RCC). Indeed, apart from mutations in the well studied von Hippel-Lindau gene (VHL), the mutation fr...

journal_title：Genome medicine

authors： Morris MR,Maher ER

更新日期：2010-09-03 00:00:00

abstract：BACKGROUND:For circadian medicine to influence health, such as when to take a drug or undergo a procedure, a biomarker of molecular clock phase is required--one that is easily measured and generalizable across a broad population. It is not clear that any circadian biomarker yet satisfies these criteria. METHODS:We ana...

journal_title：Genome medicine

authors： Wu G,Ruben MD,Francey LJ,Smith DF,Sherrill JD,Oblong JE,Mills KJ,Hogenesch JB

更新日期：2020-08-21 00:00:00

abstract：:Tumor heterogeneity is of growing importance in the treatment of cancers. Mutational hot spots are prime locations for determining number and proportions of low variant allele frequency (VAF) tumor subclones by next generation sequencing. Low VAF detection is complicated by poor mapping efficiency in regions with high...

journal_title：Genome medicine

authors： Spence JM,Spence JP,Abumoussa A,Burack WR

更新日期：2015-03-12 00:00:00

abstract：UNLABELLED:Bibliographic records in the PubMed database of biomedical literature are annotated with Medical Subject Headings (MeSH) by curators, which summarize the content of the articles. Two recent publications explain how to generate profiles of MeSH terms for a set of bibliographic records and to use them to defin...

journal_title：Genome medicine

authors： Andrade-Navarro MA

更新日期：2012-10-30 00:00:00

abstract：:The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and disease due to its interaction with the human immune system. Its overall composition and mic...

journal_title：Genome medicine

authors： Börnigen D,Morgan XC,Franzosa EA,Ren B,Xavier RJ,Garrett WS,Huttenhower C

更新日期：2013-07-31 00:00:00

abstract：:We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms,...

journal_title：Genome medicine

authors： Chan Y,Chan YK,Goodman DB,Guo X,Chavez A,Lim ET,Church GM

更新日期：2018-04-19 00:00:00

abstract：:Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype a...

journal_title：Genome medicine

authors： Farhat MR,Shapiro BJ,Sheppard SK,Colijn C,Murray M

更新日期：2014-11-15 00:00:00

abstract：BACKGROUND:While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no...

journal_title：Genome medicine

authors： Chatrath A,Przanowska R,Kiran S,Su Z,Saha S,Wilson B,Tsunematsu T,Ahn JH,Lee KY,Paulsen T,Sobierajska E,Kiran M,Tang X,Li T,Kumar P,Ratan A,Dutta A

更新日期：2020-02-17 00:00:00

abstract：BACKGROUND:The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer's disease, whilst the ε2 allele confers protection. Previous studies report differential DNA methylation of APOE between ε4 and ε2 carriers, but associations with epigenome-wide methylation have not previously...

journal_title：Genome medicine

authors： Walker RM,Vaher K,Bermingham ML,Morris SW,Bretherick AD,Zeng Y,Rawlik K,Amador C,Campbell A,Haley CS,Hayward C,Porteous DJ,McIntosh AM,Marioni RE,Evans KL

更新日期：2021-01-04 00:00:00

abstract：BACKGROUND:Efforts to improve research outcomes have resulted in genomic researchers being confronted with complex and seemingly contradictory instructions about how to perform their tasks. Over the past decade, there has been increasing pressure on university researchers to commercialize their work. Concurrently, they...

journal_title：Genome medicine

authors： Caulfield T,Harmon SH,Joly Y

更新日期：2012-02-27 00:00:00

abstract：BACKGROUND:Clinical laboratory (lab) tests are used in clinical practice to diagnose, treat, and monitor disease conditions. Test results are stored in electronic health records (EHRs), and a growing number of EHRs are linked to patient DNA, offering unprecedented opportunities to query relationships between genetic ri...

journal_title：Genome medicine

authors： Dennis JK,Sealock JM,Straub P,Lee YH,Hucks D,Actkins K,Faucon A,Feng YA,Ge T,Goleva SB,Niarchou M,Singh K,Morley T,Smoller JW,Ruderfer DM,Mosley JD,Chen G,Davis LK

更新日期：2021-01-13 00:00:00

abstract：BACKGROUND:Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes. METHODS:We ...

journal_title：Genome medicine

authors： Mordaunt CE,Jianu JM,Laufer BI,Zhu Y,Hwang H,Dunaway KW,Bakulski KM,Feinberg JI,Volk HE,Lyall K,Croen LA,Newschaffer CJ,Ozonoff S,Hertz-Picciotto I,Fallin MD,Schmidt RJ,LaSalle JM

更新日期：2020-10-14 00:00:00

abstract：:Technological advances over the past several years have dramatically reduced the cost of whole-genome sequencing. At the same time, understanding of the functional significance of genetic variation has advanced considerably. The routine generation of whole-genome sequence data for individual patients will soon be suff...

journal_title：Genome medicine

authors： Belmont J,McGuire AL

更新日期：2009-05-08 00:00:00

abstract：BACKGROUND:DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic "mitotic" clocks that can measure the lifetime number o...

journal_title：Genome medicine

authors： Teschendorff AE

更新日期：2020-06-24 00:00:00

abstract：BACKGROUND:Phenotypic changes during cancer progression are associated with alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. However, it is not yet known whether the relative abundance of transcript isoforms may be informative for clinica...

journal_title：Genome medicine

authors： Trincado JL,Sebestyén E,Pagés A,Eyras E

更新日期：2016-08-17 00:00:00

abstract：BACKGROUND:Organic cation transporters (OCTs) determine not only physiological processes but are also involved in the cellular uptake of anticancer agents. Based on microarray analyses in hepatocellular carcinoma (HCC), SLC22A1/OCT1 mRNA seems to be downregulated, but systematic protein expression data are currently mi...

journal_title：Genome medicine

authors： Schaeffeler E,Hellerbrand C,Nies AT,Winter S,Kruck S,Hofmann U,van der Kuip H,Zanger UM,Koepsell H,Schwab M

更新日期：2011-12-23 00:00:00

abstract：BACKGROUND:Evidence for genetic contribution to complex diseases is described by recurrence risks to relatives of diseased individuals. Genome-wide association studies allow a description of the genetics of the same diseases in terms of risk loci, their effects and allele frequencies. To reconcile the two descriptions ...

journal_title：Genome medicine

authors： Wray NR,Goddard ME

更新日期：2010-02-02 00:00:00

abstract：:Next-generation sequencing (NGS) methodology allows for a major expansion in current carrier screening tests. NGS testing has been shown to be analytically accurate and cost-effective, but major challenges include educational and counseling issues. ...

journal_title：Genome medicine

authors： Prior TW

更新日期：2014-08-26 00:00:00

abstract：:Prenatal diagnosis of fetal aneuploidies and chromosomal anomalies is likely to undergo a profound change in the near future. On the one hand this is mediated by new technical developments, such as chromosomal microarrays, which allow a much more precise delineation of minute sub-microscopic chromosomal aberrancies th...

journal_title：Genome medicine

authors： Hahn S,Jackson LG,Zimmermann BG

更新日期：2010-08-05 00:00:00

abstract：:The anticonvulsant carbamazepine has a high incidence of cutaneous adverse drug reactions. A recent prospective clinical trial in Taiwan has indicated that HLA-B*1502 screening will reduce the incidence of life-threatening adverse reactions to carbamazepine, while a genome-wide association study has identified the HLA...

journal_title：Genome medicine

authors： Mushiroda T,Nakamura Y

更新日期：2011-05-30 00:00:00

abstract：:The identification of somatic mosaicism in the brain lends a new perspective to our understanding of the role of gene and environment interactions in psychiatric disease risk. Somatic mutations, such as retrotransposon insertions, that are precipitated by modern environmental factors may alter neuronal function and ne...

journal_title：Genome medicine

authors： Bedrosian TA,Linker S,Gage FH

更新日期：2016-05-23 00:00:00

abstract：:The magnitude of the detrimental effects following in utero alcohol exposure, including fetal alcohol syndrome and other fetal alcohol spectrum disorders (FASD), is globally underestimated. The effects include irreversible cognitive and behavioral disabilities as a result of abnormal brain development, pre- and postna...

journal_title：Genome medicine

authors： Ramsay M

更新日期：2010-04-28 00:00:00