DawnRank: discovering personalized driver genes in cancer.

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：: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：:To help overcome the bottlenecks that limit the development of diagnostic and therapeutic products, academic and industrial researchers, patient organizations and charities, and regulatory and funding institutions should redefine the basis for sharing the knowledge collected in large-scale clinical and experimental st...

journal_title：Genome medicine

authors： Auffray C

更新日期：2009-03-04 00:00:00

abstract：BACKGROUND:Based on promising phase II data, the histone deacetylase inhibitor entinostat is in phase III trials for patients with metastatic estrogen receptor-positive breast cancer. Predictors of sensitivity and resistance, however, remain unknown. METHODS:A total of eight cell lines and nine mouse models of breast ...

journal_title：Genome medicine

authors： Tanioka M,Mott KR,Hollern DP,Fan C,Darr DB,Perou CM

更新日期：2018-11-30 00:00:00

abstract：:Osteoporosis, the most common type of bone disease worldwide, is clinically characterized by low bone mineral density (BMD) and increased susceptibility to fracture. Multiple genetic and environmental factors and gene-environment interactions have been implicated in its pathogenesis. Osteoporosis has strong genetic de...

journal_title：Genome medicine

authors： Wu S,Liu Y,Zhang L,Han Y,Lin Y,Deng HW

更新日期：2013-05-29 00:00:00

abstract：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 methylat...

journal_title：Genome medicine

authors： Cheng J,Wei D,Ji Y,Chen L,Yang L,Li G,Wu L,Hou T,Xie L,Ding G,Li H,Li Y

更新日期：2018-05-30 00:00:00

abstract：BACKGROUND:Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE...

journal_title：Genome medicine

authors： Sigurdsson MI,Saddic L,Heydarpour M,Chang TW,Shekar P,Aranki S,Couper GS,Shernan SK,Seidman JG,Body SC,Muehlschlegel JD

更新日期：2016-12-06 00:00:00

abstract：BACKGROUND:Metabolomics, the non-targeted interrogation of small molecules in a biological sample, is an ideal technology for identifying diagnostic biomarkers. Current tissue extraction protocols involve sample destruction, precluding additional uses of the tissue. This is particularly problematic for high value sampl...

journal_title：Genome medicine

authors： Brown MV,McDunn JE,Gunst PR,Smith EM,Milburn MV,Troyer DA,Lawton KA

更新日期：2012-04-30 00:00:00

abstract：BACKGROUND:The R620W variant in protein tyrosine phosphatase non-receptor 22 (PTPN22) is associated with rheumatoid arthritis (RA). The PTPN22 gene has alternatively spliced transcripts and at least two of the splice forms have been confirmed to encode different PTPN22 (LYP) proteins, but detailed information regarding...

journal_title：Genome medicine

authors： Ronninger M,Guo Y,Shchetynsky K,Hill A,Khademi M,Olsson T,Reddy PS,Seddighzadeh M,Clark JD,Lin LL,O'Toole M,Padyukov L

更新日期：2012-01-20 00:00:00

abstract：:For almost three decades, Huntington's disease has been a prototype for the application of genetic strategies to human disease. HD, the Huntington's disease gene, was the first autosomal defect mapped using only DNA markers, a finding in 1983 that helped to spur similar studies in many other disorders and contributed ...

journal_title：Genome medicine

authors： Gusella JF,MacDonald ME

更新日期：2009-08-21 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：BACKGROUND:Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic mutations resulting from various endogenous and exogenous causes, including normal DNA damage and rep...

journal_title：Genome medicine

authors： Kim YA,Wojtowicz D,Sarto Basso R,Sason I,Robinson W,Hochbaum DS,Leiserson MDM,Sharan R,Vadin F,Przytycka TM

更新日期：2020-05-29 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：BACKGROUND:Comprehensive molecular profiling has revealed somatic variations in cancer at genomic, epigenomic, transcriptomic, and proteomic levels. The accumulating data has shown clearly that molecular phenotypes of cancer are complex and influenced by a multitude of factors. Conventional unsupervised clustering appl...

journal_title：Genome medicine

authors： Arora A,Olshen AB,Seshan VE,Shen R

更新日期：2020-12-03 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:Intertumoral heterogeneity represents a significant hurdle to identifying optimized targeted therapies in gastric cancer (GC). To realize precision medicine for GC patients, an actionable gene alteration-based molecular classification that directly associates GCs with targeted therapies is needed. METHODS:A...

journal_title：Genome medicine

authors： Ichikawa H,Nagahashi M,Shimada Y,Hanyu T,Ishikawa T,Kameyama H,Kobayashi T,Sakata J,Yabusaki H,Nakagawa S,Sato N,Hirata Y,Kitagawa Y,Tanahashi T,Yoshida K,Nakanishi R,Oki E,Vuzman D,Lyle S,Takabe K,Ling Y,Okuda

更新日期：2017-10-31 00:00:00

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：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 pioneering work of Jean Dausset on the HLA system established several principles that were later reflected in the Human Genome Project and contributed to the foundations of predictive, preventive, personalized and participatory (P4) medicine. To effectively develop systems medicine, we should take advantage of the...

journal_title：Genome medicine

authors： Auffray C,Charron D,Hood L

更新日期：2010-08-26 00:00:00

abstract：BACKGROUND:Establishing the cancer type and site of origin is important in determining the most appropriate course of treatment for cancer patients. Patients with cancer of unknown primary, where the site of origin cannot be established from an examination of the metastatic cancer cells, typically have poor survival. H...

journal_title：Genome medicine

authors： Soh KP,Szczurek E,Sakoparnig T,Beerenwinkel N

更新日期：2017-11-28 00:00:00

abstract：BACKGROUND:Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A, C, W and Y) are available as plain-polysaccharide and protein-polysaccharide conjugate vaccines. Here we apply contemporary...

journal_title：Genome medicine

authors： O'Connor D,Clutterbuck EA,Thompson AJ,Snape MD,Ramasamy MN,Kelly DF,Pollard AJ

更新日期：2017-01-30 00:00:00

abstract：BACKGROUND:One of the major challenges in obesity treatment is to explain the high variability in the individual's response to specific dietary and physical activity interventions. With this study, we tested the hypothesis that specific DNA methylation changes reflect individual responsiveness to lifestyle intervention...

journal_title：Genome medicine

authors： Keller M,Yaskolka Meir A,Bernhart SH,Gepner Y,Shelef I,Schwarzfuchs D,Tsaban G,Zelicha H,Hopp L,Müller L,Rohde K,Böttcher Y,Stadler PF,Stumvoll M,Blüher M,Kovacs P,Shai I

更新日期：2020-11-16 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：:Considerable time and effort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biologic...

journal_title：Genome medicine

authors： Taub MA,Corrada Bravo H,Irizarry RA

更新日期：2010-12-10 00:00:00

abstract：BACKGROUND:Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. METHODS:We examine...

journal_title：Genome medicine

authors： Moyer K,Kaimal V,Pacheco C,Mourya R,Xu H,Shivakumar P,Chakraborty R,Rao M,Magee JC,Bove K,Aronow BJ,Jegga AG,Bezerra JA

更新日期：2010-05-13 00:00:00

abstract：BACKGROUND:The advent of direct-to-consumer (DTC) genetic testing (GT) has sparked a number of debates regarding the scientific validity of tests, their broad health and ethical implications for society as well as their legal status. To date, relatively few empirical studies have been published regarding this phenomeno...

journal_title：Genome medicine

authors： Howard HC,Borry P

更新日期：2013-05-22 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: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 datas...

journal_title：Genome medicine

authors： Anufrieva KS,Shender VО,Arapidi GP,Pavlyukov MS,Shakhparonov MI,Shnaider PV,Butenko IO,Lagarkova MA,Govorun VM

更新日期：2018-06-27 00:00:00

abstract：BACKGROUND:Preterm birth confers a high risk of adverse long term health outcomes for survivors, yet the underlying molecular mechanisms are unclear. We hypothesized that effects of preterm birth can be mediated through measurable epigenomic changes throughout development. We therefore used a longitudinal birth cohort ...

journal_title：Genome medicine

authors： Cruickshank MN,Oshlack A,Theda C,Davis PG,Martino D,Sheehan P,Dai Y,Saffery R,Doyle LW,Craig JM

更新日期：2013-10-18 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