Overcoming bias and systematic errors in next generation sequencing data.

abstract：:Selective inhibitors of the kinases BRAF and MEK for the treatment of patients with otherwise refractory BRAF mutant melanoma have demonstrated impressive efficacy, and combination treatment with these agents may prove to be even more effective. However, these drugs are not curative, mainly because of the relatively r...

journal_title：Genome medicine

authors： Settleman J

更新日期：2014-04-28 00:00:00

abstract：:CRISPR/Cas9 has revolutionized cancer mouse models. Although loss-of-function genetics by CRISPR/Cas9 is well-established, generating gain-of-function alleles in somatic cancer models is still challenging because of the low efficiency of gene knock-in. Here we developed CRISPR-based Somatic Oncogene kNock-In for Cance...

journal_title：Genome medicine

authors： Mou H,Ozata DM,Smith JL,Sheel A,Kwan SY,Hough S,Kucukural A,Kennedy Z,Cao Y,Xue W

更新日期：2019-04-16 00:00:00

abstract：BACKGROUND:Alzheimer's disease affects ~13% of people in the United States 65 years and older, making it the most common neurodegenerative disorder. Recent work has identified roles for environmental, genetic, and epigenetic factors in Alzheimer's disease risk. METHODS:We performed a genome-wide screen of DNA methylat...

journal_title：Genome medicine

authors： Watson CT,Roussos P,Garg P,Ho DJ,Azam N,Katsel PL,Haroutunian V,Sharp AJ

更新日期：2016-01-19 00:00:00

abstract：BACKGROUND:The advent of personalized medicine requires robust, reproducible biomarkers that indicate which treatment will maximize therapeutic benefit while minimizing side effects and costs. Numerous molecular signatures have been developed over the past decade to fill this need, but their validation and up-take into...

journal_title：Genome medicine

authors： Starmans MH,Pintilie M,John T,Der SD,Shepherd FA,Jurisica I,Lambin P,Tsao MS,Boutros PC

更新日期：2012-11-12 00:00:00

abstract：:Primary biliary cirrhosis (PBC) is an autoimmune hepatobiliary disease characterized by immune-mediated injury of small and medium-sized bile ducts, eventually leading to liver cirrhosis. Several studies have addressed PBC immunopathology, and the data support an immune activation leading to autoantibodies and autorea...

journal_title：Genome medicine

authors： Selmi C,Torok NJ,Affronti A,Gershwin ME

更新日期：2010-01-26 00:00:00

abstract：BACKGROUND:Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a large scale. Such effects, however, could lead to conflicts among studies, while further impacting st...

journal_title：Genome medicine

authors： Swindell WR,Michaels KA,Sutter AJ,Diaconu D,Fritz Y,Xing X,Sarkar MK,Liang Y,Tsoi A,Gudjonsson JE,Ward NL

更新日期：2017-03-09 00:00:00

abstract：:Pathogen genomic analysis is a potentially transformative new approach to the clinical and public-health management of infectious diseases. Health systems investing in this technology will need to build infrastructure and develop policies that ensure genomic information can be generated, shared and acted upon in a tim...

journal_title：Genome medicine

authors： Luheshi LM,Raza S,Peacock SJ

更新日期：2015-12-30 00:00:00

abstract：:The analysis of the genomic distribution of viral vector genomic integration sites is a key step in hematopoietic stem cell-based gene therapy applications, allowing to assess both the safety and the efficacy of the treatment and to study the basic aspects of hematopoiesis and stem cell biology. Identifying vector int...

journal_title：Genome medicine

authors： Calabria A,Leo S,Benedicenti F,Cesana D,Spinozzi G,Orsini M,Merella S,Stupka E,Zanetti G,Montini E

更新日期：2014-09-03 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：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：:Considerable progress has been made in identifying genetic risk factors for idiosyncratic adverse drug reactions in the past 30 years. These reactions can affect various tissues and organs, including liver, skin, muscle and heart, in a drug-dependent manner. Using both candidate gene and genome-wide association studie...

journal_title：Genome medicine

authors： Daly AK

更新日期：2013-01-29 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:Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approa...

journal_title：Genome medicine

authors： Duffy DJ,Krstic A,Halasz M,Schwarzl T,Konietzny A,Iljin K,Higgins DG,Kolch W

更新日期：2017-02-10 00:00:00

abstract：BACKGROUND:Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis settings. To support this informatically, previous work led to the development of the widely use...

journal_title：Genome medicine

authors： Phelan JE,O'Sullivan DM,Machado D,Ramos J,Oppong YEA,Campino S,O'Grady J,McNerney R,Hibberd ML,Viveiros M,Huggett JF,Clark TG

更新日期：2019-06-24 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：: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：: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：: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：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:Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural ste...

journal_title：Genome medicine

authors： Engström PG,Tommei D,Stricker SH,Ender C,Pollard SM,Bertone P

更新日期：2012-10-09 00:00:00

abstract：:A report on the 62nd Annual Meeting of the American Society of Human Genetics, San Francisco, California, USA, 6-10 November 2012. ...

journal_title：Genome medicine

authors： Zielinski D,Gymrek M,Erlich Y

更新日期：2012-12-19 00:00:00

abstract：:Genome-wide association analyses on large patient cohorts are generating large sets of candidate disease genes. This is coupled with the availability of ever-increasing genomic databases and a rapidly expanding repository of biomedical literature. Computational approaches to disease-gene association attempt to harness...

journal_title：Genome medicine

authors： Tiffin N,Andrade-Navarro MA,Perez-Iratxeta C

更新日期：2009-08-07 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: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:Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential. Several knowledgebases have been ...

journal_title：Genome medicine

authors： Lever J,Jones MR,Danos AM,Krysiak K,Bonakdar M,Grewal JK,Culibrk L,Griffith OL,Griffith M,Jones SJM

更新日期：2019-12-03 00:00:00

abstract：BACKGROUND:Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet-induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep s...

journal_title：Genome medicine

authors： Starrett GJ,Thakuria M,Chen T,Marcelus C,Cheng J,Nomburg J,Thorner AR,Slevin MK,Powers W,Burns RT,Perry C,Piris A,Kuo FC,Rabinowits G,Giobbie-Hurder A,MacConaill LE,DeCaprio JA

更新日期：2020-03-18 00:00:00

abstract：:Periodontitis is a common inflammatory disease that leads to tooth loss and has been linked to cardiovascular disease and diabetes mellitus. The periodontal microbiome is highly diverse, and metatranscriptomic studies have indicated that the genes that are expressed by the microbiota are more relevant than the microbi...

journal_title：Genome medicine

authors： Wang GP

更新日期：2015-04-27 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:A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS:We investigated mutation...

journal_title：Genome medicine

authors： Merker M,Kohl TA,Barilar I,Andres S,Fowler PW,Chryssanthou E,Ängeby K,Jureen P,Moradigaravand D,Parkhill J,Peacock SJ,Schön T,Maurer FP,Walker T,Köser C,Niemann S

更新日期：2020-03-06 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