Defining functional signatures of dysbiosis in periodontitis progression.

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：: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：:With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that allows comparison of all the variant calls of an exome to a high-quality reference dataset of an ethnically mat...

journal_title：Genome medicine

authors： Heinrich V,Kamphans T,Stange J,Parkhomchuk D,Hecht J,Dickhaus T,Robinson PN,Krawitz PM

更新日期：2013-07-31 00:00:00

abstract：BACKGROUND:Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS:DNA samples exacted from CD4+ T cells of 48 SSc patients and ...

journal_title：Genome medicine

authors： Li T,Ortiz-Fernández L,Andrés-León E,Ciudad L,Javierre BM,López-Isac E,Guillén-Del-Castillo A,Simeón-Aznar CP,Ballestar E,Martin J

更新日期：2020-09-25 00:00:00

abstract：:Candidate gene association studies, linkage studies and genome-wide association studies have highlighted the role of genetic factors in the development of ischemic stroke. This research started over a decade ago, and can be separated into three major periods of research. In the first wave classic susceptibility marker...

journal_title：Genome medicine

authors： Maasz A,Melegh B

更新日期：2010-09-13 00:00:00

abstract：BACKGROUND:Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these...

journal_title：Genome medicine

authors： Kolde R,Franzosa EA,Rahnavard G,Hall AB,Vlamakis H,Stevens C,Daly MJ,Xavier RJ,Huttenhower C

更新日期：2018-01-29 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：:The Killer-cell Immunoglobulin-like Receptor (KIR) gene complex has considerable biomedical importance. Patterns of polymorphism in the KIR region include variability in the gene content of haplotypes and diverse structural arrangements. Droplet digital PCR (ddPCR) was used to identify different haplotype motifs and t...

journal_title：Genome medicine

authors： Roberts CH,Jiang W,Jayaraman J,Trowsdale J,Holland MJ,Traherne JA

更新日期：2014-03-05 00:00:00

abstract：:Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequencing technologies to identify neoantigens and to create personalized immunotherapies for cancer treatment. To cr...

journal_title：Genome medicine

authors： Richters MM,Xia H,Campbell KM,Gillanders WE,Griffith OL,Griffith M

更新日期：2019-08-28 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：:Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing...

journal_title：Genome medicine

authors： Liu Q,Zhang P,Wang D,Gu W,Wang K

更新日期：2017-07-18 00:00:00

abstract：:There are still many open questions in data-analytic research pertaining to biomarker development in the era of personalized/precision medicine and big data. Among them is the question of what constitutes best practice for the extraction of prioritized lists of candidate biomarkers from smaller studies that are 'hypot...

journal_title：Genome medicine

authors： Gaile DP,Miecznikowski JC

更新日期：2013-11-29 00:00:00

abstract：BACKGROUND:Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demarcating open and closed chromatin across the genome. Additionally, large sets of genome-wide transcri...

journal_title：Genome medicine

authors： Simmonds P,Loomis E,Curry E

更新日期：2017-06-07 00:00:00

abstract：:Stem cell banks are increasingly seen as an essential resource of biological materials for both basic and translational research. Stem cell banks support transnational access to quality-controlled and ethically sourced stem cell lines from different origins and of varying grades. According to the Organisation for Econ...

journal_title：Genome medicine

authors： Knoppers BM,Isasi R

更新日期：2010-10-05 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: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: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：:Advances in mass spectrometry have allowed the high-throughput quantitative identification of human leukocyte antigen (HLA) class I ligands, and recent studies have reported on the breadth and diversity of the HLA class I immunopeptidome. These findings have far-reaching implications for immunosurveillance by T cells ...

journal_title：Genome medicine

authors： Melief CJM,Kessler JH

更新日期：2017-05-24 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：:Genome-wide association studies have shown unequivocally that common complex disorders have a polygenic genetic architecture and have enabled researchers to identify genetic variants associated with diseases. These variants can be combined into a polygenic risk score that captures part of an individual's susceptibilit...

journal_title：Genome medicine

authors： Lewis CM,Vassos E

更新日期：2020-05-18 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：: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：:National and international public-private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts will contribute to the creation of a medical information commons (MIC), a comprehensive data resource that is...

journal_title：Genome medicine

authors： Deverka PA,Majumder MA,Villanueva AG,Anderson M,Bakker AC,Bardill J,Boerwinkle E,Bubela T,Evans BJ,Garrison NA,Gibbs RA,Gentleman R,Glazer D,Goldstein MM,Greely H,Harris C,Knoppers BM,Koenig BA,Kohane IS,La Rosa S,

更新日期：2017-09-22 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：:The cancer genome is highly complex, with hundreds of point mutations, translocations, and chromosome gains and losses per tumor. To understand the effects of these alterations, precise models are needed. Traditional approaches to the construction of mouse models are time-consuming and laborious, requiring manipulatio...

journal_title：Genome medicine

authors： Mou H,Kennedy Z,Anderson DG,Yin H,Xue W

更新日期：2015-06-09 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:Cigarette smoking is well-known to associate with accelerated skin aging as well as cardiovascular disease and lung cancer, in large part due to oxidative stress. Because metabolites are downstream of genetic variation, as well as transcriptional changes and post-translational modifications of proteins, they...

journal_title：Genome medicine

authors： Spitale RC,Cheng MY,Chun KA,Gorell ES,Munoz CA,Kern DG,Wood SM,Knaggs HE,Wulff J,Beebe KD,Chang AL

更新日期：2012-02-23 00:00:00

abstract：:Large-scale cancer genomic studies have revealed that the genetic heterogeneity of the same type of cancer is greater than previously thought. A key question in cancer genomics is the identification of driver genes. Although existing methods have identified many common drivers, it remains challenging to predict person...

journal_title：Genome medicine

authors： Hou JP,Ma J

更新日期：2014-07-31 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:Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human neuronal model with a singl...

journal_title：Genome medicine

authors： Grabole N,Zhang JD,Aigner S,Ruderisch N,Costa V,Weber FC,Theron M,Berntenis N,Spleiss O,Ebeling M,Yeo GW,Jagasia R,Kiialainen A

更新日期：2016-09-21 00:00:00