PubMed Journals Articles About "Human Genome Sequencing CenterBaylor College Medicine" RSS

04:44 EDT 19th September 2018 | BioPortfolio

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Showing "Human Genome Sequencing centerBaylor college Medicine" PubMed Articles 1–25 of 37,000+

A collaborative translational research framework for evaluating and implementing the appropriate use of human genome sequencing to improve health.

In a Policy Forum, Muin Khoury and colleagues discuss research on the clinical application of genome sequencing data.

Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development.

Prenatal genetics has evolved over the last decade to include application of new 'omics technologies to improve perinatal care. The clinical utility of these technologies when applied to direct fetal specimens from amniocentesis or chorionic villus sampling is being explored. In this review, we provide an overview of use of prenatal exome sequencing and role in evaluation of the structurally abnormal fetus, potential applications of genome sequencing, and finally, use of transcriptomics to assess placental ...

Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material.

Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis, a disease that infects more than 5 million people annually. Since TPA is an uncultivable bacterium, most of the information on TPA genetics comes from genome sequencing and molecular typing studies. This study presents the first complete TPA genome (without sequencing gaps) of clinical isolate (UZ1974), which was obtained directly from clinical material, without multiplication in rabbits. Whole genome sequencing was performed usin...

Whole genome sequencing of a CTX-M-11-encoding and quinolone non-susceptible Klebsiella pneumoniae ST194 isolated from a hospitalized dog in Greece.

The emergence and spread of transferable beta-lactamases among the Enterobacteriaceae is a major problem to both human and veterinary medicine and an important contributing factor to the development of multi-drug-resistant bacterial strains. In the present study, we performed the whole genome sequencing of a Klebsiella pneumoniae resistant to first and second generation cephalosporins and non-susceptible to fluoroquinolones, isolated from a urine sample of a hospitalized dog.

Whole Genome Sequencing in Severe Chronic Obstructive Pulmonary Disease.

Genome-wide association studies (GWAS) have identified common variants associated with chronic obstructive pulmonary disease (COPD). Whole-genome sequencing (WGS) offers comprehensive coverage of the entire genome compared with genotyping arrays or exome sequencing.

Correction: A collaborative translational research framework for evaluating and implementing the appropriate use of human genome sequencing to improve health.

[This corrects the article DOI: 10.1371/journal.pmed.1002631.].

Development of the Knowledge of Genome Sequencing (KOGS) questionnaire.

Whole-genome sequencing is being implemented in research and clinical care, yet tools to assess patients' knowledge are lacking. Our aim was to develop a robust measure of whole-genome sequencing knowledge suitable for patients and other stakeholders including research participants, public, students, and healthcare professionals.

High Whole-Genome Sequence Diversity of Human Papillomavirus Type 18 Isolates.

The most commonly found human papillomavirus (HPV) types in cervical cancer are HPV16 and HPV18. Genome variants of these types have been associated with differential carcinogenic potential. To date, only a handful of studies have described HPV18 whole genome sequencing results. Here we describe HPV18 variant diversity and conservation of persistent infections in a longitudinal retrospective cohort study.

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.

Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using shor...

Clinical-grade validation of whole genome sequencing reveals robust detection of low-frequency variants and copy number alterations in CLL.

The 100 000 Genome Project aims to develop a diagnostics platform by introducing whole genome sequencing (WGS) into clinical practice. Samples from patients with chronic lymphocytic leukaemia were subjected to WGS. WGS detection of single nucleotide variants and insertion/deletions were validated by targeted next generation sequencing showing high concordance (96·3%), also for detection of sub-clonal variants and low-frequency TP53 variants. Copy number alteration detection was verified by fluorescent in...

Genome-by-genome approach for fast bacterial genealogical relationship evaluation.

Large-scale whole-genome sequencing (WGS) dataset based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed.

Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or dioxin, is commonly considered the most toxic man-made substance. Dioxin exposure impacts human health and diseases, birth defects and teratogenesis were frequently observed in children of persons who have been exposed to dioxin. However, the impact of dioxin on human mutation rate in trios has not yet been elucidated in the whole genome level. To identify and characterize the genetic alterations in the individuals exposed to dioxin, we perfomed whole genome seq...

Precision Medicine, Genome Sequencing, and Improved Population Health.

findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies.

Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation.

Umap and Bismap: quantifying genome and methylome mappability.

Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding and chemical modifications. Every region in a genome assembly has a property called 'mappability', which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. These regions have increased susceptibili...

The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations.

The Clinical Sequencing Evidence-Generating Research (CSER) consortium, now in its second funding cycle, is investigating the effectiveness of integrating genomic (exome or genome) sequencing into the clinical care of diverse and medically underserved individuals in a variety of healthcare settings and disease states. The consortium comprises a coordinating center, six funded extramural clinical projects, and an ongoing National Human Genome Research Institute (NHGRI) intramural project. Collectively, these...

A decade of genome sequencing has revolutionized studies of experimental evolution.

Genome sequencing has revolutionized studies using experimental evolution of microbes because it readily provides comprehensive insight into the genetic bases of adaptation. In this perspective we discuss applications of sequencing-based technologies used to study evolution in microbes, including genomic sequencing of isolated evolved clones and mixed evolved populations, and also the use of sequencing methods to follow the fate of introduced variations, whether neutral barcodes or variants introduced by ge...

Genome-first findings require precision phenotyping.

Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation a...

Scientists on the Spot: Sequencing the human genome to influence patient healthcare.

Draft Genome Sequencing of Extended Spectrum β-Lactamase Enterobacter aerogenes Isolates from Swine and Human.

The draft genome sequences of two Enterobacter aerogenes HN503E2II and PN108E5IIB isolated from two Cameroonian abattoirs, are reported here.

Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. ...

Assessing Asthma Medication Responses in US Minority Children by Whole-genome Sequencing.

Concordance of mitochondrial DNA sequencing methods on bloodstains using Ion PGM™.

In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicon...

Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq).

NOMe-seq (nucleosome occupancy and methylome sequencing) identifies nucleosome-depleted regions that correspond to promoters, enhancers, and insulators. The NOMe-seq method is based on the treatment of chromatin with the M.CviPI methyltransferase, which methylates GpC dinucleotides that are not protected by nucleosomes or other proteins that are tightly bound to the chromatin (GpCdoes not occur in the human genome and therefore there is no endogenous background of GpC). Following bisulfite treatment of the ...

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