Posts Categorized: Tools

Cell programming?

Posted by & filed under Part 03: GENERAL THEMES, Tools.

Cells respond to the environment and perform their different functions via computational operations performed by DNA-encoded circuits that process sensory information. More specifically, these operations are performed by networks of regulatory proteins that integrate signals and control the timing of gene expression. Cells can be programmed using synthetic genetic circuits to generate a desired operation. […]

Progress in nanopore technology

Posted by & filed under Exome sequencing, In the news, Part 06: DIAGNOSTIC APPROACHES, Tools.

Feng et al. (2015) recently reviewed the progress in nanopore technology from the past as well as the latest advances. They describe the different types of nanopores and discuss recent and potential applications. Nanopore-based sequencers have the potential to quickly and reliably sequence the entire human genome “for less than $1000, and possibly for even […]

Tissue-based map of the human proteome

Posted by & filed under Tools, Websites.

Ulen et al. used an integrative omics approach to study the spatial human proteome. Samples representing all major tissues and organs in the human body were analyzed based on 24,028 antibodies corresponding to 16,975 protein-encoding genes, complemented with RNA-sequencing data for 32 of the tissues. A genome-wide analysis of the tissue specificity of RNA and […]

CRISPR tool (treatment & mutations assessment)

Posted by & filed under Tools, Treatment.

CRISPR-Cas9-based genome editing enables the rapid genetic manipulation of any genomic locus without the need for gene targeting by homologous recombination. It can be used in the search for new treatment modalities, e.g. studies focusing on the identification of physiological targets of drugs and bioactive small molecules (Zhu et al. 2015; Kasap et al 2014). One of the […]

Genomics to accelerate diagnosis of IEM

Posted by & filed under Part 06: DIAGNOSTIC APPROACHES, Tools.

Stranneheim et al. demonstrated how Massively parallel DNA sequencing (MPS) can aid in the diagnosis and early intervention of patients with Inborn Errors of Metabolism (IEM). Their method focuses on analysing pulsed whole genome sequence data in real time, using automated analysis combined with data reduction and parallelization. The genes targeted are 474 disease genes […]

Disease modeling with iPS cell and heart-on-chip technologies

Posted by & filed under Tools.

The study by Wang et al combined patient-derived and genetically engineered induced pluripotent stem cells (iPSCs) and tissue engineering to elucidate the pathophysiology underlying the cardiomyopathy of Barth syndrome, a mitochondrial disorder caused by mutation of the gene encoding tafazzin (TAZ). Using Barth syndrome iPSC-derived cardiomyocytes (iPSC-CMs), they defined metabolic, structural and functional abnormalities associated with TAZ mutation. Barth syndrome […]

External stressors reprogramming somatic to pluripotent cells

Posted by & filed under Tools, Treatment.

A new means of reprogramming somatic cells into pluripotent cells has been recently published by Obocata et al. in Nature. The method is called stimulus-triggered acquisition of pluripotency (STAP) and, in contrast to previous methods; it does not require nuclear transfer or genetic manipulation. Rather, STAP involves exposure of the cells to an external stressor […]

Combining GWAS & Gaussian graphical modeling with metabolomics to predict the identity of unknown metabolites.

Posted by & filed under Tools.

Genetic variation in the human genome has been recently linked to differences in individual metabolite levels by combining GWAS studies and metabolomic tools. A considerable amount of the molecules currently quantified by modern metabolomics techniques are chemically unidentified. Krumsiek et al. developed a systems-level approach that combines GWAS studies and Gaussian graphical modeling with metabolomics […]

Diagnostic exome sequencing in intellectual disability.

Posted by & filed under Exome sequencing, Part 06: DIAGNOSTIC APPROACHES, Part 28: NEUROGENETICS, Tools.

de Ligt et al. evaluated patients with intellectual disability to exclude known causes and then sequenced the coding regions of more than 21,000 genes obtained from 100 patients with an IQ below 50 and their unaffected parents. The total diagnostic yield was 16%, mostly involving de novo mutations. The authors conclude that de novo mutations […]

A new approach to advance clinical genomics?

Posted by & filed under Exome sequencing, Part 02: PERSPECTIVES, Part 03: GENERAL THEMES, Part 06: DIAGNOSTIC APPROACHES, Tools.

It is now feasible to sequence an individual’s whole genome at a relatively low cost. However, for genome sequencing to be implemented clinically, a number of major challenges need to be overcome. I hereby discuss the challenges associated with integrating genomic technologies into clinical practice and describe a novel approach, namely, “Individualized Mutation-weighed On-line Phenotype […]