Evaluation of Next Generation Sequencing for Detecting HER2 Copy Number in Breast and Gastric Cancers.

Amplicon-based next generation sequencing (NGS) approaches have been preferentially adopted by the clinical laboratories on the basis of a short turnaround time (TAT) and small DNA input needs. However, little work has been done to assess the amplicon-based NGS methods for copy number variation (CNV) detection in comparison with current standard methods like immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The correlation between NGS based CNV detection and the later standard methods has remained unexplored.

Identification of MET exon14 skipping by targeted DNA- and RNA-based next-generation sequencing in pulmonary sarcomatoid carcinomas.

Background: Pulmonary sarcomatoid carcinomas (PSCs) constitutes a heterogeneous group of NSCLCs, which show poor prognosis even with aggressive surgical treatment and postoperative chemotherapy. The detection MET exon14 skipping (METex14 skipping) in PSCs suggests the targeted therapeutic opportunities with MET TKIs.

Patients And Methods: We detected MET exon14 alterations using both targeted DNA- and RNA-based Next Generation Sequencing (NGS) and elucidated the driver mutation profile of 77 Chinese PSC patients.

Performance comparison of NextSeq and Ion Proton platforms for molecular diagnosis of clinical oncology.

Purpose: Next-generation sequencing is a powerful approach to detect genetic mutations with which cancer diagnosis and treatment can be tailored to the individual patient in the era of personalized and precision medicine. Ion Torrent Systems Ion Proton and Illumina NextSeq are 2 major targeted sequencing platforms; however, not much work has been done to compare these platforms' performance for mutation detection in formalin-fixed paraffin-embedded (FFPE) materials.

Methods: We benchmarked the performance by using a collection of FFPE samples from 23 patients with different cancers for NextSeq and Ion Proton platforms.

Development and validation of an ultra-high sensitive next-generation sequencing assay for molecular diagnosis of clinical oncology.

Dramatic improvements in the understanding of oncogenes have spurred the development of molecular target therapies, which created an exigent need for comprehensive and rapid clinical genotyping. Next-generation sequencing (NGS) assay with increased performance and decreased cost is becoming more widely used in clinical diagnosis. However, the optimization and validation of NGS assay remain a challenge, especially for the detection of somatic variants at low mutant allele fraction (MAF).

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys.

Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates.

A global network-based protocol for functional inference of hypothetical proteins in Synechocystis sp. PCC 6803.

Functional inference of hypothetical proteins (HPs) is a significant task in the post-genomic era. We described here a network-based protocol for functional inference of HPs using experimental transcriptomic, proteomic, and protein-protein interaction (PPI) datasets. The protocol includes two steps: i) co-expression networks were constructed using large proteomic or transcriptomic datasets of Synechocystis sp.

Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803.

Background: Recent efforts demonstrated the potential application of cyanobacteria as a "microbial cell factory" to produce butanol directly from CO2. However, cyanobacteria have very low tolerance to the toxic butanol, which limits the economic viability of this renewable system.

Results: Through a long-term experimental evolution process, we achieved a 150% increase of the butanol tolerance in a model cyanobacterium Synechocystis sp.

Metabolomic and network analysis of astaxanthin-producing Haematococcus pluvialis under various stress conditions.

Various combinations of acetate (Ac), Fe(2+) and high light (HL) stress conditions were evaluated to maximize astaxanthin accumulation and biomass production in Haematococcus pluvialis, and then GC-MS and LC-MS based metabolomics were applied to determine molecular mechanisms responsible for enhancing astaxanthin accumulation under the stress conditions. With the optimized analytical protocols, the GC-MS and LC-MS analyses allowed identification of 93 stable and 24 unstable intracellular metabolites from H. pluvialis, respectively.

Metabolomic analysis of the salt-sensitive mutants reveals changes in amino acid and fatty acid composition important to long-term salt stress in Synechocystis sp. PCC 6803.

Early studies in cyanobacteria have found that few genes induced by short-term salt shock (15-60 min) display a stable induction in the long-term (>1 day) salt-acclimated cells; meanwhile, most of the genes responsive to long-term salt stress were different from those by short-term salt shock, suggesting that different regulatory mechanisms may be involved for short-term and long-term salt stress responses. In our previous work using the model cyanobacterium Synechocystis sp. PCC 6803, sll1734 encoding CO2 uptake-related protein (CupA) and three genes encoding hypothetical proteins (i.

Global metabolomic and network analysis of Escherichia coli responses to exogenous biofuels.

Although synthetic biology progress has made it possible to produce various biofuels in more user-friendly hosts, such as Escherichia coli, the large-scale biofuel production in these non-native systems is still challenging, mostly due to the very low tolerance of these non-native hosts to the biofuel toxicity. To address the issues, in this study we determined the metabolic responses of E. coli induced by three major biofuel products, ethanol, butanol, and isobutanol, using a gas chromatography-mass spectrometry (GC-MS) approach.