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Archive for the ‘Next generation sequencing’ Category

Launched an open access database of neuropsychiatric disease biomarker and drug discovery assays and protocols. The listed protocols are extracted from and linked to patents and journal articles. The innovative representation of protocols in this database will be a useful tool for idea/concept generation for developing innovative approaches for neuropsychiatric disease biomarker and drug discovery research. Please follow this link to see the complete list of protocols: Neuropsychiatric disease biomarker and drug discovery assays and protocols

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Bioprotocols database

The decisive goal of clinical biomarker discovery should be intended for developing high quality and low-cost disease detection/monitoring assays with high diagnostic accuracy. Innovative approaches are warranted for the discovery of clinical biomarkers, with faster bench to clinics timeline, to provide high quality and efficient patient care. At the same time, if we continue with the strategic and technological approaches that are currently being adopted for biomarker discovery and validation, most likely, it may take several years to find clinically viable biomarker/s for complex diseases like cancer or neurodegenerative or autoimmune or other human diseases. Therefore, an ideal clinical biomarker discovery platform, which can lead to the development of reliable and robust clinical diagnostics assays, should adopt an integrated approach that consists of comprehensive understanding of patients’ phenotypic, genetic and socio-environmental characteristics as well as biological and functional relevance of all biomolecules. In order to achieve these goals, two models for the discovery, selection and validation of clinically viable biomarkers are proposed in this scientific blog. Read the full blog: How to Identify Clinically Successful Biomarkers?

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This scientific blog critically analyzes potential complexities associated with current biomarker discovery approaches. According to the scientific arguments that have been put forward in this blog, thousands of biomarkers that are currently being reported may not be true biomarkers of the target disease, rather it may be a complex mixture of biomarkers, which may include target disease specific biomarker as well as biomarkers or biomolecules associated with other diseases, infections, gender, race/ethnic backgrounds, geographic-environmental factors, psychiatric condition/diseases and nutritional factors. Based on our analysis, we believe that an ideal biomarker discovery platform, which can lead to the development of reliable and robust diagnostics assays, should be developed by integrating comprehensive understanding of patients’ phenotypic, genetic and socio-environmental characteristics along with biological and functional relevance of all biomolecules that may be potentially identified and called as biomarkers. Several innovative strategies for developing rational and personalized biomarker discovery platforms have been suggested in this blog. These strategies include 1) Comprehensive genome-scale analysis based rational genetic biomarker discovery 2) Cell or tissue or organ specific function based rational or targeted biomarker discovery 3) Use of validated tissue/organ specific biomarkers or therapeutic drug targets for identifying non-invasive biomarkers, 4) Epidemiology-driven biomarker discovery for developing personalized diagnostic tools and 5) Integrated bioinformatics approaches for rational biomarker discovery. The relevance of disease prevalence and predictive value in biomarker discovery for personalized medicine, utility of rational or personalized biomarkers in clinical trials and applications of rationally identified biomarkers for diagnostics imaging or theranostics have also been discussed. Read the full blog (click on this title): Strategies for Rational and Personalized Cancer Biomarker Discovery

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Tumor and Tumor Cell Assays and Protocols

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Highlights of recent US patent applications on protein biomarkers, theranostics and molecular diagnostics.

1. Externalized phoshatidylserine as a global tumor blood vessel biomarker and a cancer theranostics target
2. Radiolabeled cyclic pentapeptide drug for the diagnosis and treatment (theranostics) of cancer
3. Glyoxalase I gene point mutation as a potential next generation sequencing diagnostics target of schizophrenia
4. T cells expressing B-Raf and K-Ras for rheumatoid arthritis theranostics (diagnostic therapy)
5. SNP markers for predicting the risk of developing antibodies against FVIII- a potential personalized medicine strategy for hemophilia patients
6. FGF23 mRNA detection- a potential next generation sequencing diagnostics target of oncogenic hypophosphatemic osteomalacia (OHO) tumors
7. FGF23 missense mutations- potential next generation sequencing diagnostics target of autosomal dominant hypophosphatemic rickets (ADHR)
8. Serum amyloid A as molecular and immunodiagnostic diagnostic biomarker of glaucoma
9. Methods for detecting a target nucleic acid and a target protein in a single assay
10. PDE10 inhibitors for schizophrenia theranostics
11. Antibodies that specifically inhibit VEGF binding to VEGFR2 receptors for cancer theranostics
12. Major adverse cardiac events risk score (MACERS) for evaluating the risk of mortality in patients with heart failure
13. Biomarkers for diagnosing and for determining the progression of osteoarthritis
14. Biomarkers for the detection of renal damage caused by chronic renal transplant rejection
15. Phosphodiesterase 4D7 (PDE4D7) for prostate cancer theransotics (diagnostics therapy)
16. Phosphodiesterase 9A (PDE9A) for prostate cancer theransotics (diagnostics therapy)
Details: http://www.sciclips.com/sciclips/biomarker-news.do

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2. Bioprotocols
3. Drug discovery news
4. Biomarker news

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2. Cancer Theranostics – Potential Applications of Cancer Biomarker Database

Following are the new categories added to the Bioprotocols section. This bioprotocol database contains a unique list of protocols that are linked to open access journal articles, patents (issued) and patent applications. More than 10,000 protocols are listed in this database.

Next Generation Sequencing Protocols: A comprehensive list of next generation sequencing protocols for human, bacteria, virus, plants and other organisms.

Nanoparticles: Drug delivery, Imaging and Theranostics Protocols: The protocol categories include:Nanoparticle based Drug delivery & assays/immunoassays/imaging and preparation & characterization of nanoparticles.

Pharmaceutical Drug Formulation Protocols: The protocols categories include:General pharmaceutical drug formulation and nanoparticle based drug formulation protocols.

Raman Spectroscopy (Biomarker,Drug discovery and Theranostics Applications) Protocols: The protocols listed are related to the applications of Raman spectroscopy in biomarker discovery/imaging, cancer diagnosis, drug efficacy evaluation, drug composition analysis, protein/DNA/metabolite analysis, drug discovery assays and theransotics. The methods include coherent anti-Stokes Raman scattering (CARS),surface enhanced Raman spectroscopy (SERS),Tip-enhanced Raman scattering (TERS) etc.

Metabolomics Protocols: A comprehensive list of metabolomics protocols related to biomarker and drug discovery.

Next Generation Sequencing Bioinformatics Tools & Databases: A comprehensive list of open access bioinformatics tools and database for next generation sequencing data analysis.

Circulating Tumor Cells (CTCs) Protocols: A comprehensive list of open access circulating tumor cells (CTCs) protocols

Mitochondrial Drug Discovery Protocols: A comprehensive list of open access mitochondrial drug discovery protocols

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2. Biomarker discovery protocols (descriptive protocols)
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5. Biomarker discovery news

Note: Following are the highlights of recent patent applications on next generation sequencing. Complete review of next generation sequencing related patent searches and data mining are available through Sciclips consultancy services.

1. Terminal tagging oligoribonucleotide (rTTO) to join a DNA sequence tag to the 3′-termini of first-strand cDNA molecules
2. A ligation-based method and a kit for preparing a template for next generation sequencing
3. Next generation sequencing method for noninvasive prenatal diagnostics
4. High-throughput next generation sequencing DNA markers for treating, diagnosing, and prognosing lung cancer
5. Next generation sequencing method of predicting the risk of a patient for developing COX-2 inhibitor lumiracoxib induced hepatotoxicity
6. Next generation sequencing method for determining the primary site of a cancer of unknown primary site (CUP)
7. Next generation sequencing method for diagnosing Noonan-like syndrome with loose anagen hair
8. Next generation sequencing method for the diagnosis of Alzheimer’s disease
9. Method for high throughput paired-end sequencing of large-insert clone libraries for next generation sequencing
10. Next generation sequencing method for determining the increased risk for developing degenerative neurological or psychiatric diseases
11. Identification of fetal nucleic acid fraction in a mixture of fetal and maternal nucleic acids using next generation sequencing
12. Next generation sequencing method for predicting the risk of developing late onset Alzheimer’s disease
13. Whole genome sequencing methods for identifying polymorphisms in blood sample
14. Next generation sequencing methods for diagnosing presence or increased risk of developing an autism spectrum disorder
15. Next generation sequencing method for determining the genome of an unborn fetus of a pregnant female

Details: http://www.sciclips.com/sciclips/biomarker-news.do

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4. Cancer Theranostics – Potential Applications of Cancer Biomarker Database

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1. Next generation sequencing bioinformatics tools and analysis
2. Comprehensive cancer biomarker database with companion diagnostics pathway
3. Drug discovery protocols
2. Bioprotocols
4. Drug discovery reagents
5. Drug discovery news


Comprehensive Cancer Bomarker Database

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A comprehensive database for stem cell researchers, Stem cell research reagents, Stem cell patents, Stem cell grants, Stem cell clinical trials, Stem cell statistics, Stem cell news and Stem cell open innovation ideas. Please visit http://www.sciclips.com/

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Drug target database (open access)

Pharmacogenomics protocols online

Proteomics and Mass spectrometry (MS) protocols online

Therapeutic drug targets database (open access)

Drug discovery, Biopharmaceuticals, HTS assays protocols online

Protein display/Protein engineering/Directed evolution protocols online

Molecular biology and Cell biology protocols online

siRNA protocols miRNA protocols online

Video protocols

Cell culture video protocols, Cytotoxicity assay video protocols, Stem cell video protocols, Molecular biology video protocols http://www.sciclips.com/sciclips/video-protocols.do

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Bioprotocols online (open access)

Combination therapy database (open access)

Therapeutic drug targets database (open access)

Bioinformatics databases (open access)

HTS assay protocols online (open access)