Road to the Biomarker discovery via NGS-based transcriptomics: a case study


Faculty Scientist, Institute of Bioinformatics & Applied Biotechnology

ABSTRACT: One of the key reasons for a slower rate of discovery of new diagnostic or therapeutic molecules, in recent years, is lack of attention to thorough screening and identification of target molecules. If researchers do not identify the right target molecule it can result in failure at later stages of R & D or during clinical trials.

Exploring gene expression profiles is key to biomarker discovery, which in turn is crucial for diagnostics, prognostics, and therapeutics. With the advent of modern techniques such as the microarrays, NGS, and mass spectrophotometry, and parallel bio-IT approaches, there is a higher potential to generate more data and a more meaningful short-listing of potential target molecules. RNA-sequencing particularly offers hope to identify key transcript- and/or protein-isoforms associated with diseases. But the data need to be carefully analyzed and interpreted. This has been a non-obvious challenge. There seems to be a tremendous gap between general biologists, health professionals, molecular biologists, pharmacologists and computational biologists/bioinformaticians. My team has been doing some research in meeting such challenges, at IBAB ( earlier developed a simple yet effective computational meta-analysis method. We also carefully compiled public transcriptomic data and developed a few software and databases for better analysis and interpretation of the data. Using the newly developed methods, we identified a list of genes and specific alternatively spliced forms of transcripts, which may be important for a type of male infertility (non-obstructive azoospermia – which we think is a good model to work towards better male contraceptives as well).Then they performed their own RNA-sequencing using clinical samples and validated the observations.  are currently performing more data analysis, particularly in terms of network analysis, and pick crucial biomarker-candidates for non-obstructive azoospermia as well as a few other disease conditions, such as lung and breast cancer, as well.

Meet Dr. Kshitish Acharya, Scientist, IBAB at Emerging Role of Next Generation Sequencing in Clinical Genomics on November 01 in Mumbai.#NGSCG#GENOMICS2017



What will make it an Overwhelming QbD Conference?

Dear Colleagues,

Many of you wonderful scientists must be having one or more of the following questions in your mind.

What is different in this QbD conference?

I have attended so many QbD conferences, why one more??

QbD is same always, what is new in this conference???

I am from XYZ department, will I gain anything????

I am busy, how should I take out time for this conference?????

However, we wish to tell you that our “QbD in Pharma Developement World Congress 2015 ” is going to be a great conference.  We have done efforts to make this conference the best possible with several happenings which have never been collectively there before at any QbD conference viz Problem Solving Software Training and discussion on the following and many more topics.

  • Question based Review and Continued Process Verification
  • Question based Approach to Product Development
  • Integration of Quality by Design from Product Development to API Production
  • Methods to Minimize the Impact of Uncertainty in Pharma Quality Attributes
  • Realization of Quality by Design in ANDA Submissions
  • How to Demonstrate the Relevant Diligence on Filing
  • Risk Based Approach for Efficient Development of the DS Control Strategy
  • QbD & QbR to Reduce Health Care Cost while Maintaining Quality
  • How to find the Robust Setpoint for Design Space Combining DOE Models, Monte Carlo Simulations and Design Space Concept
  • ATP and CQA For Analytical Methods
  • Risk Assessment In Aqbd and Design Space for Analytical Methods
  • Tools that Play a Critical Role in Implementation of Qbd for Biotech Processes
  • Five-D Concept of QbD
  • Live Demonstration on How to Utilize Tools of Qbd i.e. DoE & PAT
  • Industry Case-Studies Related to Implementation of PAT
  • How To Implement DoE & PAT Systematically & Effectively during Development & Manufacturing of Solid Oral/Liquid Orals/ Semisolids & Parenteral Dosage Forms
  • DoE for Development of a Modified-Release Tablet
  • Advanced DoE for Improved Process Understanding
  • Statistics in Product Development – Beyond DoE
  • Use of other Statistical Tools to Build Robust Products & Processes
  • Chemometric Tools in QbD -Chemometric Methods & their Advantages and Principle
  • QbD Based Systematic Development of Nanoemulsions for Natural Product
  • Analytical Quality By Design (Aqbd) Approach In RP-HPLC Method Development
  • Quality By Design (QbD) Approach in Formulation of Oral Delayed Release Tablet of LansoprazolFor details, please find attached the agenda of the conference. Looking into the above topics being covered, we feel that we have the answers to the above questions
  •  You were looking for the best QbD scientists and there they are.
  • This is not like the earlier conferences since the quality of talks is exceptionally high and specifically meant to enhance your process and product understanding.
  • QbD has to be implemented holistically and if you are a scientist from Quality assurance, Analytical development, API Development or Formulation Development, it is relevant for you.
  • You are entrusted with responsibility to develop products and processes of high quality for effective ANDA filings and that exactly the aim of this conference is.
  • You spend lot of time in sorting out QbD data related problems which your colleagues must be facing. Be there, get your data problems solved and save time.
  • Finally get tips on how to develop medicine in cost effective manner and give your company a return which is much higher than investment in this conference.

So what are you waiting for? Register now

Our worthy Speakers and we all will be doing our best and Now it is your presence which will make it an Awesome Conference.!!!

Looking forward to see you in Chandigarh.

How Question Based Development can Demonstrate Quality by Design and how it can Facilitate Continued Process Verification??

Ajaz Hussain2

How Question Based Development can Demonstrate Quality by Design and how it can Facilitate Continued Process Verification??

Recent organizational changes at CDER/FDA have created a new ‘supper’ Office of Pharmaceutical Quality to improve information and knowledge sharing and decision- making; (a) within New and Generic CMC Review function, and (b) between CMC Review and CGMP Compliance functions.  ‘Question based Review’ and ‘Continued Process Verification’ are two themes can be expected to have a significant impact over the next several years on how product development, validation and manufacturing is carried out in industry and how FDA will review and inspect these functions.

If the above issue is important for you and you would like to be enlightened on the same you ought to be in Chandiarh for “QbD in Pharma Development World Congress 2015” on April 16, 2015 in Chandigarh. Dr Ajaz Hussain, Former FDA Reviewer and Currently Executive Director, NIPTE, USA will be there to address this issue and many more.

Just SMS QbD at 7696125050 and we will get back to you with more details.

An Evening Delight in Chandigarh


Beat the intellectual heat and invigorate yourself with a Delightful Evening tour of Chandigarh after the intense sessions and thought provoking discussions during QbD in Pharma Development World Congress. SELECTBIO cordially invites all conference participants to join us for Chandigarh by Evening Sightseeing Tour on April 17, 2015 in Chandigarh Tourism Open-Roof Double-Decker Tourist Coach. This trip will begin at 05:30 pm and will take about 2 and half hours.

The trip will include visit to Rose Garden, Capitol Complex, Sukhna Lake, Garden of Silence and Terrace Garden.

Don’t Forget to Carry Your Cams !!!

How to choose right tool to implement 3D Cell-based Assays?

 The Implementation of 3D Cell based Assays and High Content Imaging in Translational Research: Choosing the right tools for the Job

High Content Screening and analysis (HCS/A) technologies have over the last 15 years become widely adopted in both the academic and industrial research sectors. The acceptance of these technologies has in the large part been due to their demonstrable utility as both drug-discovery and basic research tools, indeed these imaging technologies such as HCS/A have the capability of providing researchers with a ready means of performing both large scale primary screens as well as permitting more detailed downstream analysis.  Alongside the rapid uptake of these technologies, we have also seen a concomitant increase in the demand for more refined and flexible hardware and biologically relevant cell based assay approaches that can be utilized for translational research.  Currently one of the biggest drivers in the field is the need to improve the physiological relevance of cell based assays used within translational research campaigns. To achieve these aims many are turning their attention to the use of primary cells and/or 3 dimensional cellular assay models. In summary this presentation will cover the key technological and methodological approaches we are currently implementing within our High Content Analysis workflows to meet our translational research goals. This talk will be presented at CellTech India 2015 in Bangalore on March 2, 2015 by Dr. Anthony Mitchell Davies, Queensland, Australia. Dr. Anthony Mitchell Davies is currently the Center Director: Translational Cell Imaging, Institute of Health Biomedical Innovation, Australia

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How to integrate 3D cell cultures in biomedical research?

Advanced Cell Based Assay and Phenotype Screening Approaches in Biomedical Research and Drug Discovery – One Day Training Course with Live Demo

With the ever-increasing demand for improved productivity in research through the generation of robust analysis outputs has driven both the development and deployment of phenotypic cell-based approaches to drug discovery. In contrast to the more traditional cellular analysis and target-based approaches, here the researcher is able to evaluate the efficacy of potential therapeutics by monitoring the physiological state of cells through the simultaneous analysis of multiple cellular parameters in the context of an intact biological system. This course will cover the key features of the latest imaging technologies and the best approaches to using these technologies for phenotypic cell-based screening. As part of this course we will also cover the some of the latest approaches to 3D cell culture, lab on a chip and the analytical and methodological challenges these new methods represent to the researcher. This course will cover

  • An appraisal of the key technologies currently being utilized in this area of research
  • Presentation of research data from a few selected studies using both 2d functional and 3D assay technologies
  • Hands on demo showing demonstrating advanced analysis techniques
  • Q & A and Group Discussion

Lab Visit & Live Demo

A Lab visit and Live Demo has been arranged for the course participants at advanced high content and high throughput screening facility of C-CAMP. The visit will include a live demo of both the high end platforms.

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Conference: CellTech India 2015

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SELECTBIO is organizing its inaugural International conference on Cell Culture and Cell based assays “CellTech India 2015” scheduled to be held on March 2-3, 2015 in Sheraton Bangalore Hotel at Brigade Gateway, Bangalore, India.

This event aims to bring together scientists working in the field of 2D and 3D cell culture, cell line development and optimization, cell based assays, biomolecular screening, phenotypic screening, flow cytometry, cell imaging, high throughput screening, high content screening, new drug discovery research, cancer research, circulating tumor cells and stem cell therapies for cancer. About 100 scientists from India and abroad and from Industry and academics are expected to attend the event. With experts like Anthony Michael Davies, Director, Translational Cell Imaging, Australia, Alain Bernard, Vice President, UCB Pharma, Jeremy Simpson, University College, Dublin and several more as serving as Speakers, this event will provide an excellent platform for researchers from all facets of drug research an unprecedented opportunity to explore the advancements in the field of cell technologies.

The event will be followed by a one day post conference training course entitled “Advanced cell based Assays and Phenotypic Screening Approaches in Biomedical Research & Drug Discovery” to be conducted by Dr Anthony M Davies. This training course will also have Live demos at Advanced High Content & High Throughput Screening facility at C-CAMP, Bangalore. The training course followed by live demo has been specially arranged so as to give the participants greater and lasting learning experience.

This event is co-located with another inaugural event International Conference on ADC Development & Manufacture “Current Trends in Antibody Drug Conjugates“. Participants registered for one conference can attend both the co-located conferences. For enhanced and cost-effective learning and comfortable stay SELECTBIO INDIA has recently introduced affordable conference packages for the delegates. The details of these packages are available at