Ethnicity and Breast Cancer Risk: The Indian Saga & Role of NGS

Conference Talk by Dr. Ahmad

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Dr. Firoz Ahmad 
Research Scientist & Senior Manager-R&D,SRL Diagnostics

Talk Abstract: Carcinoma of the breast is one of the most prevalent cancers in Indian females, and the incidence of breast cancer has been increasing manifolds in India and so the burden of breast cancer on the Indian healthcare system has been steadily on rising also emphasizing the need for a cost-effective method for early detection of these cancers.

Unfortunately, it has been established that Indian patients develop breast cancer at a younger age than their Caucasian counterparts, the contributions of BRCA1 and BRCA2 (BRCA1/2) mutations in Indians are expected to be different than in Caucasians. Although identification of BRCA1 and BRCA2 has greatly increased our understanding of breast cancer genetics in populations of Western European descent, reports about the role of these genes in Indian patients are still very limited. In the current report results found by using next-generation sequencing (NGS) tools, the prevalence and distribution pattern of BRCA1/2 gene mutations in Indian patients will be discussed, this presentation also aims to present the current status of knowledge about the spectrum of BRCA pathogenic variants in Indian populations.The study highlights how Next-generation sequencing (NGS) based testing increases the sensitivity of mutation detection, and help in identifying patients at high risk of developing cancer. New advances in genomic technologies, such as next-generation sequencing (NGS), allow the sequencing and analysis of genes associated with a disease/cancer efficiently at a significantly lower cost as compared with the traditional methods.

Studies such as these will provide physicians and researchers much-needed evidence on the clinical utility of NGS for incorporation into routine genetic testing in clinical oncology practice and thrust the clinical research.

Meet Dr. Firoz Ahmad at Emerging Role of Next Generation Sequencing in Clinical Genomics in Mumbai on November 01, 2017.

 

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Newer Metabolite and Pathway Identification Approaches to Metabolomics

Conference Talk by Dr. Pal

Dr Debnath
Dr Debnath Pal, Professor, Indian Institute of Science, India

Talk Abstract: Identification of metabolites and inference of differentially regulated metabolic pathways are the key aims of metabolomics research. A common approach to this problem is to compare the experimental spectrum with the database archived metabolite information. However, databases store metabolite information at “standard condition” which are in most cases in variance to the experimental condition data is obtained. Consequently, a considerable fraction of the metabolites remains unidentified and the experimental spectrum unharvested.

Dr. Pal has developed a method based on matching the pattern of spectrum peaks rather than absolute tolerance thresholds, using a combination of geometric hashing and similarity scoring techniques. When applied to 2D NMR metabolomics data, tests with 719 metabolites from the Human Metabolome Database show that 100% of the metabolites can be assigned correctly when accurate data are available. A high success rate is obtained even in the presence of large chemical shift deviations such as 0.5 ppm in 1H and 3 ppm in 13C and missing peaks (up to 50%), compared to nearly no assignments obtained under these conditions with existing methods that employ a direct database search approach. A variation of the approach has been extended to obtain “peaks to pathways” information from NMR spectral data.

Dr. Debnath Pal is noted for his contributions in the area of protein structure, function, interaction and dynamics.

He will be speaking at Metabolomics India 2017 conference on 15 September in Hotel Le Meridien, Bengaluru.

How Fetal Cell Free DNA (cfDNA) is Expanding the Frontiers of Non-Invasive Prenatal Testing?

Conference Talk by Dr. Bhatt

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Dr. Sucheta Bhatt, Director, Genetics, Illumina, USA.

Talk Abstract: Fetal cfDNA can be reliably detected in the maternal circulation by 7 weeks gestation and its amount increases with gestational age, Cell-free DNA in maternal circulation, therefore, can be reliably used in clinical practice to screen for common aneuploidies (21,18, 13) and sex chromosome analysis.The recent advancements in DNA sequencing technology, as well as counting statistics, have also provided a timely opportunity to develop new methods for the non-invasive detection of fetal aneuploidy. Test performances and positive and negative predictive values are well established for the same.

Over the past few years, the NIPT using cell-free DNA is expanding in terms of addition of more content, specifically expanding to screening for microdeletion, rare chromosome trisomies, and copy number variation.

This presentation will give an insight into the following aspects of NIPT-

  • Methodology
  • Clinical indications
  • Test performances
  • Clinical utility aspects of the expanded NIPT platforms

Dr. Sucheta Bhatt will speak at Emerging role of Next Generation Sequencing in Clinical Genomics” scheduled to be held on 01 November 2017 in Mumbai, India.

Implementing next-generation sequencing technology for non-invasive prenatal testing (NIPT) in diagnostics

Conference Talk by Dr. Weiss

Janneke weiss ma'am
Dr. Janneke Weiss, The Netherlands

Talk Abstract: The first part of this presentation will provide background information on the biology underlying NIPT. It will explain what cell-free DNA is, the source of cf-DNA will be discussed, and the consequence for the sensitivity and specificity of cf-DNA testing. The basics of the different available technologies will be discussed briefly. Finally, a short introduction will be given on the most commonly used bioinformatics tools, based on a z-score analysis.

The second part of this presentation will cover tools, pitfalls, and tricks: causes of false positive and false negative results. NIPT analysis for the detection of Trisomy 21, 13 and 18 is rather straightforward, there are several biological factors that might cause false positive and false negative effects. Although most of them are rare, testing of large numbers of pregnant women will assure the fact that all of these causes might be encountered. The most important causes are: False negative results (Low foetal fraction, True foetal mosaics, Twin pregnancies) and False positive results (Confined Placental Mosaicism (CPM), Maternal CNVs, Maternal malignancies, Maternal mosaics, Vanishing twin). Most of these causes will be discussed based on examples from daily practice in her facility.

Furthermore, Dr. Weiss will discuss how to discern between true negative/positive and false negative/positive results based on several different bioinformatics tools that were developed at VUmc Amsterdam, such as WISECONDOR and Defrag. WISECONDOR detects smaller chromosomal deletions and duplications without increasing the need for NIPT/NGS data. It is now widely used in many countries for routine diagnostic NIPT analysis, including the Netherlands, Denmark, France and South Korea. Defrag has not yet been published but is a tool to determine foetal fraction. Defrag is based on Y-chromosome fraction. All tools are freely available for non-commercial use  (https://github.com/rstraver).WISECONDOR can also be used for the detection of tumor profiles in cf-DNA from cancer patients.Through her presentation, Dr. Weiss will share her experience in interpretation of genetic data, both sequence variants as well as copy number variations, in NIPT and clinical diagnostic setting.

Dr. Weiss is Head NGS Facility, VU University Medical Center, The Netherlands. Meet Dr. Janneke Weiss on November 1, 2017, in Mumbai, India at Emerging Role of Next Generation Sequencing in Clinical Genomics.

 

Translating Cancer Genomics to Medicine

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Dr. Amit Dutt
Scientist F
ACTREC, Mumbai

Conference Talk by Dr Amit Dutt

Talk Abstract: As we know that Massively parallel Next Generation DNA sequencing technologies has made technically feasible to interrogate the complete set of genomic alterations in a tumor in a systematic, comprehensive manner in a single run. These methodologies are beginning to transform diagnostics by allowing cancers to be classified based on molecular mechanism and allowing clinical trials to be undertaken on more homogeneous groups of patients; and, therapeutics by sparking a new generation of drugs targeted at the molecular alterations that cause cancer. Advances have been made by Dutt Laboratory leading to the establishment of TMC-SNPdb, first Indian SNPdb which is the first open source freely available, flexible and upgradable SNP database from whole exome data of 62 normal samples derived from cancer patients (hosted at ANNOVAR) from India origin. It consists of 114, 309 unique germline variants prevalent exclusively among Indian population at a variant frequency. The TMC-SNPdb comes along with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface (GUI) to deplete Indian population-specific SNPs. This will facilitate cancer research using genomics data from pure Indian origin samples. Also, beyond cancer somatic analyses,  it has utility in several Mendelian germline diseases too. It will assist the discovery of novel molecular subclasses, new therapeutic targets, and biomarkers for clinical development in head and neck and lung carcinoma. This database will prove crucial for any researcher working on genome sequencing of different carcinomas and other diseases who would wish for a normal germline SNP db from Indian population.

Meet him on 01 November 2017 in Mumbai at SELECTBIO conference “Emerging role of Next Generation Sequencing in Clinical Genomics”

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 to develop Smaller and Cheaper Cell-Based Assays for HCA?

Assay Miniaturization Strategies:  Smaller and Cheaper Cell-Based Assays for HCA

Learn from Dr Anthony Davies, Director, TCIQ, Queensland, Australia at CellTech India 2015 in Bangalore on March 2-3, 2015.

Abstract

To sustain the viability of large-scale research programs running in academia and industry (especially when considering the current global economic climate), it is essential to reduce research costs wherever possible.  With the advent of micron resolution robotics and nano-litre capable liquid handlers, assay miniaturization for large-scale High-Content Screening is now possible. The advantages of miniaturization are clear, when one considers the savings in reagents and experimental materials and experimental turnaround times.  However miniaturization can also be costly to set up and difficult to deploy.

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