Now a day’s, pharma research is facing challenges in deciphering molecular understanding of disease initiation, progress and establishment as well as performance assessment of drug molecule on such phases of disease development. Emerging of next generation sequencing bases molecular tools were found to be a key method for creating genome wide genomics landscape of gene mutations, gene expression and gene regulation events. Although NGS is a powerful tool for molecular research but same time it have its own technical challenges. Few major challenges of NGS based pharmacogenomics is summarized below

1. BIOINFORMATICS
OFFERINGS

2. Now a day’s, pharma research is facing challenges in
deciphering molecular understanding of disease initiation,
progress and establishment as well as performance
assessment of drug molecule on such phases of disease
development. Emerging of next generation sequencing
bases molecular tools were found to be a key method for
creating genome wide genomics landscape of gene
mutations, gene expression and gene regulation events.
Although NGS is a powerful tool for molecular research but
same time it have its own technical challenges. Few major
challenges of NGS based pharmacogenomics is
summarized below -
Pharmaceutical
GENOMICS CHALLENGES
Large size genomic data
Deployment of rapidly updating
annotation databases
Analysis and Interpretation of Output
generated at each analytic phase
Integration of external information/
data to evaluate the hypothesis
Selection of appropriate analysis
tools or pipeline

3. Incedo’s Bioinformatics
BASED ANALYTIC SOLUTIONS
Despite various challenges offered by NGS data generated from pharmaceutical industries, the
bioinformatics methods supported by advanced computing infrastructure have made clinicians
capable to process, analyze, interpret and validate the hypothesis. Simultaneous growth of molecular
and computing environment made it possible to deliver outputs to pharmacogenomics needs. Our
bioinformatics based analytic solutions are as follows:
Cloud based scalable computing
environment and parallel sample
processing scalable in terms of RAM,
computing and storage
Benchmarking of tools and pipelines
crucial to ensure the accuracy and
reproducibility of analytical tools and
pipelines used to characterize NGS data
Proper and elaborated reporting of
results derived from each analysis at
different analytics phase
Evaluation of hypothesis in the light of
scientific literature by automated
algorithm and manual curation
Unique
OFFERINGS
Results
validation
with published
research studies
or data – Results
validation with
cited literature
Wide range
of analytics
tools
Secondary
analysis
Tertiary
analysis
Results
validation with
published
research studies
or data
noita
cifitnauQeneG
Gene
Mutagenesis
ChIP-Seq
DNAse-Seq
FAIRE-Seq
RNA-Seq
Microarray
Exome-Seq
WGS-Seq
Targeted -Seq

4. Case Study Exome-Seq: We studied Exome
sequencing analysis on colon tumor tissue of 10
colorectal cancer patients. Genome-wide
assessment of the mutation events in these colon
tumors revealed massive alterations throughout
the genome, consisting of previously-established
and novel mutations. We found out the quality
assessment revealed high-quality of the
sequencing experiments. A large number (average
84%) of high-quality reads were perfectly aligned
with the human genome. Total 1330867 variants
were identified in the colon cancer samples out of
which 1078123 (81%) were known mutants and the
remaining 252744 were considered novel variants
specific to the colon cancer samples of this study.
Case Study ChIP-Seq: We evaluated the possible
role of transcription factors in the development
and progress of colon cancer disease. Co-
immunoprecipitation method elucidated a
comparison of genome-wide transcriptional
activity in a diseased state in comparison with
diseased vs. normal tissue. This study has been
derived from publicly- available colon cancer ChIP-
Seq repository data (PRJNA155759) entitled as
“Epigenomic enhancer profiling defines a signature
of colon cancer [ChIP-seq]”. It is largely focused on
coding sequences and promoters, despite the fact
that distal regulatory elements play a central role in
controlling transcription patterns. Histone mark
H3K4me1 was used to analyze gain and loss of
enhancer activity genome- wide in primary colon
cancer lines relative to normal colon crypts.
Representative
WORKS

5. Representative
WORKS
Case study of RNA-Seq of TCGA breast cancer data
of ER+, PR+, HER+, TNBC, Breast Tumor: We
downloaded Breast cancer data from TCGA and
used RNA-Seq Version 2 sequencing data to
determine gene expression levels from the TCGA
data portal. After analyzing around 1200 RNA-Seq
Samples we grouped the samples based on ER+,
PR+, HER2+, Triple Negative & Solid breast tumor
samples. The gene expression profile was measured
experimentally using the Illumina HiSeq 2000 RNA
Sequencing platform at the University of North
Carolina TCGA genome characterization center. We
have utilized MapSplice to perform the alignment
and RSEM to perform the gene level quantitation.
Level 3 interpreted data was also downloaded from
University of North Carolina TCGA genome
characterization data coordination center for
reference. Genes are mapped onto the human
genome coordinates using UCSC cgData HUGO
probeMap. This dataset shows gene-level
transcription estimates, as RSEM normalized
counts, percentile-ranked within each sample.
Incedo Inc.
(formerly a part of $ 4Bn Indiabulls Group)
USA: | 2350 Mission College Boulevard, Suite 246 Santa Clara, California - 95054 | Tel: +1408 531 6040
INDIA: | 248, Udyog Vihar Phase-IV, Gurgaon - 122 015 | Tel: +91 124 4345900/ 01/ 02