A Contract Research and Services Organization

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A Contract Research and Services Organization
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A Contract Research and Services Organization

• Xcelris is a Specialty Contract Research and
  Services Organization
• Delivering the best end to end solutions to
  global Genomics, Pharma and Bio-Pharma Community
• Built by team of Scientists and Management
  Professionals
• Outstanding infrastructure facilities to support
  Cutting Edge Research

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Our Vision
To  lead the way to a healthier world by
partnering with Pharma Biotech Community across
the globe and delivering high quality value added
healthcare solutions.
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Mission

• Xcelris endeavors to be a world class
  Lifesciences based innovative service
  organization built towards achieving excellence
  in
• Research Technology
• Service Delivery
• Management Capability

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Values
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Infrastructure

• cGLP and cGMP compliant Laboratory designed in
  accordance with global standards
• Spread across 50,000 square ft. area
• Fully equipped Labs conforming to global norms
• Stateoftheart equipments
• Dedicated LIMS
• Dedicated lab for Genomics and Bioinformatics.

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People

• Committed enthusiastic high performing team of
  50 members
• More than 100 man-years of experience in
  Molecular Biology, Plant Molecular Biology,
  Genome Sequencing, Animal Genetics, Virology,
  Bioinformatics, Biotech and analytics
• Alliance partner having experienced people from
  premier institutions like Sanger Labs, Baylor
  College which were part of HGP.
• Xcelris Scientific Board with a strong
  experience in the field of Genomics
  Biopharmaceuticals.

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Whole Genome Sequencing

• Next Generation Sequencing Technology Platforms
  using ABI Roche
• Whole Transcriptome Analysis and SNP Discovery

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Next Generation DNA Sequencing Technology

• SOLiD technology
• Two slide per run and up 16 samples /run.
• 2 Base encoding with higher fidelity.
• 50-75 base per run.
• 10-15 GB data per run.

• Phase I for ABI SOLiD Wet Lab
• Preparation of high quality DNA.
• Qualification of DNA using AGE/Picogreen.
• DNA Shearing and End repair.
• Fragment Library or Mate Paired Library.
• Clonal Emulsion PCR and Bead Enhancement.
• Bead Deposition and Ligation Sequencing.
• Raw data Generation.

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Whole Transcriptome Analysis
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Xcelris Capability
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Xcelris Capability
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ABI SOLiD Technoloy
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ABI SOLiD Technoloy
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GS FLX technology

• One slide per run and up 16 samples /run.
• 300-400 bp per read.
• 1.2 million reads per run
• 0.8-1.0 GB data per run.

• Phase I for GS FLX Wet Lab
• Sample Type Genomic DNA, PCR product, BAC and
  cDNA.
• Qualification of DNA using AGE/Picogreen.
• DNA fragmentation 300-800 bp and End repair and
  adaptor AB ligation.
• Water-in-oil emulsification of beads and PCR
  reagents.
• Clonal amplification in microrector.
• DNA Bead Deposition to Picotitre plate and
  Pyrosequencing.
• Raw data Generation.

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Roche GS FLX (454) Technology
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Roche GS FLX (454) Technology
Sequencing Workflow Loading of Pico Titer
Plate Device
Depositing DNA beads into the Pico Titer Plate
device
Well diameter average of 44 µm gt 400,000 reads
obtained in parallel A single clonally amplified
sstDNA bead is deposited per well
Quality filtered bases
Amplified sstDNA library beads
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Roche GS FLX (454) Technology
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Roche GS FLX (454) Technology
Sequencing-by-synthesis
Repeated dNTP flow sequence
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nucleotide flow cycles are completed.
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Anneal Primer
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Xcelris Capability

• Phase IV Bioinformatics
• Assembly and Annotation.
• Location of genes/promoters
• Transcribed Regions
• Function of Motifs/other DNA seq
• Screening of data against bacteria/virus and
  vector data bases.
• Detection of sequence variations
• SNP/CNV/Dupli/In-Del

• Phase II Data processing
• Genome Data processing,
• Align Create color space consensus
• Convert color space consensus to base space for
  SOLiD.
• Draft Assembly.
• Final Assembly and Annotation.
• Removal/Identification of the gaps.
• Phase III Genome Finishing
• Gap closure by PCR-assisted contig extension
  (PACE) methodology.
• Contig Gap filling and customized

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ABI SOLiD Technoloy
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Whole Transcriptome Data Analysis
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Deliverables

•  Alignment Report -A summary of the mapping
  results, including score distribution.
•   Filter report (Optional)
•    Score distribution plots
•   MAX file -A MAX file contains all the reads
  that map to genomic reference. Does not include
  mapping to splice junctions.
•   General Feature Format (GFF) file -A GFF file
  containing all the reads that were mapped
  uniquely, including those mapped to splice
  junctions.
•   Counts file-A file in GFF format, containing
  information regarding the number of reads hitting
  the corresponding region (Figure 2).
•    Annotation wig file-Coverage file in wiggle
  format for regions contained in the annotation
  file, one for each genomic region (chromosome)
• -- Predicted Transcribed Region (PTR) GFF files
• -- Optimization plots-These plots are
  used in selecting the optimal parameters for
  detecting Novel Transcribed Regions (NTR).
• -- Annotated Transcribed Regions (ATR) plots
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Thanks...