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A Contract Research and Services Organization. Ideas to Life! A Contract Research and Services Organization  Xcelris is a Specialty Contract Research.

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Presentation on theme: "A Contract Research and Services Organization. Ideas to Life! A Contract Research and Services Organization  Xcelris is a Specialty Contract Research."— Presentation transcript:

1 A Contract Research and Services Organization

2 Ideas to Life! 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

3 Ideas to Life! 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.”

4 Ideas to Life! Mission “Xcelris endeavors to be a world class Lifesciences based innovative service organization built towards achieving excellence in;  Research & Technology  Service Delivery  Management Capability”

5 Ideas to Life! Values

6 Ideas to Life! 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  State–of–the–art equipments  Dedicated LIMS  Dedicated lab for Genomics and Bioinformatics.

7 Ideas to Life! 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.

8 Ideas to Life!

9 Whole Genome Sequencing  Next Generation Sequencing Technology Platforms using ABI & Roche  Whole Transcriptome Analysis and SNP Discovery

10 Ideas to Life! 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.

11 Ideas to Life! Whole Transcriptome Analysis

12 Ideas to Life! Xcelris Capability

13 Ideas to Life! Xcelris Capability

14 Ideas to Life! ABI SOLiD Technoloy

15 Ideas to Life! ABI SOLiD Technoloy

16 Ideas to Life! GS FLX technology  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 A&B 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.  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.

17 Ideas to Life! Roche GS FLX (454) Technology

18 Ideas to Life! Roche GS FLX (454) Technology Sequencing Workflow : Loading of Pico Titer Plate Device Well diameter: average of 44 µm > 400,000 reads obtained in parallel A single clonally amplified sstDNA bead is deposited per well Depositing DNA beads into the Pico Titer Plate device Quality filtered bases Amplified sstDNA library beads

19 Ideas to Life! Roche GS FLX (454) Technology

20 Ideas to Life! Roche GS FLX (454) Technology A A T C G G C A T G C T A A A A G T C A C TA Repeated dNTP flow sequence: GGT C AGT C AGTTTT C AGGAT CCC GATT G C TA Anneal Primer Process continues until user- defined number of nucleotide flow cycles are completed. Sequencing-by-synthesis

21 Ideas to Life! 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

22 Ideas to Life! ABI SOLiD Technoloy

23 Ideas to Life! Whole Transcriptome Data Analysis

24 Ideas to Life! Deliverables   A lignment 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 

25 Thanks...

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