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WELCOME
Norma J. Nowak, PhD
Executive Director,
NY State Center of Excellence in
Bioinformatics and Life Sciences (CBLS)
Director,
UB Genomics and Bioinformatics Core
(GBC)
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Grow Your Business: Assistance for Industry Partners
CBLS
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UB Genomics and Bioinformatics Core
Mission
Strive to offer latest advances in next-generation sequencing
and gene expression services to UB, external researchers and
private entities to help facilitate research, discovery, and
product development.
Bioinformatics Team
• Jie (Jessie) Wang, Ph.D
• Jonathan Bard
• Brandon Marzullo
Laboratory Technicians
• Sujith Valiyaparambil
• Natalie Waldron
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How can High-throughout Sequencing work for you?
ChiP-seq
RNA-seq miRNA-seq
DNA-seq (whole
genome and exome)
Kahvejian et.al., Nature biotechnology, 2008
16S Amplicon
GBC…continued
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QIASymphony automated nucleic acid
purification platform
Advanced Analytics Fragment Analyzer
Biotek Synergy plate reader for
picogreen quantitation
Sage Biosciences Blue Pippin Prep
Diagenode SX-8G Automated system
GBC…continued
Technology Platforms
Nucleic Acid Purification, QC, Library preparation
Illumina Hiseq 2500
Illumina Miseq
Affymetrix Genechip 450
Biorad digital droplet PCR (QX100)
Sequencing and Gene Expression
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Illumina Sequencing Workflow Genomic DNA RNA/miRNA
GBC…continued
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Bioinformatics Support
−600 −400 −200 0 200 400 600
0.0
0.1
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0.3
Peak Model
Distance to the middle
Perc
en
tag
e
forward tags
reverse tags
shifted tags
d=147
Data Hosting and Visualization
Assay Specific Analysis Quality Monitoring Initial Data Processing
Illumina base pipeline generating FASTQ files
Sequencing run quality assessment and metrics
Automated analysis pipelines dependent on sample type
Viewable aligned sequence data and analysis via UCSC genome browser
GBC…continued
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)
Leveraging CCR Resources for Data Storage and Analysis
GBC…continued
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The Relevancy of “Classic” Techniques
Differential Gene Expression
• Northern blotting (1977) : 1 Probe – 20 samples
• Dot Blots (1987) : 100s of probes – 1 sample
• RT-PCR (1992) : 100s of probes – 10 -100 samples
• Microarrays (1995 ) : 100,000s of probes – 1 sample
• Next-gen sequencing (2005) : 250 x 106 reads – 1 sample
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Research and Development
Product development
Lab-on-chip testing and development for Rheonix.
Clinical diagnostics
Development of diagnostic gene panels for Multiple Sclerosis and Autism Spectrum Disorder in partnership with Lineagen.
Translational research
Global miRNA sequencing of plasma from animals with Traumatic Brain injury. Project led by Sinapis Pharma.
Microbiome Sequencing
V1-V3 and V3-V4 16S amplification and sequencing of oral microbiota samples
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Copyright Rheonix, Inc. 2016 All Rights Reserved
®
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Copyright Rheonix, Inc. 2016 All Rights Reserved
®
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Copyright Rheonix, Inc. 2016 All Rights Reserved
® Successful Integration of NGS
Library Prep on CARD
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Copyright Rheonix, Inc. 2016 All Rights Reserved
®
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Copyright Rheonix, Inc. 2016 All Rights Reserved
®
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Using Advanced Proteomic Analysis to Identify Optimal Clinical Applications for Novel Cancer Therapies
TREAT CELLS WITH DRUG X ISOLATE TOTAL PROTEIN
IDENTIFY AND QUANTITATE INDIVIDUAL PROTEINS
DEFINE PATHWAYS/PROCESSES AFFECTED BY DRUG X
PATHWAY 1: COMBINE WITH DRUG Z
PATHWAY 2: AVOID DRUG Y
PATHWAY 3: NEW INDICATION?
PATHWAY 4: NEW DOSING REGIMEN?
USE DATA TO REVEAL/DESIGN OPTIMAL THERAPEUTIC
APPLICATIONS
VALIDATE WITH PRE-CLINICAL MODELS
ADAPT TO CLINICAL PRACTICE
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S TAT E U N I V E R S I T Y AT B U F FA L O
UB CCR's Industry Cluster C e n t e r f o r C o m p u t a t i o n a l R e s e a r c h
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HPCNY: NYS High Performance Computing Consortium
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Powered by ESD/NYSTAR
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UB Center for Computational Research
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The UB CCR industry cluster
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Current Industrial Partners (18)
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molecular modeling fluid dynamics genomics data analytics
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Where to go for more information
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3/30/2016
Introduction to Sentient Science
Webware Infrastructure for Rapid Conversion and Implementation of
Predictive Modeling Approaches in a Web-Based Tool
HPC Enabled Meta-model
High Fidelity
High Accuracy
Tests
Fast
Screening
Real Time
Tests
HPC Database
Physics-based Model
• Web-based computational lifing tool • Engineering components: bearing, gears • For general users as well as experts • Rapid Meta-model based tests • High accuracy physics-based tests • Turkey solution for O&M, buy on life
Meta-Model
DigitalCloneTM UX
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Thank You
Q&A