welcome [] · lab-on-chip testing and development for rheonix. clinical diagnostics development of...

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

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

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

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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

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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

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwj8sq_x0dXLAhVLGB4KHQzvBG0QjRwIBw&url=http://www.biosonda.cl/producto/qiasymphony-1&psig=AFQjCNEviz_obHwaWoF0A5yYOnlikZC21w&ust=1458782087480884

Illumina Sequencing Workflow Genomic DNA RNA/miRNA

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http://bitesizebio.com/?attachment_id=9393

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwit67mamNXLAhXHSSYKHdo0AcIQjRwIBw&url=http://rnaseq.uoregon.edu/&bvm=bv.117218890,d.eWE&psig=AFQjCNENptzpWnNd7RgSIDJM-CAnuz5aZA&ust=1458766852481793

Bioinformatics Support

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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

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Leveraging CCR Resources for Data Storage and Analysis

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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

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

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwjpia2XztfLAhUMFT4KHfykBpMQjRwIBw&url=http://www.ihub.co.ke/blogs/17838&psig=AFQjCNFyYQov2o2S2Rxh7gLtndfszs68Jg&ust=1458850064884952

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Copyright Rheonix, Inc. 2016 All Rights Reserved

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® Successful Integration of NGS

Library Prep on CARD


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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

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

HPCNY: NYS High Performance Computing Consortium

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Powered by ESD/NYSTAR

UB Center for Computational Research

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The UB CCR industry cluster

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– Industry Cluster Node Rack

Current Industrial Partners (18)

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molecular modeling fluid dynamics genomics data analytics

Where to go for more information

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http://www.hpc-ny.org/



http://www.hpc2.org/

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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

Thank You

Q&A

welcome [] · lab-on-chip testing and development for rheonix. clinical diagnostics development of...

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