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1:00PM – 2:00PM, January 26, 2015 – Clinical Methodologies of NGS – LIVE @Silicon Valley 2015 Personalized Medicine World Conference, Mountain View, CA

Real Time Conference Coverage with Social Media

@Computer History Museum by Dr. Aviva Lev-Ari, PhD, RN

1:00PM – 1:15PM Mike Snyder, Stanford (Chair)

Analyzing Complex Diseases Using Integrative Omics Technologies

LIVE FROM THE PODIUM

Complex Disease

• Highest prevalence: Diabetes and Autism as examples
• Personal “Omics” Profiling – Molecualr measurement: Microbiome, metabolomics via Urine
• Principles
• Genome Sequence(Illumina, Complete Genomics): Predict Diabetes
• Life Time change if the Genome sequencing find risk for diabetes
• Metabolic Disorder can be familial
• Molecules and Biochemical Pathways that change during acquisition of Diabetes: Insulin, Biosynthetic pathway
• Microbiome is important for health: implicated in IBD: Crohn’s and Enterical Colitis
• in Nasal microbes: Streptococcus pneumonie
• Stool microbiome: during fever Respiratory infection: Gut microbiome changes
• 70 Prediabetics: Personal Omics profile – data sensors:
• other data types sensors: Insulin Resistance –>>> obesity — Diabetes
• AUTISM: protein in patients –
• Cetificate in Genomics

 

1:15PM – 1:30PM Patrick Roche, HTG Molecular -mRNA and MiRNA

NGS-based Molecular Profiling from a Single FFPE Section

LIVE from the PODIUM

Molecular Profiling is slow: the alternative is

HTGEdge CHemistry

• Nuclease protection – HTG EdgeSeq – No DNA or RNA: extraction of RNS for adoptors like Illumina Sequencer
• HTG and NGS – Edge Chemistry is optimized for NGS workflow
• miRNA Asssay – Whole Transcriptome (HTG EdgeSeq WTA
• Reproducability Tissue microarrays (TNAs)
• Lung Fusions Assay: Measure expression of HERs microarrays
• Fusion Measurement Techniques
• Cellline carrying – Lung Fusion – HTG EdgeSeq: ALK, ROS1, RET, NTRK1 Fusion
• Analytics Software: Rearrange for 5’/3′ length
• HERs insertion
• Comprehensive Molecular Profiling: The Product
• Profile expression of 2500 cancer related genes
• Oncology Biomarker Panel:
• COmprehensive molecular profiling

 

1:30PM – 1:45PM Michael Ball, GenoLogics

The Impact of Informatics on Clinical NGS Services

LIVE from the PODIUM

• Informatics market is $Billion
• 23andMe
• Informatics
• Operations in multiple locations
• From Start Up to Genome Factory
• ClarityLIMS
• 8 weeks kickoff to production
• Future is in the CLOUD
• Informatics: prevention of errors

 

1:45PM – 2:00PM Jason Merker, Stanford University School of Medicine

Using Genome Sequencing in the Clinical Setting

LIVE from the PODIUM

• WOrlflow: Stanford CLinical Genomics Service
• MD order a test
• Genetics Counsellor counsalt
• question posed to patient and treating team
• insurance authorisation
• biobanking
• results of Illumina sequencer
• Data analysis (MedGAP)
• variants analysis
• curation meeting
• genomics Review Group
• Genomics Review Board – Bioethic/legal, additional genetics expertise
• FINAL report generation: coverage of metrics, meeting with genetic COunselor
• Multidisciplinary team – more precise clinical genetic care
• GS is a test for AUNEXPALINED GENETIC DISEASES
• potential methodology improvements
• CNV and other SV detection

 

2:00PM – 2:15PM John Ryals, Metabolon, Inc. CLIA

Getting More from NGS: Metabolomics as a First-line Phenotyping Tool

LIVE FROM THE PODIUM

Where knowing COmes to Life?

• Discovery HD4 platform launched in 4/2014
• 200 molecules are derived from bacterial metabolism
• Metabolon’s proprietaty technologydevelopment
• Human Metabolome Individually
• Metabolon GWAS Study- Nature 477, 54-60 (2011)
• 145 Associations
• Conclusiono: Genetic Origins of Individual Variations in Metabolosm

200 patients – blood and urine tests

70 unaffected cases

Correct Disease assessment

• Patient 11315: thymidine – Maple Syrup Urine Disease mutation on an ENZYME
• Metabolic signatures in Patients: Gzene Penetrations
• case 3905 – Fructose intollerence vs sorbitol Case 3958: Urea Case 3976: Liver – shows tylenol toxicite

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