Advances in NGS Library Preparation and Target Enrichment
Belynda Hicks
Wednesday, December 7, 2016
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Chapters
Introduction
Outline
CGR: Support from Planning to Publication
CGR Focus Areas Today…
Primary Sequencing Instrumentation @ CGR
Development/Optimization of Production-scale Exome Sequencing Pipeline
Current CGR Exome Sequencing Pipeline
New expansion to support somatic analyses
Utilization of FFPE derived biomolecules
Challenges of FFPE Sequencing pt.1
Challenges of FFPE Sequencing pt.2
Opportunities!
Preparations for FFPE Utilization
FFPE Extraction Methods Work
DNA Purity Variability pt.1
DNA Purity Variability pt.1
Amplifiable DNA Variability
Impact of collection protocols/age, FFPE repair methods
Evaluation of damage-repair techniques
Exome coverage results
Concordance with GiaB
Specimen Type, Study, Age
Specimen Age: DNA Library yield, size, FFPE Repair +/-
Specimen Age: RNASeq Library Yield
Specimen Age: RNASeq Quality Metrics
Integration and optimization of HyperPlus enzymatic shearing
Rationale for Change
Library Yield, Exonic Coverage (gDNA)
Primary Analysis/Sequencing Metrics
Optimization of KAPA HyperPlus for FFPE Samples
Research Rigor and Reproducibility
What is truth? pt.1
What is truth? pt.2
Sources of Variability
Genome in a Bottle
Utilization of GiaB
Other Reference Materials
Summary
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