Mitochondrial and STR DNA Analysis by Mass Spectrometry Workshop Outline Day 1

Time
Topic
Instructor(s)
8:30–8:45 Welcome & Introduction
  • Purpose of the workshop
  • Instructors
  • Facilities
  • Agenda Review
NIJ Staff
NFSTC Staff
Hofstadler, Lowery, Hall, Planz, McCurdy, Budowle
8:45–9:45 Introduction to Biological Mass Spectrometry
  • History
  • Components
  • Applications

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Hofstadler
9:45–10:15 High Throughput Analysis of Amplified Nucleic Acids with Mass Spectrometry: The Ibis Platform
  • Applications
  • Ibis T5000
  • Ibis T6000

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Hofstadler
10:15–10:30 Break  
10:30–11:00 Introduction to Mitochondrial DNA Analysis

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McCurdy
11:00–11:30 Overview of the Ibis mtDNA Tiling Assay
  • Ibis mtDNA assay format
  • Base composition analysis of mtDNA samples
    - Data processing and analysis
    - Blinded samples
  • Information content relative to sequencing
  • Heteroplasmy detection
    - Length
    - SNP
  • Sensitivity
  • Reproducibility

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Hall
11:30–12:15 Mitochondrial DNA Mixture Detection, Analysis, and Interpretation
  • Definition of an mtDNA mixture Heteroplasmy vs. multiple donors
  • Current approaches to handling mtDNA mixtures
    - Advantages / Limitations
  • mtDNA mixtures using the Ibis mtDNA assay
    - Technological / theoretical basis
    - Interpretation guidelines
    - Advantages / limitations

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McCurdy
12:15–1:15 Lunch  
1:15–1:45 Overview of the Ibis STR Assay
  • Assay format
  • Comparison to traditional STR analysisThird party comparison to CE
  • Polymorphic STR alleles

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Hall
1:45–2:30 Enhanced Resolution and Statistical Power Through SNP Distribution Within the Short Tandem Repeats
  • Nature and structure of STR loci
  • SNP distributions with the STR repeat structure
  • Population and statistical implications of expanded allele definitions
  • Assumptions and implications for database searching

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Hall
2:30–2:45 Break  
2:45–3:15 Analysis Software for the mtDNA Tiling Assay Overview
  • General interface
  • Software features
  • Data processing
  • Data analysis

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Hall
3:15–3:45 Laboratory Tour Lowery, Hofstadler
3:45–4:00 Ibis Assay System Workflow Overview
  • Workflow
  • Throughput

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Lowery
4:00–4:30 Laboratory Exercise Overview
  • Objectives
  • Samples
  • PCR Setup
  • Ibis T5000 setup

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Lowery

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