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The DNA Bead String Exercise. Anita L DeStefano, PhD Department of Biostatistics BU School of Public Health Co-Director Biostatistics Program Associate Director Genome Science Institute. Innovation Inspiration.

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the dna bead string exercise

The DNA Bead String Exercise

Anita L DeStefano, PhD

Department of Biostatistics

BU School of Public Health

Co-Director Biostatistics Program

Associate Director Genome Science Institute

innovation inspiration
Innovation Inspiration
  • National Heart Lung and Blood Institute (NHLBI) funded Summer Institute in Training in Biostatistics (SIBS)
  • 6 week intensive summer course for undergraduates
  • Addressing dearth of Biostatisticians
innovation inspiration3
Innovation Inspiration
  • Modules in
    • Biostatistics
    • Epidemiology
    • Clinical Trials
    • Statistical Genetics
innovation inspiration4
Innovation Inspiration

Lisa Sullivan, Chair

Department of Biostatistics

Associate Dean of Education, SPH

Metcalf Award Winner

  • Modules in
    • Biostatistics
    • Epidemiology
    • Clinical Trials
    • Statistical Genetics

Wayne LaMorte,

Assistant Dean of Education, SPH

Presenting later today

Me

innovation inspiration5
Innovation Inspiration
  • Need to keep up with excellent faculty
    • Hands on activities
    • Counting M&M colors to assess statistical distribution
  • I teach the last week
    • Even highly motivated students start to wane a bit
innovation inspiration6
Innovation Inspiration
  • Statistical Genetics
    • Application of statistical tests to genetic data
    • Often to identify variation in the human genome that confers risk for disease
    • Requires understanding of both the statistical and genetic concepts
  • SIBS students have varying background in biology and genetics
how do i
How do I…
  • Provide a hands on way to “see” DNA?
  • Show students how DNA is analyzed without taking them into a lab?
  • Bring students of varying background to the same level
  • Cover both genetic and statistical concepts?
  • Have students interact with each other?
  • Have students interact with me?
dna bead exercise
DNA Bead Exercise
  • In the laboratory can examine a small segment of DNA and characterize
  • Recreated a small DNA segment with beadsincorporating key genetic concepts
    • Non-coding region
    • Promoter region
    • Coding region
    • Restriction enzyme cut site
    • Tetranucleotide repeat
    • Single Nucleotide Polymorphism (SNP: missense)
  • Carefully constructed to incorporate statistical concepts
    • Disease association
    • Linkage disequilibrium
slide9
promoter

region

codons

ECOR1

cut site

A

T

G

C

String color indicates disease status

ECOR1

cut site

GATA

repeat

dna bead exercise implementation
DNA Bead Exercise: Implementation
  • Randomly hand out bead strings to student
    • Half blue strings (unaffected with disease)
    • Half yellow strings (affected with disease)
  • Students must pair based on same string color
  • Characterize their “individual”
    • Affected/Unaffected with disease
    • Length of DNA segment (based on GATA repeats)
    • Presence or Absence of ECOR1 cut site
    • Amino Acid sequence
  • Aggregate data across the class
slide12
promoter

region

codons

ECOR1

cut site

A

T

G

C

String color indicates disease status

ECOR1

cut site

GATA

repeat

dna bead exercise implementation13
DNA Bead Exercise: Implementation

Table 1. Allele Frequencies based on 12 individuals(24 chromosomes)

  • Discuss correct statistical test
    • No association with disease status
dna bead exercise implementation14
DNA Bead Exercise: Implementation
  • Create similar tables for other genetic characteristics
  • Association between presence/absence of ECOR1 cut site and disease status
  • Stronger association between amino acid change and disease status
  • Correlation between the ECOR1 cut site and amino acid change
    • Linkage disequilibrium
dna bead exercise implementation15
DNA Bead Exercise: Implementation
  • Exercise used in
    • Summer Institute for Training in Biostatistics (undergraduates)
    • SPH BS858 Statistical Genetics I (graduate students)
    • Upward Bound (high school students)
  • Well received by students
  • Helps achieve learning objectives
  • Could be adapted for your course in genetics, medical genetics, population genetics, bioinformatics
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