dna testing & ancestry - tufts...

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

DNA Testing & AncestryHigh school applications: An Array of Possibilities

Diane Perito, Ph.D. and Meredith KnightMalden High School

Tufts University

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Workshop Overview

1. Introduction to genetic testing• Activities you can use in your classroom

2. Science of genetic testing• Mitochondrial DNA mutations, Haplogroups

3. Technology behind genetic testing• Microarray technology

4. Bringing the science and technology to high school classrooms• The ARRAY Project

5. Outreach partnerships

6. Next steps

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Game Time!!!

• Game Name: It’s In Your Genes!• Rules: Respond to Questions using colored

cards– Green = Genetic– Red = Not Genetic

• Prizes? Learning more about genetics…….– (P.S. everybody wins……)

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Genetic or Not Genetic?

Relatively poor verbal memory.

It’s genetic!!!!!!!!!!

Whether you prefer chocolate or strawberry ice cream.Not genetic.

Your ability to taste certain bitter flavors

It’s genetic!!!!!!!!!!

Whether you are an early riser.It’s genetic!!!!!!!!!!

Your IQNot genetic. Or is it?????

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

What ELSE can be done with this data?

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Genetic Testing – the future is now……

The DNA Age: Insurance Fears Lead Many to Shun DNA Tests February 24, 2008 Afraid of having genetic information used against them, many Americans do not take advantage of its growing availability.

My Genome, Myself: Seeking Clues in DNANovember 17, 2007 For as little as $1,000 and a saliva sample, customers of an infant industry will be able to learn what is known about how their biological code shapes who they are.

In DNA Era, New Worries About PrejudiceNovember 11, 2007 Research is exploring how DNA explains racial differences, but it could give discredited prejudices a new potency.

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Questions to Ponder

• In your assigned group, discuss the following -Group 1: Both your mother and your grandmother have been diagnosed with breast cancer. Your health insurance company will pay for a genetic test which will determine whether you have the gene for this condition, but your premiums may go up. What do you do?Group 2: Some relatives from your father’s side of the family have a condition which makes them prone to blood clots. Knowledge of this condition is important when considering prescription drugs, but could also effect your health insurance coverage. What do you do?

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Issues of Genetic Testing

• Tests give a probability of whether person may express the condition, do not give “yes or no” answers

• The severity of the phenotype (expressed gene) may differ among different people

• Many genetic tests only do a scan of the genome for the most common variants; they may miss other less common mutations

• Many diseases, even genetic diseases have a blend of nature (genes) and nurture (environment)

• Legal and privacy issues are also important to consider– What happens to archived information about patients?– Should individuals have to disclose information to insurance co?Source: http://www.labtestsonline.org/understanding/features/genetics-

10.html

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

More on Genetic Testing

How does it work? – the Mechanics– Send in a swab from your cheek and (usually) a check ($88-

$1000)– Wait a few weeks– Companies will email/ or mail you your results

• Some companies offer genetic counseling, others do not• Some will link you with other people with similar scenarios• Not all genetic tests look at the entire genome!

What is the science behind this?

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

DNA – structure and composition

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

DNA Replication

•Each backbone forms a new strand

•Genetic information is inherited from both mother and father

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Single Nucleotide Polymorphisms - SNPs

• Single nucleotide is switched out (spelling error)– ACCTTGCGCGCTATA– ACCTTGGGCGCTATA

• Occur throughout the genome• Passed down from generation• Can be used as a genetic marker• Traits can be linked to SNPs

– Our genetics game

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

DNA and Cells

• Where is the DNA inside the cell?

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Mitochondrial DNA (mtDNA)

• Mitochondria – “energy source” of the cell• A remnant of an ancient parasitic bacteria (due to structure) • Has own DNA (loop structure) – does not recombine when

mitochondria replicates• Lacks a proofreading mechanism• 16,569 base pairs long• Human genome = 3 billion bp

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

HV Section of mtDNA

• Focus on hypervariable sections of DNA – HVS 1 and 2• HVS 1 = 359 base pairs HVS 2 = 315 base pairs• Haplogroups = Groups of people who share a common SNP• Hap Map project – fewest number of SNPs needed to characterize

individuals

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Steps to creating a haplogroup

• 1. Identify SNPs from multiple people• 2. Create haplotypes• 3. Tag SNPs are identified which can be used to put people into

haplogroups

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

The Hap Map – Patterns of Human Migration

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Microarray Technology

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Microarray – SEM image

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Different DNA probes are first attached to beads

DNA Base Pairing

A

T

G

Chttp://upload.wikimedia.org/wikipedia/en/f/f0/DNA_Overview.png

A

T

G

CA

T

G

C A

T

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Probe A Probe B Probe C

Microwells etched on distal fiber face

CCD chip2) Probes are combined into a library

1) Different DNA probes arefirst attached to beads

3) Probe bead library is distributed randomlyinto wells on fiber array surface

Optical Fiber-based Microsphere Array

Fiber bundle

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

3) Specific Hybridization of Complement to Probe C

DNA Hybridization

4) Increased Signal for Probe C Sensors

1) Encoding image

2) Background Image

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Microarrays in High School???

• Time: typical high school laboratory period between 1-2 hours

• Level of Difficulty: should take into consideration science background

• Cost: School laboratories are often subject to strict budget restrictions

• Sensitivity: The assay needs to be sensitive enough to circumvent PCR due to time limits

• Technologically Feasible: Successful hybridization needs to be clearly visible with naked eye or naked eye and inexpensive equipment

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Advancing Real Research Among Young ScientistsARRAYS Project

• Tufts Undergraduates developing mtDNA microarray + protocols and instruments

• Allow high schools to interface with DNA testing• Working on cost effective solutions• Work in progress!

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

High School Outreach Portion

HHMI Outreach Initiative

Tufts/ Malden Partnership

ResearchExperience forHS teachersHS student

Campus visitsfor HS

students

Grads/ Postdocvisit H.S.

Co-developmentof curriculum

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Biology Curriculum Development

Malden High School Students:

- Completed a series of experiments to extract and isolate their own mitochondrial DNA

- Were introduced to new laboratory techniques (use of micropipettes, PCR, gel electrophoresis)

- Able to apply their prior knowledge of genetics

- Able to analyze experiments and identify sources of error

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Using Alu Insertion Polymorphism to Study Human Populations

PV92 Alu Insertion Polymorphism detects the presence or absence of a "jumping gene" on chromosome 16. This simple genetic systemhas only three alleles and nine genotypes. Despite this simplicity, allele frequencies vary greatly in different world populations.

Goals of experiment…• Examine human Alu dimorphism at PV92 locus• Sample human cells with saline mouthwash• Extract DNA with Chelex resin (binds contaminating metal ions)• Polymerase Chain Reaction (PCR) to amplify desired region• Gel electrophoresis to separate alleles

(+) allele is 300 nucleotides longer than the (-) non-insertion allele

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Benefits and Drawbacks

What Worked Well What to ConsiderStudent exposure to real-life techniques they otherwise would not encounter until college

Outreach to local colleges and universities for resources and knowledge support

Students engaged and interested in the process because it connected directly to them

Scheduling requirements to enable all students to participate – allotted time for lab period is too short

Collaboration with fellow teachers outside of own discipline

Having sufficient common planning time to optimize use of resources (ideas, people and equipment)

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Tufts University Field Trip – March 13 2008

• Lab group meeting• Optics Activity• Lab Tours• Lunch w/ Tufts students• Campus Tour• Science Course

“Talking to graduate and undergraduate students during lunch allowed me to learn more about college life. – Howard”

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

Student Comments

Just listening to the mentors and professors at a casual level allowed me to become comfortable with asking questions and wanting to learn more from them. - Dario

The best part was going to the labs where the graduate student perform their research.– Katie

HHMIHoward Hughes Medical Institute

Tufts UniversityDepartment of Chemistry

For more information: meredith.knight@tufts.eduOr dperito@malden.mec.edu

Questions?