Transcript The Genomics Education Partnership, 2011 (pptx)

The Genomics Education Partnership, 2011
Charles Hauser1, Wilson Leung3, Chris Shaffer3, David
Lopatto2, Sarah Elgin3
and faculty and students of the GEP
1St.
Edward’s University, Austin TX, 2Grinnell College, Grinnell, IA, 3Washington
University, St. Louis
Genomics Education Partnership (GEP)
2011-12 additional schools
Participating TX Institutions
Texas Wesleyan University
Chitra Chandrasekaran
Austin College
Kelynne Reed
St. Edward’s University
Charles Hauser
Prairie View A&M
Gloria Regisford
University of the Incarnate Word
Christy MacKinnon, Russell Raymond
University of St. Thomas
Donald Frohlich
Supporting undergraduate research in genomics
Broad consensus:
1.
We need to bring more genomics into our curriculum, and increase
student familiarity with computer-based tools
2.
Students need to know how new knowledge is created in their field
3.
AAMC/HHMI Future Physicians Competencies:
“Apply quantitative knowledge and reasoning—including integration
of data, modeling, computation, and analysis—and informatics tools
to diagnostic and therapeutic clinical decision making.”
The Genomics Education Partnership uses a lab
course centered on genomics research during
the academic year to address these aims.
Individual projects, common tools, pooled
results
The Drosophila melanogaster fourth chromosome exhibits an
amalgam of heterochromatic and euchromatic properties
Heterochromatic properties:
- Antibody staining of HP1, H3K9me2/3
- Lack of recombination
- High repeat density
Euchromatic properties:
- Banded structure in polytene chromosomes
- Gene density similar to other euchromatic domains
(~80 genes in the distal 1.2Mb)
- Transcriptionally active
C
C
Phase
HP
1
James
et al,1989
GEP research goal:
Use comparative genomics to learn more
about heterochromatic domains, analyzing the
dot chromosomes and a control euchromatic
region of Drosophila genomes
Status
Reference
Completed
Annotation
Sequence
Improvement
FlyBase: http://flybase.org
St. Edward’s
Research Explorations in Genomics
Course Structure:
•
•
•
•
Meet 6 hrs/week (MW 5-8pm)
Max of 10 students, 1 TA
Finishing Projects (~8 weeks)
Annotation Projects (~7weeks)
Finishing
• Select overlapping set of fosmids (scale: 7-10)
• Each student finishes a fosmid
• Class reassembles completed overlapping set at end
Annotation
• Select overlapping set of contigs (scale: 7-10)
• Each student annotates a contig
• Class reassembles completed overlapping set at end
Finishing a fosmid (40 kb):
Typical challenges with 6X coverage
• Design needed experiments (choice of primers,
template for additional data); view result;
redesign, repeat experiment as needed
• Advantage: concrete goal, clear endpoint
• Final verification- compare in silico restriction digests to
actual restriction digest
• Report process to group, defend conclusions
• Satisfaction of solving challenging problems, making an
original contribution
• Each project finished twice independently by GEP partner
schools (75% congruence)
Initial project
1st round
2nd round
Finished fosmid
D. grimshawi DGB15A19
Annotation: Create gene models using sequence similarity and
computational predictions
Finished
Sequence
Sequence
Homology
Gene
Predictions
Benefits of the annotation process…
Student
Gene
Predictors
• Become familiar with tools available for finding genes, manage data
• Identify genes, create accurate models (start, exons, stop etc.)
• Analyze genome organization (synteny), repeats
• Use power of comparative genomics; reference D. melanogaster
• Address questions of evolution
• Experience presenting data, supporting conclusions based on
available evidence
• Making an original contribution
• Each project done twice independently
•~75% congruence (D. erecta), ~60% (D. mojavensis)
Adding second generation sequencing data to
the genome browsers
RNA-Seq
modENCODE
Constraints, solutions…. to achieve
institutionalization
• Need large time blocks
• Need appropriate lab: computers, internet access.
• Generating letter grades: graded training exercises;
lab reports that argue results from data.
• Is it cost-effective, in dollars and personnel?
– Yes, similar or significantly lower costs compared with
individual mentored lab experience.
– Student work is of high quality!
• Student ownership is essential!
• Problem - things change! New problems every year.
GEP assessment
5
Understanding the
research process
Tackling real
problems
Lab techniques
GEP
Summer Research
Courses without research
Mean scores
4
3
2
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
Learning Benefits
For most gains, a GEP course is as effective as a summer research experience.
Comments from GEP students
• The class was very intellectually challenging
for me. It taught me to think in a way that I
had never thought before.
• The thing that sparked me the most was the
fact that I was able to perform the BLAST
searches on my own and was able to explain
to my instructor what I had done.
More comments from GEP students
• I learned to fight through the frustration and
eventually figure out the problem.
• It would have been helpful if the instructor
had attempted to be more helpful.
•
I know if I could survive this class then I
could survive just about anything.
Lessons Learned - Faculty
• Students need ownership
• Generating letter grades works
• Challenging - things change!
• Quality of the experimental work is very good.
Distributed projects, collaborative effort
Use systems where
- unfinished sequence data available on web
- BACs/fosmids available from resource center
Web-based system for training materials,
- video of WU Genome Sequencing Center
- data in/out
Workshops for faculty and TAs
Publication goals:
- deposit sequencing results in Genbank
- deposit annotation results with Flybase
- scientific literature (Genetics, 2010; Genome Biology,2006)
- science education literature (CBE Life Sci Educ, 2010;
Science,2008)
The format is flexible
• Can be initiated as part of an existing course, as part
of a lab in molecular genetics, or as a new course
• Technology requirements:
– for annotation, a computer lab with internet access;
– for finishing, Macs or unix based system.
• Washington University staff provide tech support as
needed
• Needed background:
– an understanding of genetics
– ability to type, use a Mac or PC, use the internet.
Resources & Support
• Faculty, TA workshops
• Curriculum resources
• Forum, wiki
– Finishing guidance
– Annotation questions
• Tools
– UCSC browser
– Gene model checker
Website
Genomics Education Partnership
http://gep.wustl.edu
WU Science Outreach
http://so.wustl.edu
References:
Leung, W. et al. (2010). Evolution of a Distinct Genomic Domain in Drosophila: Comparative
Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis.
Genetics, Vol. 185, 1519-1534.
Lopatto, D. et al (2008) “Genomics Education Partnership” Science Oct 31, 2008.
Lopatto, D. (2004) “Survey of Undergraduate Research Experiences (SURE): First Findings”
Cell Biology Education, vol. 3, pages 270-277, Winter 2004 (available on line at
http://www.cellbioed.org)
• We are looking for interested faculty to join our Genomics
Education Partnership ([email protected]).
• Next workshop August 4-6, 2011 and January 8-13,2012 (TA)
Acknowledgements
Sarah C.R. Elgin
Chris Shaffer, Wilson Leung,
GEP faculty
Students!
Putative Polymorphisms
Aligned Reads Window
Putative SNP
Trace Window
Annotation
Contig 11
Contig 12
Contig 13
Contig 14
Contig 16
Contig 17
Contig 19
Contig 21
Contig 22
Increased Independence
SURE follow up: I feel I have become better able to think
independently and formulate my own ideas.
GEP: Taking this course has helped me learn to think independently.
45
Percent of sample
40
35
GEP
SURE
30
25
20
15
10
5
0
None/Strongly
Large/Agree
Figure
8. ComparisonSmall/Disagree
of SURE follow up Moderate/Neutral
(N = 609) results with the
current GEP results. Very
Disagree
Large/Strongly
Agree
Increased Independence
Shaffer et. al., 2010
More Active Learner
SURE follow up: I feel that I have become a more active learner.
GEP: Taking this course has helped me to become a more active
learner.
50
45
Percent of sample
40
35
GEP
SURE
30
25
20
15
10
5
0
Figure 10.
None /Strongly
Disa gre e
Sm a ll/Disa gre e
Mode ra te /Ne utra l
La rge /Agre e
Ve ry
La rge /Strongly
Agre e
More Active Learner
Shaffer et. al., 2010
Student evaluation of future plans
Percent
0
20
40
60
80
Plan for post-BA education in life sciences no change
Plan for post-BA education in life sciences confirmed
Plan for post-BA education will have genomics emphasis
Dropped plan due to course
Dropped plan due to other reasons
Did not have plan but now will develop a plan
Still have no plan
GEP 2010
GEP 2009
Dave Lopatto, 2011
D. grimshawi DGB15A19
Students must evaluate the available evidence, create the best
gene model and defend their conclusions