A Bachelor’s degree in BioMolecular Engineering prepares you for graduate-level studies and industry positions in a wide variety of disciplines. Bioinformatics is one such field, which integrates mathematics, statistics, and principles of computer science in order to solve biological questions. One of the most exciting areas of bioinformatics is clinical genomics, the usage of DNA sequencing to inform patient diagnosis and treatment. The BloodCenter of Wisconsin provides clinical diagnostic tests that utilize Next-Generation Sequencing (NGS) and bioinformatics software to accurately discover and interpret mutations found in patient samples. In this talk, details about this new exciting area of BioMolecular Engineering will be presented along with discussion about the transition from university to the workforce.

1. BIOINFORMATICS: MY
JOURNEY INTO THE
GENOME
Ibrahim Vazirabad
EB 2100
12/7/15

2. STORY
• 1st treatment of patient based on “NGS”.
• Nic Volker
12/12/2015 2
http://www.jsonline.com/news/health/111224104.html

3. BIOINFORMATICS-RELATED
COURSEWORK
•Coursework:
• BE 2200 - Matlab
• CS 2550 - Java
• Bioinformatics I/II
• These classes essential for my
current job.
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4. BLOOD RESEARCH INSTITUTE
• Worked at BRI over summer Soph-Junior
year.
• Opportunity to practice wet-lab research.
• PCR, Western Blotting, “molecular scissors”.
• Project management skills. Presented to lab.
• “The Liquid Nitrogen story”
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5. THE “LIQUID NITROGEN” STORY
• Filling up the containers of liquid N2.
• Special goggles, stored mine in my front
pocket.
•When filling the containers, I had to lean
over…
•Didn’t even know until later, needed my
supervisor to extract my glasses with
tongs.
•Glasses ruined.
•I cannot stress enough the importance of
lab safety.
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6. BIOINFORMATICS @ MSOE
• NCBI GenBank, OMIM, dbSNP, etc.
• Inferring common ancestry via seq. alignment, algorithms
of alignment.
• Tools I use on a daily basis at my job.
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7. WORKING FOR WORTHEY: MEDICAL
COLLEGE
• Senior year, Dr. Worthey came to CBM.
• Was able to talk to her about becoming a
bioinformatician.
•I ended up in her laboratory as an intern.
• Worked on bacterial typing using DNA sequencing
and mutation discovery pipeline.
• MCW laid off workers, didn’t give up.
• Message: Networking pays off, but continue
to strive.
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8. MICROBE DETECTIVES
•Worked in a start-up that performs DNA
testing of water samples for microbes.
• Worked as Bioinformatics Data Analyst.
•Invited to the Rice Business Plan
competition.
• Richest student start-up competition in the
world.
• Introduced to the entrepreneurial realm.
Monetizing ideas.
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9. GOOGLE SUMMER OF CODE
•While working at Microbe Detectives, got
involved with bioinformatics
programmers through Google Summer of
Code.
• Two mentors in San Diego and one in Japan.
• Metabolic Network Modeling
• L.A. at end of summer.
•Programming skills and presentation
confidence.
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10. MARQUETTE
• Went back to school to get my Master’s in
Bioinformatics:
• Wanted more coursework related to statistics and
computer science.
• Statistical Methods
• Software Engineering Methods
• High Performance Computing
• Epigenetics
• Intro to Bioinformatics
• Biochemistry
•My experience: MSOE prepared me for graduate
studies:
• Introduced to difficult concepts.
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11. UW-MILWAUKEE
•At Marquette, I was connected to researcher at UWM.
•I was able to work with WES data from children with
genetic diseases.
• Looking at something impossible to see 10 years
ago and that these analyses could help children in
need.
• Were able to find causative mutations leading to
syndromes.
• I was hooked.
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12. BACK TO THE BLOOD CENTER
• Found out that the BloodCenter of Wisconsin needed a Bioinformatics
Analyst.
• Couldn’t find anyone for a year.
• They were developing genetic tests to diagnose inherited genetic
diseases and looked to develop pipelines for the interpretation and
reporting of test results.
• I sent in my application, not really expecting to hear back.
• After a phone interview and 2 in-person interviews: I was hired.
• I was told many people know biology or know computers. Developing hybrid skills
is crucial.
• Bioinformatics hub being developed in Milwaukee.
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13. WHAT IS BIOINFORMATICS?
-Jung Lee 201112/12/2015 13

14. BIOINFORMATICS AND THE DATA
TORRENT
• 2001: HGP draft.
• 2007: First personal
genome
• 2011: 1000th genome
• Today: ~600k?
• Tomorrow: Millions
• More genomes: more info
on what is dangerous or
benign.
• Mutation data freely
available.
• Not enough Analysts.
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15. CLINICAL GENOMICS
• Key: finding mutations between
the patient sample and the
reference; annotate the
mutation.
• Coding region?
• Non-synonymous?
• Has it been seen before? Linked to
disease?
• Real?
• All needed for actionable results.
G  A
Sample DNA
Human Reference genome
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16. LEVERAGING THE TORRENT
• BloodCenter has gene panels that physicians order in the case of
genetic diseases:
• Kidney disease panel: 15 Blood Cancer panel: 30 Upcoming panel: 115+
• Need mutation data to assess clinical merit of discovered mutations.
• I work to make the existing panels easier to analyze while working
on the new panel’s development.
• Automate procedures. Run 3rd party tools. Utilize publically available databases.
“Get it Done”
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17. PROGRAMS: IGV
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18. PYTHON PROGRAMMING
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19. LINUX
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20. MICROSOFT ACCESS
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21. WHAT DOES IT TAKE?
• The workforce requires:
• Technical
knowledge/documentation.
• A trouble-shooting
mentality/perseverance.
• Strong inter-personal skills.
• Life-long learning.
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22. CONCLUSION
•The torrent of genomic data has wealth of health information which
can change lives.
• Dr. Worthey and Nic
• Children at UWM
• We need more people who can analyze this data.
• Excited for what the future holds.
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