journey into the genome: bioinformatics
TRANSCRIPT
BIOINFORMATICS: MY JOURNEY INTO THE
GENOME
Ibrahim Vazirabad
EB 2100
12/7/15
STORY
• 1st treatment of patient based on “NGS”.• Nic Volker
12/12/2015 2
http://www.jsonline.com/news/health/111224104.html
BIOINFORMATICS-RELATED COURSEWORK
•Coursework:• BE 2200 - Matlab
• CS 2550 - Java
• Bioinformatics I/II
• These classes essential for my current job.
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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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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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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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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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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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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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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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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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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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WHAT IS BIOINFORMATICS?
-Jung Lee 201112/12/2015 13
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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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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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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PROGRAMS: IGV
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PYTHON PROGRAMMING
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LINUX
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MICROSOFT ACCESS
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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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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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