BIOINFORMATICS: MY JOURNEY INTO THE

GENOME

Ibrahim Vazirabad

EB 2100

12/7/15

STORY

• 1st treatment of patient based on “NGS”.• Nic Volker

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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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