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Tuesday, June 5 • 1:15pm - 2:00pm
Calculating Genetic Diversity for a Registry of More Than 8 Million Bone Marrow Donor Volunteers

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Be The Match, based here in the Twin Cities, is the largest Donor Registry in the US for people willing and able to donate their stem cells to people facing life- threatening illnesses like leukemia and lymphoma.  We have been collecting genetic information on these volunteer donors for thirty years.

Before Next-Generation (DNA) Sequencing, large numbers of marrow donor volunteers were genetically typed using techniques that did not resolve ambiguities for the highly variable region of our genome called HLA (Human Leukocyte Antigen). This is the region of our genome that governs the body’s immune response to disease and affects marrow transplant outcomes.

In order to estimate genetic match probabilities between volunteers and patients under these conditions, an elaborate process of estimating HLA genetic diversity frequencies and imputing potential genetic combinations was necessary for each volunteer and patient.  This was an almost intractable problem which has been easily overcome using cloud computation technology.

We experimented with various tools to set up a Hadoop ecosystem and trained our existing staff in tools such as Spark.  Our presentation focuses on determining the amount of genetic diversity we have in the Registry, and the sometimes-meandering path we took to get there.  Our presentation would be for anyone interested in our experience of developing internal staff in Big Data techniques.  

Speakers
avatar for Pradeep Bashyal

Pradeep Bashyal

Bioinformatics Software Architect, Be The Match (Operating the National Marrow Donor Program)
avatar for Debra Turner

Debra Turner

Data Analyst, Be The Match (Operating the National Marrow Donor Program)
avatar for Eric Williams

Eric Williams

Senior Bioinformatics Scientist, Be The Match (Operating the National Marrow Donor Program)


Tuesday June 5, 2018 1:15pm - 2:00pm
P1838 Normandale Partnership Center, 9700 France Ave So, Bloomington, MN 55431