HASUG MEETING ANNOUNCEMENT AND DIRECTIONS
Our next meeting is Thursday, December 6, 2012 at
Boehringer Ingelheim Pharmaceuticals
AOB Building Auditorium
39 Briar Ridge Road
Danbury, CT 06810 from 9:00am to noon
Refreshments to be served, and time for conversation, beginning at 8:30 AM
NOTE: Boehringer Ingelheim security requires that every attendee must RSVP with a response by Dec. 4th using the Online HASUG Registration Form
Our Topics and Speakers will be:
Using the SAS System as a bioinformatics tool: a macro that calls the standalone Basic Local Alignment Search Tool (BLAST) setup, by Kevin Viel, Pharmanet/i3
Aligning DNA and RNA sequences is an integral task in genomics research. For brief and practical purposes, DNA and RNA can be thought of as character strings comprised of A, C, G, and T (DNA) or U (RNA). Within the constraints of the SAS System, namely 32,767 bytes for a character variable, patterns can be matched or "aligned" using, for example, regex expressions (PRXMatch). This size limit typically suffices even for the state of the art sequencing projects, in which read lengths may be well under 15,000 base-pairs. For larger sequences, a SAS programmer may have to consider calling a perl program or use a tool like Basic Local Alignment Search Tool (BLAST(r)), a popular tool for alignments. An example of an alignment to a sequence larger than the SAS limit might be the need to determine the start position of a primer within a gene, for instance 186 Kb F8. The National Center for
Biotechnology Information (NCBI) of National Institutes of Health (NIH) provides the blast+ software package. The goals of this paper are to describe a SAS macro that calls BLASTn using the X statement and demonstrate an example alignment using the macro.
Kevin Viel obtained his PhD from the Department of Epidemiology in 2007 while working under Laura Almasy of the Texas Biomedical Research Institute (formerly, the Southwest Foundation for Biomedical Research). TBRI has some of the largest pedigrees and family-based studies in the world, which were exceedingly important to map genes and their variants (linkage analyses) due to the technological constraints of obtaining high throughput, fine genotyping necessary for each work, but also important to determine parent of origin effects. His research has always included the genomics of coagulation; with recent focus on the immune response to biologics, particularly Factor VIII, which is infused into Hemophilia A patients. Kevin has been writing code, including using the SAS System, to obtain, process, and create databases for DNA sequence data. These concepts could be one of the first
successes of the era of personalized medicine; potentially, an important contribution since approximately 1 in 10,000 males world-wide are Hemophilia A patients and the average cost of treating these patients in the United States exceeds $100,000 per year.
Data Edit-checks Integration using ODS Tagset, by Vinodh Paida, SAS Consultant
In the Clinical trials data analysis and reporting work, though the Data Management works hard to ensure high quality data as per the Good Clinical Practices, data issues still can exist. The study programmers extract data for the study and checks for potential data issues to ensure the data integrity by executing edit check programs. This paper demonstrates how to effectively integrate all different edit checks into one output file. Also, this article talks about some important and very common edit checks. This paper incorporates the use of ODS tagset feature that is available in SAS® 9.1.3 and later versions.
Vinodh Paida is a seasoned programmer in SAS with over 10 years of experience in Information Technology and over 7 years of consulting experience within the Pharmaceutical Industry in clinical reporting space. He has authored various technical papers and presented at the NESUG and PharmaSUG conferences in last couple of years.
The most recent HASUG Flash is also available for reading on the HASUG.org website, and you can get directions for the upcoming meeting as well.
Look foward to seeing you there. And feel free to invite your colleagues at work.
The HASUG Steering Committee
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