BI202 SNP Genotyping
From Bioinformatics.Org Wiki
This course helps to demystify Affymetrix analysis so that any researcher can take the basic steps to go from a chip image to genotypes, for each SNP, and to the copy number or linkage associated with the SNPs in given samples. Various tools will be covered, such as GCOS, GTYPE, BRLMM, CNAT, Excel, MATLAB, and free tools like dChip. It is geared towards researchers who conduct microarray-based SNP genotyping experiments to study genome-wide polymorphisms and then use the information for genotyping and linkage analysis. Most scientists are not able to analyze resulting microarray data themselves and are not able to get desired results using traditional tools like Microsoft Word and Excel, or the advanced software provided by commercial vendors. The free solutions come either with a steep learning curve or as black-box interfaces that provide limited functionality, with little or no technical support. In the midst of all this is the fundamental lack of understanding among scientists on how the technology works and what the fundamental parts of the analysis are.
No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful.
- Sessions 1 & 2: Introduction to GCOS – the environment, creating and saving experiments, importing and exporting data, normalization settings, from DAT->CEL->CHP files and their significance, importing and exporting data, SNP chip layout and algorithms for generating genotypes
- Sessions 3 & 4: GTYPE, BRLMM for generating genotypes, sample mismatch report, gender calls, pedigree check, creating virtual sets, and copy number analysis
- Sessions 5 & 6: dChip software: importing SNP data and annotation information into dChip, LOH analysis, copy number analysis, linkage disequilibrium analysis, allele sharing analysis, and exporting to Excel
- Sessions 7 & 8: MATLAB: importing SNP data in MATLAB, manipulating and filtering SNP genotypes, automating tasks using API to Affymetrix SDK, building custom user interfaces for advanced applications, and exporting to Excel
If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)
- Step 1
- If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
- Step 2
- Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).
Please also check the course tuition rates and discounts.
Registration deadline: When full
Tuition & discounts
- Live instruction held on-line
- For-profit & government: $1,000 USD
- Non-profit & self-pay: $600 USD
- Live instruction held on-site
- For-profit & government: $1,200 USD
- Non-profit & self-pay: $800 USD
- On-demand instruction held on-line
- For-profit & government: $600 USD
- Non-profit & self-pay: $400 USD
Additional discounts are available as follows:
- Professional members: 20% discount
- Limited scholarships may also be available for those residing in low-income economies (please inquire).
The necessary software, lecture notes and exercises will be provided.
Live instruction held on-line
On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, depending on the topics covered.
For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as AVI video files each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and Java. A microphone and webcam are not required but may be used.
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.
Please contact us for questions or additional information.