SNP-Related Toolboxes and Database Searching
Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that represent critical molecular markers for dissecting the biological mechanisms underlying complex diseases, as well as for pharmacogenomic studies. SNPs in protein-coding DNA regions can potentially lead to changes of the protein structure and in turn, changes of the biological functions of the encoded proteins, whereas SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific fashion. With the rapid advancement of high-throughput SNP genotyping platforms such as TaqMan or SNPlex, SNP-related toolboxes and databases have become increasing important for researchers. This tutorial will illustrate the usages of several SNP-related toolboxes - (1) SNPHunter, (2) SNPper, and (3) SNPicker through practical examples, and will cover several major SNP searching databases: (1) NCBI dbSNP, (2) SNP500Cancer, (3) SeattleSNPs, (4) HGVbase, (5) GeneSNPs, and (6) IIPGA
Training session: August 10, 2005. At Kresge LL-6, training slides, tutorial notes.
Analysis of large scale 'omic data
John Quackenbush, Ph.D. Department of Biostatistics and Computational Biology invites you to a course in Expression Data Analysis.
Come and participate in this informative training session. The goals of this workshop will be to provide an overview of techniques for analysis of these large scale datasets along with hands on application to real data sets. The workshop will be driven by simple biological questions and approaches that can help arrive at meaningful answers. A CD with the software and presentations will be provided to all participants.
Registration is required and seats are limited.
Date: June 13, 2005
Time: 9:00am to 5:00pm
Location: Harvard School of Public Health, Kresge Bldg., LL6, 677 Huntington Avenue
Event email: johnq@jimmy.harvard.edu
Haplotype Determination
Haplotype-level analysis provides significant new insights than genotype-level analysis. Current high-throughput genotyping and sequencing methods do not provide information on linkage phase in diploid organisms. In order to resolve haplotype phase, traditional methods rely on laborious molecular techniques such as allele-specific PCR or typing in close family relatives, but such methods can be prohibitively expensive and error-prone. Thus, in silico haplotype determination is an attractive alternative. This training session covers basic concepts and applications of our widely used haplotype determination software programs - Clark's algorithm, HAPLOTYPER, PHASE, and PL-EM. Attendants will get hands-on experience in using these software packages to address haplotype phasing problems encountered in their research.
Training session: April 6, 2005. at Kresge LL-6, training slides, tutorial notes