Download - Snps and microarray
SNPs and Gene expression
Sucheta Tripathy
schedule
• 6 classes• 2 for SNP and 4 for gene expression• 2 per group and will present in each class.• Subjects and groups will be chosen randomly.• Todays class is introductory, we will discuss
fundamental aspects.
Terminologies
• Forward genetics – understanding a genotype by understanding the phenotype.
• Reverse Genetics -
How often SNPs occur?
• One in 300 bases – 10 M.
Not all single-nucleotide changes are SNPs, though. To be classified as a SNP,
two or more versions of a sequence must each be present in at least one percent of the general
population.
Each combination is a haplotype!!!!Not necessarily all 8 haplotypes exist!!!!
dbSNP and Hapmap project
• dbSNP: 2.5 million variations• http://www.ncbi.nlm.nih.gov/SNP/
• Haplotypes are blocks – hapmap focuses on those blocks
• http://hapmap.ncbi.nlm.nih.gov/thehapmap.html.en – 2002– Nigeria, Japan, China, USA
Gene Expression
• Yeast 1997.
Cy3: 570
Cy5: 670
Two Channel and single Channel microarrayTwo channel – two conditionsSpike-in control probes are thereUsed for Normalization-Agilent dual mode; Eppendorf with dualchip
Single channel: One condition at a time.Abundance of a transcript will not be known only relative abundance.Affymetrix: Genechip; Illumina BeadChip
Microarray and Bioinformatics
• Experimental design.• Standardization.• Statistical data analysis.• Data storage and visualization.
Contd…
• Experimental design:– Biological replicates.– Technical replicate.– Randomization
• Standardization:– Difficult – cant be easily replicated.– Minimum Information About a Microarray
Experiment" (MIAME); 2001, nature genetics• http://fged.org/projects/miame/
Contd..
• Data Analysis:– Image Analysis – gridding of the spots– Data processing:
• Background correction• Visualization (MA Plot)
– M is log transformation and A is mean average scale
Most gene should not change -> Y is 0
Contd..
• Data Processing:– Normalization (Remove non-biological variation)• Simplest way: Assume all arrays have same median
gene expression• Subtract median from each array• Quantile normalization:
– Order values in each array– Take average across probes– Substitute probe intensity with average– Change the original order
Contd..
• Class discovery– Unsupervised methods.– Supervised methods
• Draw hypothesis
Papers
Group1: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3830805/ -> ABO allele – international journal of evolutionary biology
Group5:http
://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990764/ -> Semantic modelling associated with SNPs from hapmap data – Genomics and informatics
Papers
• Group 2:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992869
/ Group 3:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219629
/ Group 4:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022823
/
Next class…
• We will discuss this paper.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805859
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