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Office hours Wednesday 3-4pm 304A Stanley Hall Review session 5pm Thursday, Dec. 11 GPB100 Association vs. linkage Unrelated individuals Common but weak effects; need 1000’s of samples to detect. If no common cause, can fail. Related individuals Strong, easy to detect, but rare in population; may not be reflective of common disease. Also, hard to collect family data. Association vs. linkage small number of generations; individuals share big chunks of genome; can get coinheritance between distant markers many recombinations have happened since common ancestor; shared region is small; no coinheritance between distant markers So you need very high density of markers to get signal in an association study, but you get very high spatial resolution. Association and admixture Cases Controls = = At any one of these loci, Caucasian-like allele will be enriched in control samples. Genotyping by array Fig. 11.8 Expression microarrays Fig. 1.13 Labeled DNA sample vs. labeled mRNA (cDNA) sample Labeled DNA sample vs. labeled mRNA (cDNA) sample (reverse transcription in the test tube) Coding sequence array Fig. 1.13 Coding sequence array say, with chemotherapeutic Fig. 1.13 Coding sequence array Fig. 1.13 Coding sequence array Fig. 1.13 Coding sequence array expression expression expressed not expressed Fig. 1.13 Why measure expression of all genes at once? “Regulon” expression response (e.g. cortisol) QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. http://www.mcb.mcgill.ca/~hallett/GEP/Lecture2/Image17.gif “Regulon” expression response QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. http://www2.kenyon.edu/Depts/BioEllipse/courses/biol114/Chap06/week08a_files/regulon.gif Finding regulatory response on a large scale Oligo expression array (soybean component) transcripts QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Expression profiles Time since drug administered QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Expression profiles Time since drug administered QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Time since drug administered Expression profiles Time since drug administered QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Each color is a regulon, or “cluster,” of coregulated genes Time since drug administered Expression effects of cancer QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Cancer classification QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Cancer classification QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Histological classification is finicky: can we do better? Diagnosis via transcriptional profile QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Diagnosis via transcriptional profile patient samples transcripts QuickTime™ and a TIFF (Uncompressed) decompressor Diagnosis via transcriptional profile QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Diagnosis via transcriptional profile QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Natural variation among “normals” Two human chromosomes differ at ~1/1000 bases. 96% of these differences are not in protein-coding sequence. Why? Natural variation among “normals” Two human chromosomes differ at ~1/1000 bases. 96% of these differences are not in protein-coding sequence. Most protein coding mutations are deleterious; appear but are culled by natural selection. Natural variation among “normals” Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Natural variation among “normals” Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Genetic variation in mRNA levels G kinase TF TF TF ORF Genetic variation in mRNA levels G Likely to be a complex trait. kinase TF TF TF ORF Many mRNA differences at once Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse ~10% mRNA levels significantly different Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse 111 F2 progeny … Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse 111 F2 progeny … Microarray each F2 liver Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse 111 F2 progeny … Microarray each F2 liver Genotype each F2 Linkage mapping of mRNA levels “Black 6” mouse x “DBA” mouse 111 F2 progeny … Microarray each F2 liver Genotype each F2 Looking for linkage (coinheritance) between marker and mRNA level. Marker is linked to polymorphism in expression regulation cascade G kinase TF TF TF ORF Marker is linked to polymorphism in expression regulation cascade G kinase TF TF G G TF ORF Marker is linked to polymorphism in expression regulation cascade G kinase TF TF G G TF ORF Marker is linked to polymorphism in expression regulation cascade G kinase TF TF G TF ORF One allele = high mRNA, the other = low mRNA G Marker is linked to polymorphism in expression regulation cascade G kinase TF TF TF ORF Marker is linked to polymorphism in expression regulation cascade G kinase TF TF TF ORF Marker is linked to polymorphism in expression regulation cascade G kinase TF TF TF ORF mRNA level shows linkage to locus of polymorphic regulator(s). Marker is linked to polymorphism in expression regulation cascade G kinase TF TF TF ORF mRNA level shows linkage to locus of polymorphic regulator(s). Locally acting polymorphisms QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Locally acting polymorphisms QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Locally acting polymorphisms QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Polymorphism responsible for mRNA difference is at the locus of the gene itself Locally acting polymorphisms G kinase TF TF TF ORF Locally acting polymorphisms G kinase TF TF TF ORF Locally acting polymorphisms QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Polymorphism responsible for mRNA difference is at the locus of the gene itself Locally acting polymorphisms ~25% of varying mRNAs are caused by locally acting polymorphism QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Polymorphism responsible for mRNA difference is at the locus of the gene itself Nonlocal polymorphisms QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Nonlocal polymorphisms One polymorphism in a key regulator can affect a regulon: 100’s of related mRNAs. Clinical applications “Black 6” mouse x “DBA” mouse 111 F2 progeny … Microarray each F2 liver Genotype each F2 Measure fat pad each F2 Quic kT i me™ and a T IFF (Unc ompres s ed) dec ompres s or are needed t o s ee thi s pi c ture. Quic kT i me™ and a T IFF (Unc ompres s ed) dec ompres s or are needed t o s ee thi s pi c ture. Quic kT i me™ and a T IFF (Unc ompres s ed) dec ompres s or are needed t o s ee thi s pi c ture. Clinical applications QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Clinical applications Colored curves = fat mass at different body QuickTime™ and a TIFF (Uncompressed) decompressor locations are needed to see this picture. Clinical applications Finding polymorphism responsible for difference in macroscopic phenotype is hard Clinical applications Finding polymorphism responsible for difference in macroscopic phenotype is hard If mRNAs change too, can learn mechanism from known function of encoded proteins Clinical applications Clinical applications Clinical applications QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Clinical applications Counts allele 1/allele 2, cases = 1.5 Counts allele 1/allele 2, controls QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Clinical applications Clinical applications Marker predicts quantitative expression level = association Can we map expression traits first, disease afterward? Linkage of human transcripts QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Linkage of human transcripts QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Association of human transcripts QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Association of human transcripts linkage (families) assoc (unrelated) QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Association in multiple populations European-Americans in Utah QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Han Chinese and Japanese Association in multiple populations QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.