Gene Regulation-Polymorphisms-Haplotype-LOD

Gene Regulation-Polymorphisms-Haplotype-LOD - 7.03 Genetics...

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Unformatted text preview: 7.03 Genetics – Lectures 24-27 TA: Yun Song 912-484-2511 | [email protected] Main Concepts Genomic Regulatory Circuits G2 ON OFF ON n1 n2 G1 OFF n3 n4 Determining Dependence / Independence of Genes: - Test used: χ 2- H : expression of genes is independent H A : expression of genes is dependent - Expected values in χ 2 test given data: G2 ON OFF ON P(G1 on ) x P(G2 on ) x T P(G1 on ) x P(G2 off ) x T G1 OFF P(G1 off ) x P(G2 on ) x T P(G1 off ) x P(G2 off ) x T P(G1 on) = (n1 + n2)/T P(G1 off) = 1 – P(G1 on) P(G2 on) = (n1 + n3)/T P(G2 off) = 1 – P(G2 on) Why do we multiply probabilities to get the expected numbers in each category? Multiplying probabilities assumes independence of the two probabilities. Independence of the genes is the null hypothesis we are testing, so expected values should be generated based on this assumption.- Observed values in χ 2 test: n1, n2, n3, n4 - χ 2 = ∑ (O-E) 2 obtain uncorrected p-value at df=1 E - Bonferroni correction for multiple hypothesis testing o p corrected ≥ p x (number of tests) o Number of tests = (n-1) + (n-2) + … + 1 (n genes studied) = n x (n/2 -1) + (n/2) - Compare p corrected to critical p value = 0.05. o If p corrected < 0.05: reject H Determining Negative/Positive Dependence - Positive dependence: P(G2 on | G1 on) > (PG2 on | G1 off) - Negative dependence: P(G2 off | G1 on) > P(G2 on | G1 on) - Remember conditional probabilities : P(A|B) = P(A AND B) / P(B) 7.03 Genetics – Lectures 24-27 TA: Yun Song 912-484-2511 | [email protected] Genetic Polymorphism – SNPs and SSRs - Polymorphism : genetic variation among chromosomes (of same type)- What is the difference between a SNP and an SSR ? SNP: single nucleotide polymorphism, one base pair change in sequence SSR: simple sequence repeat, repeats of certain bases, alleles have different length repeats- Where might you find a SNP in the genome? And SSR? SNP: coding (most often silent mutations or missense mutations that do not affect protein function) or non-coding regions SSR: non-coding DNA - Does an SSR affect phenotype? No, in non-coding regions of genome - How do we assay someone genotypically at an SSR? Isolate DNA, PCR-amplify region using primers designed for that region, analyze PCR products using DNA electrophoresis - Why might one say that SNPs/SSRs are “codominant”? SNPs: can sequence and observe any variation present at certain locus SSRs: for heterozygote, both bands show up on gel - What is the main use of poymorphisms in human genetics? Determine linkage of genes to polymorphism markers to map gene locus and assess likelihood of diseases. Haplotyping Genotype : alleles from both homologous chromosomes Haplotype : haplo id geno type , alleles assigned to a particular chromosome Why is the purpose of haplotyping?...
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This note was uploaded on 02/06/2009 for the course 7 7.03 taught by Professor Fink during the Spring '09 term at MIT.

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Gene Regulation-Polymorphisms-Haplotype-LOD - 7.03 Genetics...

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