Human Genomic Variation

1. Human Genomic Variation The Story of SNPs

2. Single Nucleotide Polymorphisms (SNPs) • In addition to variation in microsatellites (VNTRs), genetic variation takes the form of SNPs (point mutations) • The SNP Map Working Group has identified about 1.5 million SNPs • There is about 1 SNP / 2 kb of genome • Each ethnic group has its own collection • SNPs have been classified as major or minor, depending on frequency

3. Is a SNP really a SNP? • False positives can result from 1) inclusion of paralogs and 2) errors in sequencing • Warren Gish at Wash U. developed a procedure to minimize false SNPs • Initially, 80,469 SNP candidates were found in 1.3 Mb of finished sequence • Paralogs were identified by their high frequency of variation (1 base in 50, instead of 1 in 1000) • This left 69,756 positions, only 59 of which were given a high probability of not resulting from sequencing error (20 were later confirmed)

4. SNP Prevalence & Importance • 98% of all genes are within 5 kb of a SNP • 93% of all genes contain at least 1 SNP • 59% of all genes have 5 or more SNPs • 39% of all genes have 10 or more SNPs • How is SNP data useful? • the study of evolution • DNA fingerprinting • markers to map polygenic traits • developing genotype-specific medication

5. SNPs and Disease • Linkage- how close 2 loci are on a chromosome • Linkage disequilibrium- when 2 alleles are inherited together more often than expected • Haplotype- the set of alleles on a chromosome Each person has 2 haplotypes in a given region If we track SNPs that are in linkage disequilibrium and correlate this with a disease phenotype, we have identified SNP markers that form a particular haplotype associated with this disease

6. Two Populations with Different Frequencies of a Disease

7. Polygenic Traits • For monogenic traits, there are 3 different genotypes • For polygenic traits, there are 3N different genotypes • Traits that are polygenic but can be measured in some quantitative way can be mapped to QTL (Quantitative Trait Loci) • Traits such as schizophrenia, high blood pressure, diabetes, cancer and Alzheimer’s may someday be mapped to QTL

9. One Polygenic Trait: Hypomagnesemia • People with this disease are unable to maintain sufficient levels of Mg in their blood • One contributing factor is the Na/K pump • ATPase of this protein is composed of a, b & g subunits (the former is the actual pump) • A family which carried this disease had a SNP which mapped to 11q23 (the g subunit) • The SNP changed Gly to Arg in the only transmembrane domain. • Caused all 3 subunits to localize to cytoplasm

10. Mitochondrial SNPs • >50 disease-causing SNPs map to mitochondria • Phenotypes mostly affect cardiac & skeletal muscle • 13 genes required for ETC are encoded by mitochondria, as are 22 tRNA and 2 rRNA • 2000 patients suspected of having diseases caused by mitochondrial SNPs were screened • 108 had known SNPs • More SNPs may be yet to be discovered or some diseases may not be due to SNPs

11. Incorrect mRNA Splicing • BRCA1 has been linked to breast cancer • SNPs which do not alter the aa sequence of a protein are considered “silent” • Adrian Krainer (CSH) identified SNPs which lead to alternate splicing • 5’, 3’ ends of exons as well as internal sequences contribute to splicing • ESEs are exonic splicing enhancers and ESSs are exonic splicing silencers • SNPs in these regions lead to breast cancer

12. Nondisease SNPs • “What is food to some men may be fierce poison to others” - Lucretius Caro • About 10% of people experience RBC lysis upon consuming fava beans • These people lack G6P dehydrogenase • Fava beans act to increase a RBC’s sensitivity to oxidants such as H2O2 • NADPH is required to break down H2O2 • RBC’s produce NADPH using G6PD, which is encoded on the X chromosome

13. G6PD SNPs • 20% of Mediterranean population has 563C » T (no activity) • 20% of African population has 202G » A (reduces activity by 10%) • 20% of African males have 376A » G (produces normal activity)

14. Response to Medications • Many drugs must be metabolized to intermediates before they become active • Optimum dosage for drugs is determined for the “average” person • People can typically be divided into poor, typical, and ultra-rapid metabolizers • Cytochrome P450 is one enzyme used for drug metabolism • This enzyme is encoded for by two genes, 2C19 & 2D6

15. SNPs in Cytochrome P450 • 2D6 has 12 SNPs that have been identified • G » A in exon 4 is the most common, it leads to inactivity • >40 different drugs require 2D6 to become active, including: antiarrhythmics, opioids, antidepressants, and antipsychotics • 2C19 is required to metabolize mephenytoin, an epilepsy drug • While only 2% of Caucasians have a 681G » A SNP, 23% of Asians have this SNP

16. Pharmacogenomics • The study of a gene which affects drug metabolism, transport, or reception is called pharmacogenetics • The study of all genes in this category is another of the “omics” sciences • Traditional drug development was aimed at delivering medications which were safe and effective for everyone • Now, genome-specific medicine may be developed which is more effective in individuals with specific SNP combinations

17. Two Classes of Drug Metabolizing Enzymes

18. Efficacy vs. Toxicity for a Drug • Drug response is usually polygenic • Response determined by just 2 alleles (ie. metabolism & receptor) will have 9 (32) genotypes • Different #s of people will experience a therapeutic vs. a toxic effect, depending on genotype

19. mmRR mmRr mmrr MmRR MmRr Mmrr MMRR MMRr MMrr

20. You Don’t Need a SNP to Inactivate Cytochrome P450! • Cytochrome P450 3A is used to convert drugs to a form that will be excreted • Grapefruit juice contains an unknown component which destroys this enzyme • 1 glass can block activity for about 24 hours • While normal breakfast amounts slightly elevated levels of a cholesterol-lowing drug, concentrated juice 3 times a day increased concentrations by 12 fold!