Human Genomic Variation The Story of SNPs

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

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)

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? 1) the study of evolution 2) DNA fingerprinting 3) markers to map polygenic traits 4) developing genotype-specific medication

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

Two Populations with Different Frequencies of a Disease

Polygenic Traits  For monogenic traits, there are 3 different genotypes  For polygenic traits, there are 3 N 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

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 ,  &  subunits (the former is the actual pump)  A family which carried this disease had a SNP which mapped to 11q23 (the  subunit)  The SNP changed Gly to Arg in the only transmembrane domain.  Caused all 3 subunits to localize to cytoplasm

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

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

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 H 2 O 2  NADPH is required to break down H 2 O 2  RBC’s produce NADPH using G6PD, which is encoded on the X chromosome

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)

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

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

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

Two Classes of Drug Metabolizing Enzymes

Efficacy vs. Toxicity for a Drug  Drug response is usually polygenic  Response determined by just 2 alleles (ie. metabolism & receptor) will have 9 (3 2 ) genotypes  Different #s of people will experience a therapeutic vs. a toxic effect, depending on genotype

mmRR mmRr mmrr MmRR MmRr Mmrr MMRR MMrr MMRr

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!