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Single Nucleotide Polymorphisms. Arthur M. Lesk Bologna Winter School 2011. What are SNPs and why are they important?. SNP = Single nucleotide polymorphism, an isolated change in a single nucleotide SNPs are one type of mutation Some have obvious functional consequences - PowerPoint PPT Presentation

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Single Nucleotide Polymorphisms

Single Nucleotide PolymorphismsArthur M. LeskBologna Winter School 20111What are SNPs and why are they important?SNP = Single nucleotide polymorphism, an isolated change in a single nucleotideSNPs are one type of mutation Some have obvious functional consequencesSickle-cell haemoglobin: gaggtg (6 GlnVal)First molecular disease sickle-cell anaemiaSome are silentSome are in non-coding regionsaffect splice sites?affect regulatory sites?some have no known phenotypic effect

2What is a SNP?The genomes of individuals in a population contain a particular base at some position most of the time.That is, there is a normal sequenceA SNP is a deviation from the normal sequence. Many people require that a variation occur in at least 1% of the population, to be considered a SNP

But: what population? What if two distinct populations have a consistent polymorphism?

3SNPs in human genomesSNPs are about 90% of all inter-human variationOccur on the average once in every 300 bases 2/3 of SNPs are CT changes (perhaps because C can easily deaminate)

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cytosineuracilSNP density varies across human genomeSome high-density patchesSome desertsSNPs in coding regions ~1/3 as many as in non-coding regionsSNP density correlated with recombination rate (which causes which??)AT microsatellites: long (AT)n repeat tracts tend to appear in regions of low SNP density

5Figure 14 SNP density in each 100-kbp interval as determined with Celera-PFP SNPs.

J C Venter et al. Science 2001;291:1304-1351Published by AAASSNP density in each 100-kbp interval as determined with Celera-PFP SNPs. The color codes are as follows: black, Celera-PFP SNP density; blue, coalescent model; and red, Poisson distribution. The figure shows that the distribution of SNPs along the genome is nonrandom and is not entirely accounted for by a coalescent model of regional history.What is normal?Obviously we all differ genomicallySwedes and Chinese have obviously different phenotypesMost Swedes and Chinese are healthy indvidualsTherefore genetic differences do not necessarily cause diseasePointless to check for differences from a single reference sequenceOf course, many genetic differences not just SNPs7Variation in human and other speciesAny two humans ~99.5% identical in sequenceChimpanzees, gorillas: twice as variable, despite much smaller population sizeImplies prehistoric bottleneck in human population, recent common originMost SNPs (> 5%) shared among human populations from around the worldMost populations (e.g. British) contain 85-90% of all known variation8Variation in human and other speciesSome variation is population-specificIn some cases, there is local selective pressureFor example, adult lactose tolerance, malaria resistanceAfrican populations have greatest genetic diversitySupports Out of Africa theory of human origin and migration9Identification of geographical origin, phenotypeA criminal leaves a blood sample at a crime sceneHow much can we tell about him or her?Not perfectly, but:Ethnic groupEye and hair colour (hair colour easier to change)Family name?10Types of SNPsTransitions:purine purinepyrimidine pyrimidine (cytosineuracil) Transversions:purine pyrimidineTransitions are more common than transversions

11Prevalence of SNPs in human genomesapproximately 1 in 300 bp (0.001%)compare difference between human / chimpanzee genomes:4% different (not all SNPs!)

12Life cycle of a SNPGeneration of a mutationInitial survival, against sampling lossIncrease in frequency survival until become homozygous in some individuals; chance of loss reduced (helped by bottlenecks, founder effects population size dependent)Fixation13Initial survival of a SNPSuppose a person is heterozygous for a novel, selectively-neutral mutation. Suppose the person has 2 children that survive to reproductive age. The probability of loss of the mutation is 25%. If each descendant has 2 children that survive to reproductive age, probability of loss in 200 years = 94%14Where do SNPs occur in the human genome?Distributed throughout the genome50% in non-coding regions NOT the same as non-functional!!!25% missense mutations (amino acid substitution)25% silent (amino acid unchanged)silent = no change in encoded amino-acid sequenceNOT the same as no phenotypic effect!!!would be better to call them synonomous SNPs rather than silent SNPs

15SNPs in non-human genomesOf course other species have SNPsHere we will focus on human SNPs because of relevance to human diseaseHowever, SNPs in pathogens are sometimes associated with antibiotic resistance, and therefore related to human diseaseSNPs in some plants give clues to domestication16Organised efforts to collect SNPsThe HapMap is a catalogue of common human genetic variants HapMap Project = international collaboration among Japan, the United Kingdom, Canada, China, Nigeria, and the United StatesNOT EuropeCarry out measurements, provide databaseOther projects collect SNPs in other species17HapMap projectInternational consortium: International HapMap Projecthttp://hapmap.ncbi.nlm.nih.gov/Catalogue of human genetic variants :What sites?How distributed frequency in different populationsRaw material for linking genomics with disease 18Origin of samplesTotal of 270 people. The Yoruba people of Ibadan, NigeriaJapan (Tokyo)China (Beijing)U.S. residents with Northern and Western European ancestry19What is a haplotype?Often, a set of SNPs appear nearby on the same chromosomeIn absence of recombination, they will be inherited in blocksPattern of SNPs in a block is called a haplotypeA block may contain many SNPs, but only a few are needed to identify a haplotypeThese signature SNPs within a haplotype block are called `tag SNPs20

http://www.riken.go.jp/engn/r-world/info/release/news/2003/nov/image/frol_06.gif

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http://img.medscape.com/fullsize/migrated/553/400/ncpcard553400.fig1.gif22Guide to SNP databasesSNPlinks: http://www.snpforid.org/snpdata.htmlNCBI dbSNP http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snpThe SNP Consortium http://snp.cshl.org/HapMap http://www.hapmap.org/Applied Biosystems http://myscience.appliedbiosystems.com/cdsEntry Assays-on-Demand /Form/assay_search_basic.jspEnsembl http://www.ensembl.org/Homo_sapiens/HGVBase http://hgvbase.cgb.ki.se/SeattleSNPs https://gvs.gs.washington.edu/GVS/23dbSNP database at NCBInon-redundant datasetnomenclature: rs numberrs = reference SNP.24General human mutationsHuman Gene Mutation Database http://www.hgmd.cf.ac.ukover 100000 mutations, in 3700 genes6.2% of total ~23000 genes about 10000 new mutations found per yearOMIM (Online Mendelian Inheritance in Man)database of mutations associated with human diseaseOMIA (Online Mendelian Inheritance in Animal)

Databases with important related informationOnline Mendelian Inheritance in Man (OMIM) [NCBI]Comprehensive compendium of human genes and associated phenotypesNot limited to SNPsSNPs3D http://www.snps3d.org/SNPs3D assigns molecular functional effects to non-synonymous SNPs based on structure and sequence analysis. SNPper http://snpper.chip.org/Retrieve SNPs by position or gene association

26Quality of sequence information is importantSNPs appear in human genome at approximately 1 in 300 basesObviously error rate in resequencing must be substantially lower than this if SNP data are to be meaningfulMeasure of DNA sequencing quality: PHRED27PHRED measure of sequence qualityPhred scores accepted to characterize the quality of DNA sequencesOriginally Phred was a program, that determined accurate quality scores indicating error probabilities. Accepted as general standardPhred quality score Q. Let P = probability of base errorQ = -10 log10 P28Phred quality score QProbability of incorrect base callBase call accuracy 101 in 1090% 201 in 10099% 301 in 100099.9% 401 in 1000099.99% 501 in 10000099.999%29Phred quality score QProbability of incorrect base callBase call accuracy 101 in 1090% 201 in 10099% 301 in 100099.9% 401 in 1000099.99% 501 in 10000099.999%A method that gave an averaged phred score Q = 30 would give approximately as many errors as there are SNPs!30What can SNPs tell us?Causes of disease -- dysfunctional proteinCorrelation with disease prognosis, success of particular treatmentUseful genetic markers, to locate some gene of phenotypic interest; for instance, a gene correlated with a diseaseCharacterise individualsCharacterise populations (SNP distribution)Applications in anthropology -- tracing of migrations, human evolution

31Use of SNPs as genetic markersBefore 1980, genetic maps were constructed by measuring recombination frequencies between genes giving measurable phenotypic traitsThis goes back at least to Sturtevandt and Morgan, if not to MendelAt that time, phenotypes were the only visible aspect of the genome32Use of SNPs as genetic markersIn 1980, Botstein, Davis, Skolnick & White proposed using polymorphic DNA markers for genetic mapping, even if they had no known phenotypic effectExample: (then) restriction sites SNPs restriction fragment length polymorphisms (RFLPs)Did linkage mapping with restriction sitesNow we can use SNPs33Traits depending on multiple lociUse of SNPs to identify traits, including but not limited to diseases, that depend on multiple lociSingle genes for diseases showing simple Mendelian inheritance (for instance, cystic fibrosis) can be isolatedDiseases that depend on interaction with multiple loci can be studied with enough SNP linkage information34SNPs tell us about human historyDevelopment of ability to digest lactose past infancy correlated with domestication of cattle, increased (non-fermented) dairy products in human dietSource of calcium and caloriesMany Asian populations retain adult lactose intolerance Where do they get calcium? The soybean is the cow of Asia.35Ability to digest lactose in adulthoodDigestion of lactose depends on enzyme lactase-phlorizin hydrolase, which catalyzes hydrolysis of lactose glucose + galactose36

Ability to digest lactose in adulthoodIn many people, the ability to digest lactose is a juvenile characteristicExpression declines after age 2 varies among individualsConsistent with lifestyle involving breast feeding until this age, followed by weaning followed by diet not including (non-fermented) milk and other dairy productsTo form yoghurt, bacteria cleave lactose37Evolution of adult lactase expressionDomestication of cattle, with concomitant rise of milk in the diet, led to selective pressure for lactose toleranceMutation arose among cattle-raising people:the Funnel Beaker culturenorth-central Europe ~5,000-6,000 years agoMost common mutations in Europeans: SNPsC/T-13910G/A-22018Not surprisingly, in control regions for lactase gene

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Prevalance of lactose-tolerance SNP39Danes and Swedes90%Spanish and French50%Chinese1%

http://gseorlando.files.wordpress.com/2010/09/j.jpgGroup Study ExchangeMultiple development of lactose toleranceDevelopment of lactose tolerance apparently appeared four times, independentlyEurope: C/T-13910 and G/A-22018Pastoral areas of Africa three independent mutations:G/C-14010 East AfricaT/G-13915 North SudanC/G-13907 North Kenya4041

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672153/bin/ukmss-4417-f0002.jpg42

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672153/bin/ukmss-4417-f0001.jpgSNPs in anthropologyUseful in tracing relationships between populations, migration routesInitially used mitochondrial DNA (16569 bp)Maternal inheritance only(Y chromosome gives paternal inheritance only)Important argument for out of Africa theory of human origins and dispersalCan choose non-selected regions, in contrast to previous work on blood groups, MHC haplotypes43Migration routes into Asia and the Pacific based on SNPs44

http://i49.tinypic.com/2d0j2py.jpgDNA sequences and language groupsProposal by L. L. Cavalli-SforzaShowed consistency between trees based on genetic markers and trees based on linguistic groupingsControversial!In some cases, genomics has confirmed hypotheses of population affinity based on language similarity / dissimilarityBasques are outliers in both genes and language45Recommended readingTomasz KamusellaThe Politics of Language and Nationalism in Modern Central Europe Palgrave Macmillan, 2008

46What happens after invasions?Hungary invaded by Magyars in 896 AD. Country converted to speaking Uralic languageRome fell to vandals in 476 AD but did NOT impose their language. (Perhaps recognising superiority of Italian culture which their descendants dont)England invaded by Anglo-Saxons in about 5th century. Anglo-Saxon pushed Celtic languages to far reaches of British Isles + BrittanyNorman invasion of 1066 did NOT entirely replace Anglo-Saxon by French.47Possible effects of SNPsIn protein-coding sequences silentmissensecoding stop codonstop codon codingSNPs can dysfunctional proteinsIn splice sites15% of disease-causing mutations in human genome are point mutations in vicinity of mRNA splice junctionsIn regulatory sequences48What are possible effects of SNPs in coding sequences?Change in amino acidExample: sickle-cell anaemia

sense codon stop codon protein truncatedstop codon sense codon protein extended49

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SNPs in coding regions can do more than change one amino acidChange of codon for an amino acid to STOP codon produces truncated proteinExample: common mutation causing phenylketonuriaChange of STOP codon to codon for an amino acid produces extended proteinExample: haemoglobin Constant Spring -chain variant termination codon TAA is mutated to CAA (glutamine)produces extension of haemoglobin -chain from 142 to 172 amino acidscauses mild anaemia51Possible consequences of silent (synonymous) SNPsNothing detectableChange in proportions of variable spliced proteinsChange in stability of mRNAEffect on protein folding (translational pausing)52SNPs can affect variable splicing

Almost all multiexonic genes show variable splicingChange in isoform can have severe effectsSusceptibility to West Nile VirusSNP in 2',5'-oligoadenylate synthetase-like gene common in susceptible individualsoligoadenylate synthetase implicated in viral resistanceSNP present in exonic splice enhancerIncreases level of truncated protein enhanced susceptibility to virus

53SNPs can affect mRNA stabilityExpression levels of proteins depend on mRNA half-life (among other things)ATP-binding-cassette (ABC) transporters are membrane proteinsfunction in translocation of compounds out of cellsDisease associates with SNP in this family54Dubin-Johnson syndromeautosomal recessive disorderincrease in conjugated bilirubindefect in hepatocyte secretion of conjugated bilirubin into bilemany patients asymptomatichormonal birth control or pregnancy can jaundiceSome cases caused by synonymous SNP in gene for ABCC2 increased mRNA stability increased expression levels

55Synonymous SNPs can affect protein folding and even native structureSynonymous SNPs do not affect amino acid sequenceTherefore should not alter native structureHowever, affects kinetics of foldingmRNA secondary structure affect translational pausing

56Cotranslational folding is affected by translational pausingCan affect not only kinetics but tertiary structureExample: SNPs in Multidrug Resistance1 MDR1Encodes P-glycoprotein, an ABC transporterFunction to pump molecules out, including chemotheraputic agents used in cancerHaplotype C1236T, G2677T (nonsynonymous), C3435T Affects interactions of protein with: cyclosporine A -- fungal cyclic peptide, immunosuppressant, used post-transplantverapamil -- calcium channel blocker, used in treatment of high blood pressure

Ref: Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007). A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science. 315, 525-528.

5758

Verapamil

Cyclosporin AReferencesKimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007). A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science. 315, 525-528.Erratum in: * Science. 2007 Nov 30;318(5855):1382-3. Comment in: Science. 2007 Jan 26;315(5811):466-7.Bioessays. 2007 Jun;29(6):515-9.* Epilepsia. 2007 Dec;48(12):2369-70.

59Prediction of functional effects of non-synonymous SNPsPolyPhen: (EMBL, Heidelberg)http://coot.embl.de/PolyPhen/SNPs3D (Baltimore) http://www.snps3d.org/Pmut (Barcelona) http://mmb2.pcb.ub.es:8080/PMut/SIFT (University of Washington) http://blocks.fhcrc.org/sift/SIFT.htmlMAPP (Stanford)http://mendel.stanford.edu/SidowLab/downloads/MAPP/index.html

60Sorting Intolerant From TolerantDatabase and server at University of WashingtonSIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acidsLimited to non-synonymous SNPs (or more generally, amino acid substitutions)61SNPs in MedicineGenomic sequence analysis can provide a lot of information about health risks of any individualSo far, part of the problem is that sequences usually just give bad newsIndications of optimal therapy useful: the U.S. health care industry faces huge costs in treatment of side effects of medication62SNPs and diseaseSome SNPs (and of course other mutations) are consistent with a healthy life, and typical life-span, provided the individual carries on a reasonable lifestyle.Some SNPs directly and unavoidably cause diseaseOthers cause disease only in combination with unusual lifestyle or specific eventsExample: fever in children with Z-mutation of 1-antitrypsin protein somewhat unstable, denatures and aggregatesEssential to keep infants free of high feverIn many cases we cant tell extent of genetic basis of disease or how it interacts with environmental effects63Copy-number variations may mask disease genesGenes in which nonsense SNPs detected belong to gene families of higher than average size. Genetic robustnessEvery individual is heterozygous for some deleterious mutations that, if homozygous, would be lethal.Interaction of SNPs with environment/experience1-antitrypsin is a natural elastase inhibitor in the lungelastase in lung protects against bacteriainhibitor prevents elastase from acting on human tissues, notably elastin in the lungZ-mutation of 1-antitrypsin: glu342lysCauses enhanced risk of emphysemaZ-mutation + smoking = GUARANTEE of early death from emphysemaGenetics loads the gun; environment pulls the trigger (J. Stern)Discussion of following diseasesSickle-cell anaemiaPhenylketonuriaAlzheimers diseaseCancer66SNP causing disease: Sickle-cell anaemia6ValGln creates hydrophobic (sticky) patch on surface of chains of haemoglobinCommon SNP: gag gtgcauses aggregation of deoxyhaemoglobin

67PhenylketonuriaInborn deficiency in phenylalanine hydroxylaseAutosomal recessive (12q24.1)1/10000 sufferers1/50 carriersSubject of neonatal screening in many countries

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Mutations causing PKUPhenylalanine hydroxylase is a tetramerKnown mutations include:Over 200 affecting catalysisAbout 50 affecting regulationAbout 10 affecting tetramerization(Some involve cofactor -- tetrahydrobiopterin -- processing) Most common mutation in Caucasians:ga in intron 12causes truncation (sense codon to stop codon)fails to tetramerizeMcGill database: http://www.pahdb.mcgill.ca/69Testing for PKUPhenylalanine, and degradation products such as phenylpyruvate build up in blood and urine(Phenylpyruvate is a ketone, hence the name of the disease.)

Blood sample from neonate, mass spec to detect phe, tyr levelsCan also do genomic sequencing detection of carriers, counselling of potential parents

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Symptoms if untreateddevelopmental defects:mental retardationmicrocephalyseizures71TreatmentLow phenylalanine dietnot entirely satisfactory (unpalatable?)tricky to manage PKU women in pregnancyGene therapy (works in mice )Enzyme replacement therapy72

http://newenglandconsortium.org/wp-content/uploads/2009/12/PKU-Food-Diagram-copy.jpgPKU in pregnancyRemember that PKU is an autosomal recessive traitA woman with PKU must be homozygous for defective phenylalanine hydroxylase (not necessarily same mutation) If such a woman becomes pregnant, it is likely that the foetus is only a carrier (unless father also a carrier)Tricky to control phe levels in mother to give foetus adequate nutrition but not toxic levels73Enzyme replacement therapy for PKUadminister functional phenylalanine hydroxylase itself But: requires cofactor, complex regulatory controls (2) phenylalanine ammonia-lyaseconverts phenylalanine to trans-cinnamic acidtrans-cinnamic acid:has low toxicity and does not cause developmental defectsconverted by liver to benzoic acid, detoxified and excreted in urinestable

phenylalanine ammonia-lyase found in many plants; and fungi, including yeastsAnabaena variabilis enzyme in phase II clinical trials74Comparison of reactions catalysed by phenylalanine hydroxylase (PAH) and phenylalanine ammonia-lyase (PAL)75

http://www.nature.com/mt/journal/v10/n2/images/mt20041219f1.jpgGenomics of phenylalanine hydroxylaseRhesus macaque and chimpanzee phenylalanine hydroxylases differ from normal human PAHOn difference: Human Y356 = H in macaque and chimpThe mutant is in the list of mutations in the PKU database: http://www.pahdb.mcgill.ca/But chimps and rhesus macaques do not suffer from PKUWhy not?

76Alzheimers diseaseLoss of cognitive function, characterised by: Loss of train of thoughtProgressive memore problemsMiss important appointmentsEarly-onset Appears at age < 65Late-onset Alzheimers most common typeAffects people over the age 65~50% of people over age 85 suffer from it. Familial Alzheimers < 1% of cases, appears at age 40-60Alzheimers diseaseEarly-onset -- age < 65associated with mutations in presenilin 1, presenilin 2 and amyloid precursor protein Late-onset Alzheimers age > 65most common type: ~50% of people over age of 85 suffer from it. Propensity associated with ApoE (apolipoprotein E SNPs)Familial Alzheimers < 1% of cases, appears at age 40-60ApoE SNPs and risk of late-onset Alzheimer diseaseApoE = apolipoprotein EGene on chromosome 19; therefore we have two allelesBasic function: remove cholesterol from bloodFour common alleles, differ by SNPs:ApoE1 [minor variant], ApoE2, ApoE3 [~55%], ApoE4E3 most prevalent( normal)At least one E4 allele increased risk of AlzheimersAt least one E2 allele decreased risk of Alzheimers

ApoE allelesApoE = 317-residue proteinFour common ApoE alleles, differ by SNPs:ApoE1 = rs429358(C) + rs7412(T) [minor variant]ApoE2 = rs429358(T) + rs7412(T) ApoE3 = rs429358(T) + rs7412(C) [~55%]ApoE4 = rs429358(C) + rs7412(C)

Allele112168E1ArgCysE2CysCysE3CysArgE4ArgArgSNPs and CancerSNPs are relevant to cancer research and treatment in several ways:Mutations detectable in the genome indicate propensity for development of cancersMutations in BRCA1 and BRCA2, as indicators for likelihood of breast/ovarian cancer development probably best knownSequence analysis can predict progression and outcomeSequence analysis can help choose optimal treatmentProgression of tumour often involves mutations and divergence of cell lines81Formation of cancer associated with loss of genome integrityCancer results from accumulated mutations that break down the controls on cell growthThree classes of genes can promote cancer:Genes that regulate cell proliferationGenes required for repair of DNA damageGenes that control apoptosis82RetinoblastomaRare childhood tumour of eyeSporadic / familial (30-40%)Characteristics of familial retinoblastoma:Early onset Multiple tumoursAffect both eyesAutosomal dominant inheritance pattern83Two-hit hypothesisNon-familial cases require inactivation of both copies of retinoblastoma geneRequire separate and independent mutationsFamilial cases inherit one defective copy, one functional copyThat is, first hit is inherited, all that is needed is second hit 8485

SNPs and cancerA number of genes are known as tumour suppressor genesWell-known examples: BRCA1, BRCA2Not all common mutations are SNPsSome SNPs in tumour suppressor genes cause predisposition to development of cancerOther SNPs correlated with Progression of diseaseEfficacy of certain drugs86Tumour suppressor genesEncode proteins that inhibit tumor formationNormal function: inhibit cell growthMutations take foot off cell-growth brake

87Mutations in BRCA1 and BRCA2In general population: ~ 12% of women will develop breast cancerWomen with harmful mutation in BRCA1 or BRCA2: ~ 60% will develop breast cancerIn general population: ~1.4% of women will develop ovarian cancerWomen with harmful mutation in BRCA1 or BRCA2: ~ 15-40% will develop breast cancer88Some common BRCA1 mutationsVaries with population: showing strong founder effectMany not SNPsNot all of these are necessarily harmful mutations

89Population Common mutationAshkenazi Jewish185delAG, 188del11, 5382insCItalian5083del19African-Americans943ins10, M1775RSpanishR71GFrench3600del11, G1710X French CanadiansC4446TOther tumour suppressor genes correlated with predisposition to develop cancerTP53, PTEN, STK11/LKB1, CDH1, CHEK2, ATM, MLH1, and MSH2But BRCA1 and BRCA2 have the strongest correlation with predisposition to breast and ovarian cancerImportance of early detection in treatment of cancerAt-risk individuals should be sure to undergo frequent checkups90PharmacogenomicsTailoring of treatment to individual patient, based on genetic sequences

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PharmacogenomicsTailoring of treatment to individual patient, based on genetic sequencesChoice of optimal drug, and dosageUse of drugs inappropriate for the patient:risks side effects: discomfort or even deathloses time in treating a condition which may become progressively worseat best, wastes money and health care resources; may require additional resources to cure side effects and more severe conditions

92Thiopurine methyltransferaseAcute lymphoblastic leukemia is a childhood cancer treated by thiopurinesThiopurine methyltransferase breaks down the drugsGenetic variant leading to inactive enzyme threatens toxic levels of drug in patientScreening patients for deficiency allows monitoring to determine appropriate dosage levels

93Sensitivity to abacavir94Abacavir used in treatment of AIDS4-8% of patients have serious, potentially-fatal hypersensitivity reactionHypersensitivity correlated with MHC allele HLA-B*5701Genetic screening can detect, guide treatment

Cytochrome P450 and drug metabolismCytochrome P450 is a family of enzymes in the liverResponsible for metabolizing a wide variety of drugsVariations in sequences affect activity of these enzymesLowered activity or loss of activity can cause drug toxicityGenetic tests for variations in cytochrome P450 genes warn of potential overdose dangersPharmaceutical companies screen compounds for rates of metabolism by cytochrome P450 enzymes 95J.D. Watson lessons from genomeThe sequence of J.D. Watsons DNA has been determined. He is homozygous for an unusual allele of the important drug metabolizing cytochrome gene (CYP2D6)Individuals with his genotype metabolise some drugs more slowly than other people.Watson has been taking blockers to lower his blood pressure.Side effect: made him unacceptably sleepy.Now he is taking a lower dosage.96