1、12Bimodality:Hallmark of a major gene effect on a quantitative trait.3Bimodality:Hallmark of a major gene effect on a quantitative trait.4 Polygenic Traits1 Gene 3 Genotypes 3 Phenotypes2 Genes 9 Genotypes 5 Phenotypes3 Genes 27 Genotypes 7 Phenotypes4 Genes 81 Genotypes 9 Phenotypes5Complex Trait M
2、odelDisease PhenotypeCommonenvironmentMarkerGene1IndividualenvironmentPolygenicbackgroundGene2Gene3Linkage Linkagedisequilibrium Mode ofinheritance LinkageAssociation 67CHGA genetic variation:Risk factor for hypertensive ESRD in blacksJ Am Soc Nephrol.2008 Mar;19(3):600-14.Chromogranin A polymorphis
3、ms are associated with hypertensive renal disease.Salem RM,Cadman PE,Chen Y,Rao F,Wen G,Hamilton BA,Rana BK,Smith DW,Stridsberg M,Ward HJ,Mahata M,Mahata SK,Bowden DW,Hicks PJ,Freedman BI,Schork NJ,OConnor DT.89“Intermediate”intime and causality MechanismTwinsCardiorenal disease trait(later life)Tim
4、e(decades.)Gene(fixed at conception)10Twins:window into heritability(h2)of any phenotypeMonozygotic(MZ,identical)twins:Billy and Benny.VP=VG+VEh2=VG/VP=2(RMZ-RDZ)Source:Guinness Book of World Records.11 Total mole count for MZ and DZ twins01002003004000100200300400Twin 2Twin 101002003004000100200300
5、400Twin 2Twin 1MZ twins-153 pairs,r=0.94DZ twins-199 pairs,r=0.601213Family studies(twin pairs,pedigrees).Fam hx as a risk factor.In 1st degree relatives:Parents,siblings.Heritability(h2):Fraction of trait variance accounted for by genetic variance.VP=VG+VE h2=VG/VP Estimate h2 from twin pair(or ped
6、igree)studies:Type of twin pairAllele sharing across the genome.MZ=monozygotic=identical.100%DZ=dizygotic=fraternal50%(on average),like any sib pair Quick-and-dirty algorithm:h2=VG/VP=2(RMZ RDZ)1415 West J Med.1984 Dec;141(6):799-806.Understanding genetic and environmental risk factors in susceptibl
7、e persons.Williams RR.Family history as a risk factor for complex traits.Familyhistory161718Linkage=Meiotic co-segregationA2A4A3A4A1A3A1A2A2A3A1A2A1A4A3A4A3A2Marker allele A1cosegregates withdominant disease 19Linkage Markers20Thomas Hunt Morgan discoverer of linkage21Idiosyncratic features of genet
8、ic linkage(=meiotic co-segregation).Units.Metric=meiotic recombination(50 meioses/generation).Units of genetic distance=recombination during meiosis(cM).cM=(recombinant meioses/total meioses)*100 E.g.:8/(8+86)*100=(8/94)*100 =8.5 cM1 cM 1 Mb Range 0.5-2.0 Varies by species,sex,chromosomal region(mei
9、otic“hot spots”)Significance.“LOD”scores.LOD=Log10 of the odds ratio for linkageOdds ratio:Co-segregation(marker and trait)NotSignificant:LOD 3.0(i.e.,odds ratio 1000/1)Why 3.0?50“linkage groups”(meiotic breaks/generation),target=0.05.1/50*1/20=1/1000.22Genetic linkage:Meiotic recombination distance
10、 in cMcM=(recombinant meioses/total meioses)*1008/(8+86)*100=(8/94)*100 =8.5 cMMahata SK,Kozak CA,Szpirer J,Szpirer C,Modi WS,Gerdes HH,Huttner WB,OConnor DT.Dispersion of chromogranin/secretogranin secretory protein family loci in mammalian genomes.Genomics.1996 Apr 1;33(1):135-9.1 cM 1 MbRange 0.5
11、-2.0Varies by species,sex,chromosomal region(meiotic“hot spots”)23Mouse SBP crosses:“Genome scan”linkage.Wright FA,OConnor DT,Roberts E,Kutey G,Berry CC,Yoneda LU,Timberlake D,Schlager G.Genome scan for blood pressure loci in mice.Hypertension.1999 Oct;34(4 Pt 1):625-30.2425J Clin Invest.1996 May 1;
12、97(9):2111-8.Quantitative trait locus mapping of human blood pressure to a genetic region at or near the lipoprotein lipase gene locus on chromosome 8p22.Wu DA,Bu X,Warden CH,Shen DD,Jeng CY,Sheu WH,Fuh MM,Katsuya T,Dzau VJ,Reaven GM,Lusis AJ,Rotter JI,Chen YD.Genetic linkage:What the data(marker,tr
13、ait)look like.26J Clin Invest.1996 May 1;97(9):2111-8.Quantitative trait locus mapping of human blood pressure to a genetic region at or near the lipoprotein lipase gene locus on chromosome 8p22.Wu DA,Bu X,Warden CH,Shen DD,Jeng CY,Sheu WH,Fuh MM,Katsuya T,Dzau VJ,Reaven GM,Lusis AJ,Rotter JI,Chen Y
14、D.Genetic linkage:What the data(marker,trait)look like.2728The catecholamine biosynthetic pathway.T Flatmark.Regulation of catecholamine biosynthesis.Acta Physiol Scand 168:1-17,2000.29Figure 8:TH haplotypes in vivo303132Figure 7:Intermediate phenotypesMechanismTimeGene Biochemical trait Physiologic
15、al traitDisease traitHypertension:“Intermediate”phenotypes and candidate genes.Tyrosine hydroxylase C-824T Catecholamines Baroreceptor function Stress blood pressure Hypertension3334pter qter5 3ChromosomePaternalMaternalT C A G C T G A Haplotype:Ordered array of alleles along a single chromosome.Bia
16、llelic SNPs(single nucleotide polymorphisms).Typically“transitions”:Purine Purine(G A)Pyrimidine Pyrimidine(C T)355 3PaternalMaternalT A C G T A C GC G T C C G T A“Linkage disequilibrium”(LD):Local,marker-on-marker locus Equilibrium=randomness(no correlation,r2=0)Disequilibrium=non-random(correlated
17、,r20)Marker-on-trait locus:Mapping tool0.9 0.9 0.9 0.0 0.9 0.9 0.9 0.5 0.50.0Ancestral(shared)Meiotic recombinationr2BiallelicSNPs36 In population genetics,linkage disequilibrium is the non-non-randomrandom association of alleles at two or more loci.Linkage disequilibrium describes a situation in wh
18、ich some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a randomrandom formation of haplotypes from alleles based on their frequencies.Non-randomNon-random associations between polymorphisms at different loci are measured by the d
19、egree of linkage disequilibrium(LD).The level of linkage disequilibrium is influenced by a number of factors including the rate of meiotic recombination meiotic recombination(crossovers(crossovers)and the rate of mutation.Linkage disequilibrium(LD).Marker trait Marker marker37HapMap:View variation p
20、atternsTriangle plot shows LD values using r2 or D/LOD scores in one or more HapMap population38The International HapMap Project(Identification of SNPs that tag haplotypes within blocks)Daly,M.J.,Rioux,J.D.,Schaffner,S.F.,Hudson,T.J.and Lander,E.S.(2001).High-resolution haplotype structure in the hu
21、man genome.Nature Genet.29:229-232.39Linkage disequilibrium(LD)“blocks”on human chromosome 14q32 100 kbp displayed,from 3 short-range(30 kbp)LD blocksNo long-range(100 kbp)LD40Region of the genome around around SNP rs9941339 in CDH13(T-cadherin=novel adiponectin receptor)on 16q24 associated with int
22、ra MZ pair differences in HDL cholesterol(GWAS in n=1662 MZ pairs).Black points represent SNPs genotyped in the study and gray points represent SNPs whose genotypes were imputed.In middle panel,red line shows the fine-scale recombination rate(centimorgans per Mb)estimated from Phase II HapMap and th
23、e black line shows the cumulative genetic distance(in cM).Association p=8.5x10-8.Gene-by-Environment(GxE)interaction probed by MZ twin intra-pair trait differences:HDL-cholesterol effect of T-cadherin(CDH13,novel adiponectin receptor)genetic variation revealed by dense,genome-wide profiling in 1662
24、MZ pairsp=8.5x10-8 100 kbp4142Accumulation of deleterious rare amino acid substitution variants at extremes of human body mass index(BMI)Ahituv N,Kavaslar N,Schackwitz W,Ustaszewska A,Martin J,Hebert S,Doelle H,Ersoy B,Kryukov G,Schmidt S,Yosef N,Ruppin E,Sharan R,Vaisse C,Sunyaev S,Dent R,Cohen J,M
25、cPherson R,Pennacchio LA.Medical sequencing at the extremes of human body mass.Am J Hum Genet.2007 Apr;80(4):779-91.4344Drilling down to the“QTN”(“Quantitative Trait Nucleotide”)Haplotype“block”is the lower limit of resolution of marker-on-trait mapping.Switch to studies of associated variants:In ce
26、lla.E.g.,transfected/expressed variants.In vitro.E.g.,kinetic properties of variants.In vivo:transgenic mice(BAC haplotype variant expression on knockout background).45Positional candidate genetic loci.46“Positional candidate”locusWong C,Mahapatra NR,Chitbangonsyn S,Mahboubi P,Mahata M,Mahata SK,OCo
27、nnor DT.The angiotensin II receptor(Agtr1a):functional regulatory polymorphisms in a locus genetically linked to blood pressure variation in the mouse.Physiol Genomics.2003 Jun 24;14(1):83-93.47“Positional candidate”locusWong C,Mahapatra NR,Chitbangonsyn S,Mahboubi P,Mahata M,Mahata SK,OConnor DT.Th
28、e angiotensin II receptor(Agtr1a):functional regulatory polymorphisms in a locus genetically linked to blood pressure variation in the mouse.Physiol Genomics.2003 Jun 24;14(1):83-93.48“Positional candidate”locusWong C,Mahapatra NR,Chitbangonsyn S,Mahboubi P,Mahata M,Mahata SK,OConnor DT.The angioten
29、sin II receptor(Agtr1a):functional regulatory polymorphisms in a locus genetically linked to blood pressure variation in the mouse.Physiol Genomics.2003 Jun 24;14(1):83-93.49Wild-typeAgtr1a promoterLuciferasereporterTranscriptionPromoter/reporterplasmid(pGL3-Basic)VariantAgtr1a promoterLuciferaserep
30、orterTranscriptionPromoter/reporterplasmid(pGL3-Basic)LuciferasetranscriptionNucleusLuciferasetranslationCytosolChromaffin cellFirefly luciferaseenzymatic activity assayTransfectionCelllysisPromoter variant characterization50Wong C,Mahapatra NR,Chitbangonsyn S,Mahboubi P,Mahata M,Mahata SK,OConnor D
31、T.The angiotensin II receptor(Agtr1a):functional regulatory polymorphisms in a locus genetically linked to blood pressure variation in the mouse.Physiol Genomics.2003 Jun 24;14(1):83-93.“Positional candidate”locus5152ExposureDzStableRapid declineInitiation(case/control study)Outcome(longitudinal stu
32、dy)Gene:SusceptibilityGene:ModifierSwitchGenomics in Dz risk:Two kinds of Gene-by-Environment interactions.NotSwitch DrugTime(decades)53Figure 3AKCNMB1 Glu65Lys effect on rate of GFR declinein hypertensive nephrosclerosis(NIDDK AASK)54KCNMB1 Glu65Lys predicts long-term loss of renal functionin hyper
33、tensive nephrosclerosis(NIDDK AASK)E/K+K/KE/K+K/K censoredE/EE/E censoredLog rank p=0.0190Event:ESRD requiring dialysis or doubling of serum creatinineMonths after enrollmentCumulative survivalFigure 3BE/EE/K+K/K55VOCCBKCa2+K+b b1 1 subunit(Glu65)VOCCBKCa2+K+b b1 subunit(65Lys)1 subunit 1 subunitContracted mesangialor smooth muscle cellRelaxed mesangialor smooth muscle cellK+K+:Ca2+ions :InhibitionKCNMB1 Glu65Lys:Hypothesis for effect on GFRFigure 4Higher fluxLower fluxWild-typeVariant56575859
