bluegrey 2 hazelgreen 3 brown in 502scan 400757 markers W - PDF document

blue/grey, 2 = hazel/green, 3 = brown) in 502scan (400Ð757 markers). We analyzed eye color as been previously implicated in eye color variation. Weeffects. However, a large shoulder on this peak other loci.Skin, hair and eye colors are some of the most obviousforms of human diversity (Sunderland, 1956), yet thecomplexities of the genetic mechanisms underlying thedifferences of these pigmentation phenotypes withinindividuals remain largely unknown. It is expectedthat a relatively small set of major genes contribute tothe color variation of these cutaneous tissues withindiverse human populations. These pigmentary genesare also expected to be specifically expressed withinthe melanocyte cell and act to regulate the synthesis, 197 A Genome Scan for Eye Color in 502 TwinFamilies: Most Variation is due to a QTL , Grant W. Montgomery Received 17 December, 2003; accepted 4 February, 2004.Address for correspondence: Nick Martin, Queensland Institute of MedicalResearch, Brisbane Qld 4029, Australia. Email: nickM@qimr.edu KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV estimated to be 26% (Hasstedt, 1995). Recently,(MZ) pairs respectively, with corresponding dizygotic(DZ) correlations of .26 and .43. However, they esti-is the OCA2 gene which is mutated in Type II oculo-over, polymorphism of the OCA2 gene almost certainlyMohr, 1996). Two OCA2 coding

region variant alleles,Arg305Trp and Arg419Gln, were recently shown torespectively (Rebbeck et al., 2002). To date, however,tion. To address this issue we estimated heritabilityand conducted a genome-wide linkage scan in asample of 502 twin families assessed for eye color. study of melanoma risk factors, including hair, skinal., 1999; Zhu et al., 1999). Twins were enlisted bymouth. It is estimated that approximately 50% oftheeligible birth cohort were recruited into the study. Thecount (Zhu et al., 1999) and IQ (Wright et al., 2001)and it seemed reasonable, therefore, to suppose thatpopulation with respect to eye color. Informed consentto testing. This paper concerns data collected fromEye color was rated on a 3-point scale (1 = blue/grey,twins who were tested at age 12 were also tested atthere were two and even three ratings of eye color.can be handled statistically. One is to treat the cate-variables, namely, blue/grey versus other, green/hazelversus other, and brown versus other. This is theeumelanin varies between different colored irises. Wetending toward normal. As we shall see, however,bivariate normality.Zygosity Testing and Genotypingfrom peripheral venous blood samples. Before selec- 198April 2004 KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV plex marker set (AmpFLSTRR Profiler PlusT, AppliedBiosystems, Foster City, CA). All

twins were alsotyped for ABO, Rh and MNS blood groups by theAGRF, PCR was performed on 30 ng of DNA andGenotyper 2.5 (Weeks et al., 2002).course of the adolescent twin study. Numbers in thispaper. Use of the full sample improves allele frequencythe three marker sets in Figure 2. The first scan wastwins and siblings from the first 274 families (642with a high degree of certainty. The markers used in 199April 2004 A Genome Scan for Eye Color in 502 Twin Families Figure 1 AGRF 2 +71 familiesAGRF 1 + CIDR242 families518 individualsCIDR only180 families1237 individuals AGRF only32 families 124 individuals Total AGRF and/or CIDR:525 families2123 individuals244 KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV typed (D2S2313; see Figure 2). Finally, five new, five new)all samples at AGRF and integrated in the marker mapfor the genome scan. Marker locations were deter-were accurate using RELPAIR (Boehnke & Cox, 1997;different methods. RELPAIR calculates the multipointmarker allele frequencies, inter-marker distances) andalso the presumed relationship of the pair. The inferredships (GRR) is a Windows-based application designedanceof zero (since they will share two alleles acrossthe program RELPAIR in that it will identify MZtwin pairs who share most but not all of their allelesbe flagged by RELPAIR since they do not share 200April 2004 Total AGRF a

nd/or CIDR:796 markers AGRF 1 and AGRF 2364 STR markers Only in CIDR354 STR markers(incl 3 Y markers) Only in AGRF 1D2S2313XRCC5 CIDR AGRF batchAL133411,,AndRD6S265, D6S276 & D6S291 35 markers KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV the latest version of RELPAIR.) GRR is also useful inprogram Sib-pair (Duffy, 2002) was used to correctdata from X-linked loci, the program ASPEX (Davis& Weeks, 1997) was used for this chromosome.which were inconsistent between scans were deletedfrom the dataset. However, three loci (markersNext, the combined dataset was examined forthemselves in the form of spurious Òdouble recombi-is much more likely the result of genotyping error.Mendelian inconsistent errors only. However, it is consistent errors are thought to constitute greater thanbe under-estimated. One strategy is to use a haplotyp-ing program such as ALLEGRO (Gudbjartsson et al.,that an individualÕs genotype is incorrectly specifiedhood function (i.e., the allele frequencies and markerthe calculation of the total posterior probability.criterion for which a genotype was considered anerror. That is, an individualÕs genotype was deleted error in the pedigree, but the particular individual 201April 2004 A Genome Scan for Eye Color in 502 Twin Families cM Distribution of intermarker distances in (a) AGRF, (b) CIDR, and (c) KWWSVGRL

RUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV �(i.e., with 80% probability), marker information forAnalyses were performed using the ILINK andnant fraction at each marker, and then MLINK wasrun at a recombination value of zero in order to iden-The MLINK option revealed 11 individuals who werefamily structures at each locus; while there was greater0.5 cM upstream. Similarly, a high degree of linkagegroup. Two individuals were recombinant betweenthe D9S164 locus. The presence of recombinationbetween two very tightly linked loci may indicate thating (AGRF & CIDR) was a dense map consisting ofof raw ordinal data were used (Neale et al., 2002). Inour case, the observed values were eye color cate-expected to affect eye color, unless through rater bias.th DZ twins and sibs only, we were unable tofamilial effect, F. Since we have some MZ pairs whothe QTL effect Q, at each marker, so for the presenteach of the markers were estimated using MERLINAmos, 1994; Eaves et al., 1996; Fulker & Cherny,QTL which is linked to the genotyped marker, F is and shared environment (C) if MZ twins are includedas P[IBD = 2] + as P[IBD = 2] + )ponents linkage analysis was performed using the MINXprogram of Abecasis (http://www.sph.umich.edu/csg/in which Q is free. Twice the difference in natural log 202April 2004 KWWSVGRLRUJWZLQ

 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV lent to the classical lod score of parametric linkageanalysis (Williams & Blangero, 1999).form the main part of the data (419 families, 1,025in the linkage analysis if they had at least one sib although parents were not phenotyped, their genotypes 2003) are shown for each twin group in Table 1a are in agreement with a purely additive genetic model= .31). Consequently, our initial model forwhich pairs that were IBD = 2, 1, and 0 at a given, and 0 respectively.However, we realise that an additive polygenic vari-effects which behave non-additively.the dataset, we fitted an AEQ model at each marker,needs to be fitted only once. Little difference was seenbetween linkage results for the two scoring systemsment using only the nurse rating from the first visit isare shown in Table 2. The change of fit in dropping an= 88.4, equivalent to a lod of 19.2.variance in eye color liability, with 18% due to famil-ial (polygenic) background and 8% due to uniqueenvironment (of which most is probably measurement 203April 2004 A Genome Scan for Eye Color in 502 Twin Families LowerUpperMZF2030.9880.9800.993MZM1860.9990.9951.000DZF1390.6550.4780.778DZM1380.4510.2610.607DZFM2540.5430.4090.653all MZ3890.9920.9870.995all DZ5310.5430.4500.625 otal920 Heterogeneity of Three DZ Correlations: 22 ACE Model Fit ModelÐ2LLA%C%E%ACE3082.9789.89.40.8 AE3084.021.05.3199.20.8 Results of Fitting A

dditive (Q) and Dominant (D) QTLs Linked to D15S1002. Variance Components (95% Confidence Interval) Due to Familial Correlation (F) and Unique Environment (E) are Also Shown as Percentages Model#Ð2 LLFEQDFEQD12393.541258315.8818.2(3.5Ð33.8)7.9(4.3Ð13.3)73.9(41.4Ð89.6)0.0(0Ð21.7)FEQ22393.54125910.0018.2(3.5Ð31.9)7.9(4.3Ð13.3)73.9(58.8Ð89.6)FED32409.421259472.5443.4(33.5Ð52.5)7.5(4.1Ð12.9)49.1(38.9Ð59.8) FE42481.961260288.4255.8(48.1Ð62.8)44.2(37.2Ð51.9) KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV 204April 2004 Results of genome-wide linkage scan for eye color measured on a 3-point scale, using variance components analysis for a multifactorial thresh-old model implemented in Mx. Note.Results of the scan using a one-locus additive QTL model are shown in red.Results of the scan for a second additive QTL given the QTL linked to D15S1002are shown in green, and the additive additive interaction term between the 15pQTL and the second locus is graphed in blue.Also shown are the positions of someloci known to influence pigmentation in mammals.Position of centromeres is indi-cated by KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV 1, and 0 respectively. This is in addition to the additiveproduced no change. Further, dropping

D from the= 72.5. From this we con-QTL to variation in eye color, we thought we mightgreen lines in Figure 4), and an additive model,notablydirectly over the pro-opiomelanocortin gene (POMC).shift, or be refined (7q, 3p). However, the mainthe 15q linkage was allowed for, there was very littlecolor. This was true a fortiorifor additive There was a hint of interaction at 3pter, 20qter, on 6pand, most interestingly, on 11p close to the TYRLconfounding (Mather, 1974).Consequently, when we fit the full two-locusmodel (Mather, 1974; Tiwari & Elston, 1997), allow-two-locus model is likely to be much more informa-with low power. under the assumption of normally distributed liability,a trait measured with negligible error, and almostperfect genetic additivity. The slight suggestion wesaw of shared environmental effects in females is pos-rating, or possibly to assortative mating for eye color,variance between both MZ and DZ pairs to imitatetotal DZ correlation in that sample to suggest sharedenvironmental influence, although there is not a hintConsequently, and despite classical evidence thatwere IBD1. Not surprisingly, given the low resolvingwas inconclusive, and other, more powerful methodsbe the subject of future reports. Since the QTL at 15qthe case, but Lynch and Walsh (1998) point out that 205April 2004 A Genome Scan for Eye Color in 502 Twin Families KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQH

E\&DPEULGJH8QLYHUVLW\3UHVV QTL to variation in eye color, we thought we mightget better resolving power for secondary QTLs byscan (notably, chromosome 14) does not necessarilyterms. However, we recognise that the power to detectthe opportunity to fit these terms as fixed effects whenin coat color, less is known about the genetics ofhuman skin and eye color. It must be noted that eye color, while others with effects on eye color maybecause of lack of power. In future papers we shallcolor. The peak on 15q lies directly over OCA2, whichthere, and it is interesting that both the MYO5A andated transport protein (MATP; Newton et al., 2001).than one might expect if this were the locus responsi-the MC1R receptor regulating pigment type switchingsmaller than that toward the q terminus of 9, wheregunmetal coat color gene RABGGTA is at 14q11.2zones. It is worth noting, however, that since any(browns) and was demonstratedat the turn of 206April 2004 KWWSVGRLRUJWZLQ 3XEOLVKHGRQOLQHE\&DPEULGJH8QLYHUVLW\3UHVV responsible for eye color, with blue eyes resultingImesch et al., 1996; Wilkerson et al., 1996). It is theeye, which determines iris color. Thus it is expectedblue eye color.suggests that it might transport a critical substancemice have also been noted to exhibit an abnormalTYR activity. In studies designed to examine the dist

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