Three papers on genome wide association studies & height. Identification of ten loci associated with height highlights new biological pathways in human growth, Genome-wide association analysis identifies 20 loci that influence adult height and Many sequence variants affecting diversity of adult human height. Dan MacArthur hits the major point:
ScienceDaily puts a positive spin on the story ("Scientists are beginning to develop a clearer picture of what makes some people stand head and shoulders above the rest"), but the real story is this: despite the massive scale of these studies, they're still only capturing less than 5% of the total variance in a trait that is almost entirely (90%) genetic. This is a powerful demonstration of the inability of current GWAS technology to access the genetic variants responsible for the vast majority of heritable variation in at least some complex traits, for reasons I have previously discussed in detail.
I was wondering if there was any recent selection in the genomic regions pinpointed in the three papers, so I turned to Haplotter. Below the fold are the results.... I set Haplotter so that it looked around a 1 MB window fixed on the gene I queried. X = a hit within that window, while XX = a hit on that specific gene. The columns are pretty self-explanatory, but do note some of these genes are very close to each other. Also, I had to use aliases, and I can't guarantee that a gene isn't listed twice because of the usage of aliases. All in all, note much selection, huh? I wasn't expecting much, but nice to confirm expectations.... .g {text-indent:3px;padding-right:3px;overflow:hidden;white-space:nowrap;letter-spacing:0;word-spacing:0;background-color:#FFFFFF; z-index:1;border-top:0px none;border-left:0px none;border-bottom:1px solid #CCC;border-right:1px solid #CCC;} .dn {display:none} .chip {background-image:url('http://www.google.com/images/spreadsheets/chip.gif'); background-repeat:no-repeat; background-position:top right;} .s1 {background-color:white;font-family:Arial;font-size:100.0%;font-weight:normal;font-style:normal;text-decoration:none;vertical-align:bottom;white-space:normal;overflow:hidden;text-indent:0px;padding-left:3px;border-right:1px solid #CCC;border-bottom:1px solid #CCC;} .s0 {background-color:white;font-family:Arial;font-size:100.0%;font-weight:normal;font-style:normal;color:#000000;text-decoration:none;text-align:left;vertical-align:bottom;white-space:normal;overflow:hidden;text-indent:0px;padding-left:3px;border-right:1px solid #CCC;border-bottom:1px solid #CCC;}
.GeneNorthern EuropeanWest AfricanEast AsianNote
.ACAN---Alias: CSPG1
.ADAMTS17---
.ADAMTSL3---
.ANAPC13---
.ANKFN1---Alias: FLJ38335
.ANKS1X--
.ATAD5---Alias: FLJ12735
.ATXN3---
.BCAS3---Fst - No diff. Euro-Asian in some regions
.BMP2---
.BMP6---
.C18orf45---
.C1orf19---
.C20orf30---
.C6orf106XX--
.CABLES1---
.CDK6---
.CENTA2---Fst - No diff. Euro-Asian in some regions
.CEP63---
.CHCHD7---
.COIL---
.CPSF2---
.CRLF3---Fst - No diff. Euro-Asian in some regions
.DCC---
.DEF6---Alias: DEFA6
.DGKE---
.DLEU7---
.DNM3---
.DOT1L---
.DYM---
.E4F1---Lots of stuff just below p-value in region
.EFEMP1---
.ERVWE1---Problem with haplotter
.FBLN5---
.FUBP3---
.GATAD1---
.GDF5XXXXMassive selection in this genomic region in Euro & Asian
.GLT25D2---p-value close in Asian
.GNA12---
.GPR126---
.GRB10---
.HHIP---
.HIST1H1D---Alias: H1F3, lots of close p-values
.HMGA1X--Signal from other gene on list
.HMGA2--
.IHH---p-value close in Euro
.LBH---
.LCORL---Alias: FLJ30696
.LIN28B---p-values close for Euro
.LOC387103---Alias: CUG2, haplotter
.LYAR---
.LYN---Asians fixed, so haplotter can't detect
.MOS---Alias: MSV
.MTMR11---Looks like lots of fixed stuff around....
.NACA2---
.NCAPG---Alias: CAPG
.NKX2-1---
.NOG---
.PAPPA---
.PENK---Asians look fixed
.PEX1---
.PLAG1---
.PNPT1---
.PRKG2XX--X as well
.PTCH1---Haplotter error
.PXMP3---
.RAB40C---
.RBBP8---Africans look fixed
.RDHE2---
.RISK---Can't find this gene?
.RNF135---p-value close for African, looks near fixed
.RPS20---Fixed in Asians?
.SCMH1---Fixed in Africans?
.SCUBE3X--
.SF3B4---
.SH3GL3---
.SOCS2---
.SPAG17---Haplotter error
.SV2A---Asians look fixed?
.TBX2---
.TBX4---
.TCP11X--Overlap with SCUBE3
.TGS1---
.TMED3---
.TRIM25---
.TRIP11---
.UQCCXXXXLots of selection in region! Alias: BFZB
.WDR60---
.ZBTB38---
.ZF HX4---
.ZNF462---
.ZNF678---
.ZNF76X--
Region overlaps with others, SCUBE3
