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Health

Selection for height genes?

Gene ExpressionBy Razib KhanApril 7, 2008 6:31 PM

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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

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