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….
| | | | | | . | Gene | Northern European | West African | East Asian | Note | . | ACAN | – | – | – | Alias: CSPG1 | . | ADAMTS17 | – | – | – | | . | ADAMTSL3 | – | – | – | | . | ANAPC13 | – | – | – | | . | ANKFN1 | – | – | – | Alias: FLJ38335 | . | ANKS1 | X | – | – | | . | ATAD5 | – | – | – | Alias: FLJ12735 | . | ATXN3 | – | – | – | | . | BCAS3 | – | – | – | Fst – No diff. Euro-Asian in some regions | . | BMP2 | – | – | – | | . | BMP6 | – | – | – | | . | C18orf45 | – | – | – | | . | C1orf19 | – | – | – | | . | C20orf30 | – | – | – | | . | C6orf106 | XX | – | – | | . | 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 | – | – | – | | . | GDF5 | X | X | XX | Massive 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 | . | HMGA1 | X | – | – | 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 | – | – | – | | . | PRKG2 | XX | – | – | 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? | . | SCUBE3 | X | – | – | | . | SF3B4 | – | – | – | | . | SH3GL3 | – | – | – | | . | SOCS2 | – | – | – | | . | SPAG17 | – | – | – | Haplotter error | . | SV2A | – | – | – | Asians look fixed? |
| | | | | | | . | TBX2 | – | – | – | | . | TBX4 | – | – | – | | . | TCP11 | X | – | – | Overlap with SCUBE3 | . | TGS1 | – | – | – | | . | TMED3 | – | – | – | | . | TRIM25 | – | – | – | | . | TRIP11 | – | – | – | | . | UQCC | X | X | XX | Lots of selection in region! Alias: BFZB | . | WDR60 | – | – | – | | . | ZBTB38 | – | – | – | | . | ZF
HX4 | – | – | – | | . | ZNF462 | – | – | – | | . | ZNF678 | – | – | – | | . | ZNF76 | X | – | – | Region overlaps with others, SCUBE3 |
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