Table 3.

Genes with amino acids under positive selection in clade A and all tumor cell lines

TissuePositive selected sitesSNP IDGeneOccurrence in cell lines
Clade AAll
BrainI391Mrs3729680PIK3CA1049
R273H*/Y/Crs28934576*TP53824
BreastE152KBIRC54042
Q349Rrs18011376BUB1B1717
H1047R/LPIK3CA915
ColonE152KBIRC54042
G12V/C/D/AKRAS2252
G13DKRAS49
R248W/Q*rs11540652*TP53728
R273Hrs28934576TP53824
BoneR72Prs1042522TP5334144
LungG12V/CS/R/FKRAS2252
I391Mrs3729680PIK3CA1049
R72Prs1042522TP5334144
Peripheral tissuesG13D/A/V/LKRAS49
G12D/V/N/CNRAS15
Q61L/K/Hrs11554290NRAS419
I391Mrs3729680PIK3CA1049
R72P*/Rrs1042522*TP5334144
R248Q*/W/stoprs11540652*TP53728
ProstateE152KBIRC54042
Q349Rrs1801376BUB1B1717
M506Trs2277283INCENP1919
G12VKRAS2252
S442Yrs17847825PIK3CG1818
P313Srs1011320PIK3R21010
KidneyI391Mrs3729680PIK3CA1049
SkinV600E/DBRAF836
Q61K/R*rs11554290*NRAS419
M326Irs3730089PIK3R12424
A420Vrs13859RPS6KB25858
R72Prs1042522TP5334144
OvarianR72Prs1042522TP5334144
PancreasG12V/D/CKRAS2252
M326Irs3730089PIK3R12424
R72Prs1042522TP5334144
R248Q*/Wrs11540652*TP53728
I255N/TTP5314
M322Trs1073123TSC12020
OtherG12D/R/CKRAS2252
I391Mrs3729680PIK3CA1049
G245STP5318
R248Q*/L/Wrs11540652*TP53728

NOTE: Based on PAML likelihood scores (see Supplementary Methods File 1), all tumor tissue types, where genes had amino acid sites under significant positive selection (BP > 0.95), are shown. Bladder and liver tumor-derived cell lines were also tested but do not have any significant positive selection sites.

  • *Positive selection sites, which are also sites of known SNPs and their corresponding SNP ID.

  • For NRAS, positive selection site Q61 is a site of a known SNP, but mutations at this site were not of the SNP variant (Q61R).