diff --git a/fh.py b/fh.py index 75e2d9e..1f04578 100755 --- a/fh.py +++ b/fh.py @@ -14,6 +14,7 @@ class PRS(object): """ Class to easily calculate Polygenic Risk Score for FH. see Talmund et al 2013 + NOTE: Talmund et al use build 37 genomic coordinates. This script uses build 38 genomic coordinates. Attributes ---------- @@ -39,57 +40,57 @@ class PRS(object): """ SCORES = { - "1:55038977": { #rs2479409 (PCSK9) build 38 + "1:55038977": { #rs2479409 (PCSK9) "GG":0.104, "GA":0.052, "AA":0 }, - "1:109275684":{ #rs629301 (CELSR2) build 38 + "1:109275684":{ #rs629301 (CELSR2) "GG":0, "GT":0.15, "TT":0.3 }, - "2:21041028":{ #rs1367117 (APOB) build 38 + "2:21041028":{ #rs1367117 (APOB) "GG":0, "GA":0.1, "AA":0.2 }, - "2:43845437":{ #rs4299376 (ABCG8) build 38 + "2:43845437":{ #rs4299376 (ABCG8) "GG":0.142, "GT":0.071, "TT":0 }, - "6:16127176":{ #rs3757354 (MYLIP) build 38 + "6:16127176":{ #rs3757354 (MYLIP) "CC":0.074, "CT":0.037, "TT":0 }, - "6:26092913":{ #rs1800562 (HFE) build 38 + "6:26092913":{ #rs1800562 (HFE) "GG":0.114, "GA":0.057, "AA":0 }, - "6:160157828":{ #rs1564348 (SLC22A1) build 38 + "6:160157828":{ #rs1564348 (SLC22A1) "TT":0.028, "TC":0.014, "CC":0 }, - "11:126374057":{ #rs11220462 (ST3GAL4) build 38 + "11:126374057":{ #rs11220462 (ST3GAL4) "GG":0, "GA":0.05, "AA":0.1 }, - "14:24414681":{ #rs8017377 (NYNRIN) build 38 + "14:24414681":{ #rs8017377 (NYNRIN) "GG":0, "GA":0.029, "AA":0.058 }, - "19:11091630":{ #rs6511720 (LDLR) build 38 + "19:11091630":{ #rs6511720 (LDLR) "GG":0.36, "GT":0.18, "TT":0 }, - "19:44908684,19:44908822":{ #rs429358,rs7412 build 38 + "19:44908684,19:44908822":{ #rs429358,rs7412 "TTTT":-0.9, "TCTT":-0.4, "TTCT":-0.4,