add biomarker mapping 07242015 from solomon

Author: boycer

linkedSPLs/LinkedSPLs-update/mappings/FDA-pharmacogenetic-info-mapping/biomarker-to-ontology-mapping-07242015.csv

@@ -0,0 +1,74 @@
+FDAReferencedSubgroup,HGNCGeneSymbol,Synonymns,AlleleVariant,Pharmgkb,URI,Ontology,CuratorComments
+Philadelphia chromosome (t(9;22)) positive,ABL1,"c-abl oncogene 1, non-receptor tyrosine kinase; JTK7; c-ABL; p150",,PA24413,http://purl.obolibrary.org/obo/PR_000003582,PRotein Ontology (PRO),BCR/ABL
+Philadelphia chromosome (t(9;22)) positive; T315I mutation-positive,ABL1,"c-abl oncogene 1, non-receptor tyrosine kinase; JTK7; c-ABL; p150",,PA24413,http://purl.obolibrary.org/obo/PR_000003582,PRotein Ontology (PRO),BCR/ABL
+BCR-ABL T315I,ABL1,"c-abl oncogene 1, non-receptor tyrosine kinase; JTK7; c-ABL; p150",,PA24413,http://purl.obolibrary.org/obo/PR_000003582,PRotein Ontology (PRO),
+Urea cycle enzyme deficient,ABL2,v-abl Abelson murine leukemia viral oncogene homolog 2; ARG,,PA24414,http://purl.obolibrary.org/obo/PR_000003583,PRotein Ontology (PRO),
+ALK gene rearrangement positive,ALK,anaplastic lymphoma receptor tyrosine kinase; CD246,,PA24719,http://purl.obolibrary.org/obo/PR_000001282,PRotein Ontology (PRO),
+ApoE2,APOE,apolipoprotein E,E2,PA55,http://purl.obolibrary.org/obo/PR_000004155,PRotein Ontology (PRO),E2 or epsilon 2 is allele that is associated with a disorder of lipid metabolism
+Urea cycle enzyme deficient,ASL,argininosuccinate lyase,,PA25046,http://purl.obolibrary.org/obo/PR_000004373,PRotein Ontology (PRO),
+Urea cycle enzyme deficient,ASS1,argininosuccinate synthase 1; CTLN1,,PA162376926,http://purl.obolibrary.org/obo/PR_000004386,PRotein Ontology (PRO),
+Philadelphia chromosome (t(9;22)) positive,BCR,breakpoint cluster region; ALL; CML; D22S662; PHL,,PA25321,http://purl.obolibrary.org/obo/PR_000004712,PRotein Ontology (PRO),BCR/ABL
+Philadelphia chromosome (t(9;22)) positive; T315I mutation-positive,BCR,breakpoint cluster region; ALL; CML; D22S662; PHL,,PA25321,http://purl.obolibrary.org/obo/PR_000004712,PRotein Ontology (PRO),BCR/ABL
+BCR-ABL T315I,BCR,breakpoint cluster region; ALL; CML; D22S662; PHL,,PA25321,http://purl.obolibrary.org/obo/PR_000004712,PRotein Ontology (PRO),
+BRAF V600E mutation positive,BRAF,v-raf murine sarcoma viral oncogene homolog B1; BRAF1,,PA25408,http://purl.obolibrary.org/obo/PR_000004801,PRotein Ontology (PRO),Testing for the variant is required for using vemurafenib.
+CCR5 positive,CCR5,chemokine (C-C motif) receptor 5 (gene/pseudogene); CC-CKR-5; CD195; CKR-5; CKR5; IDDM22,,PA26170,http://purl.obolibrary.org/obo/PR_000001201,PRotein Ontology (PRO),Testing for the tropism is required for using maraviroc.
+Urea cycle enzyme deficient,CPS1,"carbamoyl-phosphate synthase 1, mitochondrial",,PA26840,http://purl.obolibrary.org/obo/PR_000005827,PRotein Ontology (PRO),
+NADH cytochrome b5 reductase deficient,CYB5R1-4,cytochrome b5 reductase 1; humb5R2,,PA134979668,http://purl.obolibrary.org/obo/PR_000006080,PRotein Ontology (PRO),
+CYP1A2 genotypes,CYP1A2,"cytochrome P450, family 1, subfamily A, polypeptide 2; CP12; P3-450",,PA27093,http://purl.obolibrary.org/obo/PR_000006102,PRotein Ontology (PRO),
+CYP2C19 poor metabolizers,CYP2C19,"cytochrome P450, family 2, subfamily C, polypeptide 19; CPCJ; P450IIC19",,PA124,http://purl.obolibrary.org/obo/PR_000006118,PRotein Ontology (PRO),
+CYP2C19 intermediate or poor metabolizers,CYP2C19,"cytochrome P450, family 2, subfamily C, polypeptide 19; CPCJ; P450IIC19",,PA124,http://purl.obolibrary.org/obo/PR_000006118,PRotein Ontology (PRO),
+CYP2C9 intermediate or poor metabolizers,CYP2C9,"cytochrome P450, family 2, subfamily C, polypeptide 9; P450IIC9",,PA126,http://purl.obolibrary.org/obo/PR_000006120,PRotein Ontology (PRO),
+CYP2D6 poor metabolizers,CYP2D6,"cytochrome P450, family 2, subfamily D, polypeptide 6; CPD6; CYP2D; P450-DB1; P450C2D",,PA128,http://purl.obolibrary.org/obo/PR_000006121,PRotein Ontology (PRO),
+Chromosome 5q deletion,del (5q),,,,,,"Deletion of part of chr 5q; is one cause of MDS, used as indication for treatment w/ drug"
+DPD deficient,DPYD,dihydropyrimidine dehydrogenase; DPD,,PA145,http://purl.obolibrary.org/obo/PR_000006678,PRotein Ontology (PRO),"Map to DPYD, DPD is a synonym/alias"
+EGFR exon 19 deletion or exon 21 substitution (L858R) mutation positive,EGFR,epidermal growth factor receptor; ERBB1,,PA7360,http://purl.obolibrary.org/obo/PR_000006933,PRotein Ontology (PRO),
+EGFR protein expression positive,EGFR,epidermal growth factor receptor; ERBB1,,PA7360,http://purl.obolibrary.org/obo/PR_000006933,PRotein Ontology (PRO),
+HER2 protein overexpression or gene amplification positive,ERBB2,v-erb-b2 erythroblastic leukemia viral oncogene homolog 2; CD340; HER-2; HER2; NEU,,PA27844,http://purl.obolibrary.org/obo/PR_000002082,PRotein Ontology (PRO),"Map to ERBB2 (gene symbol), Her2 and Neu are synonym/aliases."
+HER2 protein overexpression positive,ERBB2,v-erb-b2 erythroblastic leukemia viral oncogene homolog 2; CD340; HER-2; HER2; NEU,,PA27844,http://purl.obolibrary.org/obo/PR_000002082,PRotein Ontology (PRO),
+HER2 protein overexpression negative,ERBB2,v-erb-b2 erythroblastic leukemia viral oncogene homolog 2; CD340; HER-2; HER2; NEU,,PA27844,http://purl.obolibrary.org/obo/PR_000002082,PRotein Ontology (PRO),
+Hormone receptor positive,ESR1,estrogen receptor 1; Era; NR3A1 ,,PA156,http://purl.obolibrary.org/obo/PR_000007204,PRotein Ontology (PRO),ESR1 and ESR2 can homo or heterodimerize to form the ER receptor
+Prothrombin mutation G20210A,F2,coagulation factor II (thrombin),,PA157,http://purl.obolibrary.org/obo/PR_000007299,PRotein Ontology (PRO),the human F2 gene
+Factor V Leiden carriers,F5,"coagulation factor V (proaccelerin, labile factor)",,PA159,http://purl.obolibrary.org/obo/PR_000007300,PRotein Ontology (PRO), human coagulation factor V (F5)  
+FIP1L1/PDGFRα fusion kinase (or CHIC2 deletion) positive,FIP1L1,FIP1 like 1 (S. cerevisiae); DKFZp586K0717,,PA134875694,http://purl.obolibrary.org/obo/PR_000007526,PRotein Ontology (PRO),
+G6PD deficient,G6PD,glucose-6-phosphate dehydrogenase; G6PD1,,PA28469,http://purl.obolibrary.org/obo/PR_000007749,PRotein Ontology (PRO), 
+Lysosomal glucocerebrosidase enzyme,GBA,"glucosidase, beta, acid; GBA1",,PA28591,http://purl.obolibrary.org/obo/PR_000007867,PRotein Ontology (PRO),
+HLA-B*1502 allele carriers,HLA-B,"major histocompatibility complex, class I, B",HLA-B*1502,PA35056,http://purl.obolibrary.org/obo/PR_000002010,PRotein Ontology (PRO),*1502 is an allele associated with drug toxicity (skin reactions)
+HLA-B*5701 allele carriers,HLA-B,"major histocompatibility complex, class I, B",HLA-B*5701,PA35056,http://purl.obolibrary.org/obo/PR_000002010,PRotein Ontology (PRO),*5701 is an allele associated with drug hypersensitivity reactions
+HLA-A*3101 allele carriers,HLA-B,"major histocompatibility complex, class I, B",HLA-B*3101,PA35056,http://purl.obolibrary.org/obo/PR_000002010,PRotein Ontology (PRO),
+HGPRT deficient,HPRT1,hypoxanthine phosphoribosyltransferase 1; HGPRT,,PA29427,http://purl.obolibrary.org/obo/PR_000008735,PRotein Ontology (PRO),the human HPRT1 gene 
+IL28B rs12979860 T allele carriers,IFNL3,"interferon, lambda 3; IL-28B; IL28B; IL28C",T,PA134952671,http://purl.obolibrary.org/obo/PR_000001470,PRotein Ontology (PRO),
+CD25 antigen positive,IL2RA,"interleukin 2 receptor, alpha; CD25",,PA29828,http://purl.obolibrary.org/obo/PR_000001380,PRotein Ontology (PRO),
+c-KIT D816V mutation negative,KIT,v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog; C-Kit; CD117; SCFR,,PA30128,http://purl.obolibrary.org/obo/PR_000009345,PRotein Ontology (PRO),Map to KIT (gene symbol). C-kit is a synonym/alias
+KRAS codon 12 and 13 mutation negative,KRAS,Kirsten rat sarcoma viral oncogene homolog,,PA30196,http://purl.obolibrary.org/obo/PR_000009442,PRotein Ontology (PRO),
+Homozygous familial hypercholesterolemia,LDLR,low density lipoprotein receptor,,PA227,http://purl.obolibrary.org/obo/PR_000009744,PRotein Ontology (PRO),familial hypercholesterolemia
+Homozygous familial hypercholesterolemia and LDL receptor mutation deficient,LDLR,low density lipoprotein receptor,,PA227,http://purl.obolibrary.org/obo/PR_000009744,PRotein Ontology (PRO),
+Homozygous and Heterozygous familial hypercholesterolemia,LDLR,low density lipoprotein receptor,,PA227,http://purl.obolibrary.org/obo/PR_000009744,PRotein Ontology (PRO),
+CD20 positive,MS4A1,"CD20 antigen; membrane-spanning 4-domains, subfamily A, member 1; B1; Bp35; MS4A2",,PA31111,http://purl.obolibrary.org/obo/PR_000001289,PRotein Ontology (PRO),"MS4A2 is an alias for MS4A1, but MS4A2 is also listed in HGNC as a separate gene. PharmGKB links CD20 Antigen to MS4A2. Requires further investigation to disambiguate."
+N-acetylglutamate synthase deficiency,NAGS,N-acetylglutamate synthase; AGAS; ARGA; NAT7,,PA134968729,http://purl.obolibrary.org/obo/PR_000010964,PRotein Ontology (PRO),Mitochondrial protein
+Urea cycle enzyme deficient,NAGS,N-acetylglutamate synthase; AGAS; ARGA; NAT7,,PA134968729,http://purl.obolibrary.org/obo/PR_000010964,PRotein Ontology (PRO),
+Slow inactivators,NAT1,N-acetyltransferase 1 (arylamine N-acetyltransferase),,PA17,http://purl.obolibrary.org/obo/PR_000010994,PRotein Ontology (PRO),
+Slow inactivators,NAT2,N-acetyltransferase 2 (arylamine N-acetyltransferase),,PA18,http://purl.obolibrary.org/obo/PR_000011001,PRotein Ontology (PRO),
+Urea cycle enzyme deficient,OTC,ornithine carbamoyltransferase,,PA32840,http://purl.obolibrary.org/obo/PR_000012070,PRotein Ontology (PRO),
+FIP1L1/PDGFRα fusion kinase (or CHIC2 deletion) positive,PDGFRA,"platelet-derived growth factor receptor, alpha polypeptide; CD140a; PDGFR2",,PA33147,http://purl.obolibrary.org/obo/PR_000012492,PRotein Ontology (PRO),
+PDGFR gene rearrangement positive,PDGFRB,"platelet-derived growth factor receptor, beta polypeptide; CD140b; JTK12; PDGFR1",,PA33148,http://purl.obolibrary.org/obo/PR_000002136,PRotein Ontology (PRO),
+Hormone receptor positive,PGR,progesterone receptor; NR3C3; PR,,PA266,http://purl.obolibrary.org/obo/PR_000012621,PRotein Ontology (PRO),
+PML/RARα (t(15;17)) gene expression positive,PML,promyelocytic leukemia; MYL; RNF71; TRIM19,,PA33439,http://purl.obolibrary.org/obo/PR_000026474,PRotein Ontology (PRO),"PML and RARA fusion gene, dependent on retinoic acid for transcription"
+PML/RARα (t(15;17)) gene expression positive,RARA,"retinoic acid receptor, alpha; NR1B1; RAR",,PA34225,http://purl.obolibrary.org/obo/PR_000013736,PRotein Ontology (PRO),"PML and RARA fusion gene, dependent on retinoic acid for transcription"
+Rh genotype,RHD,Rh genotype,,PA34387,http://purl.obolibrary.org/obo/PR_000001442,PRotein Ontology (PRO),
+Antithrombin III deficient,SERPINC1,"serpin peptidase inhibitor, clade C (antithrombin), member 1; ATIII; MGC22579",,PA35026,http://purl.obolibrary.org/obo/PR_000003252,PRotein Ontology (PRO),"human SERPINC1 gene, serpin peptidase inhibitor, clade C (antithrombin), member 1"
+CD30 positive,TNFRSF8,"tumor necrosis factor receptor superfamily, member 8; CD30 (previous symbol); KI-1",,PA36616,http://purl.obolibrary.org/obo/PR_000001964,PRotein Ontology (PRO),Map to TNFRSF8 (gene symbol). CD30 is a synonym/alias
+CD257 positive,TNFSF13B,"tumor necrosis factor (ligand) superfamily, member 13b; BAFF; BLYS; CD257; TALL-1; TALL1; THANK",,PA434,http://purl.obolibrary.org/obo/PR_000001948,PRotein Ontology (PRO),"Same as BAFF. HUGO in FDA table as TNFSF13B/BAFF, but only represents one protein"
+TPMT intermediate or poor metabolizers,TPMT,thiopurine S-methyltransferase,,PA356,http://purl.obolibrary.org/obo/PR_000016583,PRotein Ontology (PRO),
+UGT1A1*28 allele homozygotes,UGT1A1,"UDP glucuronosyltransferase 1 family, polypeptide A1; UGT1A",UGT1A1*28 ,PA420,http://purl.obolibrary.org/obo/PR_000017048,PRotein Ontology (PRO),
+(TA)7/(TA)7 genotype (UGT1A1*28/*28),UGT1A1,"UDP glucuronosyltransferase 1 family, polypeptide A1; UGT1A",UGT1A1*28; (TA)7,PA420,http://purl.obolibrary.org/obo/PR_000017048,PRotein Ontology (PRO),
+VKORC1 rs9923231 A allele carriers,VKORC1,"vitamin K epoxide reductase complex, subunit 1",A,PA133787052,http://purl.obolibrary.org/obo/PR_000017303,PRotein Ontology (PRO),
+Protein C deficient,PROC,vitamin k -dependent protein c,,PA446903,http://purl.obolibrary.org/obo/PR_000013261,PRotein Ontology (PRO),
+POLG Mutation Positive,POLG,DNA polymerase subunit gamma-1 ,,PA33500,http://purl.obolibrary.org/obo/PR_000012973  ,PRotein Ontology (PRO),
+Chromosome 17p deletion positive,del (17p),,,,,,
+HLA-DQA1*0201 or -DRB1*0701 allele carriers,HLA-DQA1,"major histocompatibility complex, class II, DQ alpha 1",HLA-DQA1*0201,PA35066,http://purl.obolibrary.org/obo/PR_000002013 ,PRotein Ontology (PRO),
+HLA-DQA1*0201 or -DRB1*0701 allele carriers,HLA-DRB1,"major histocompatibility complex, class II, DR beta 1",HLA-DRB1*0701,PA35072,http://purl.obolibrary.org/obo/PR_000002019,PRotein Ontology (PRO),
+CYP3A5 variant carriers,CYP3A5,"cytochrome P450, family 3, subfamily A, polypeptide 5",,PA131,http://purl.obolibrary.org/obo/PR_000006132,PRotein Ontology (PRO),
+CYP2B6 variant carriers,CYP2B6,"cytochrome P450, family 2, subfamily B, polypeptide 6",,PA123,http://purl.obolibrary.org/obo/PR_000006116,PRotein Ontology (PRO),
+CYP2D6 ultrarapid metabolizers,CYP2D6,"cytochrome P450, family 2, subfamily D, polypeptide 6; CPD6; CYP2D; P450-DB1; P450C2D",,PA128,http://purl.obolibrary.org/obo/PR_000006121,PRotein Ontology (PRO),
+NADH cytochrome b5 reductase deficient,CYB5R1-4,cytochrome b5 reductase,,PA134979668,http://purl.obolibrary.org/obo/PR_000006080,PRotein Ontology (PRO),"FDA biomarker is 1-4, but it looks like the focus is on 1"
+Protein S deficient,PROS,protein s (alpha),,PA33809,http://purl.obolibrary.org/obo/PR_000013269,PRotein Ontology (PRO),