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autogkb

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pmcid string	article_title string	article_path string	article_text string	variant_annotation_id int64	variant_haplotypes string	gene string	drugs string	pmid int64	phenotype_category string	significance string	notes string	sentence string	alleles string	specialty_population string	metabolizer_types string	is_plural string	is_is_not_associated string	direction_of_effect string	pd_pk_terms string	multiple_drugs_and_or string	population_types string	population_phenotypes_or_diseases string	multiple_phenotypes_or_diseases_and_or string	comparison_alleles_or_genotypes string	comparison_metabolizer_types string
PMC6714673	Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients	articles/PMC6714673.md	null	1,449,192,282	rs1799853	CYP2C9	warfarin	28,049,362	Dosage	yes	null	Genotype CT is associated with decreased dose of warfarin as compared to genotype CC.	CT	null	null	Is	Associated with	decreased	dose of	null	null	null	null	CC	null
PMC3553682	Impact of Pharmacogenetic Markers of CYP2B6, Clinical Factors, and Drug-Drug Interaction on Efavirenz Concentrations in HIV/Tuberculosis-Coinfected Patients	articles/PMC3553682.md	null	1,183,491,471	rs3211371	CYP2B6	efavirenz	23,254,426	Metabolism/PK	no	No significant difference in plasma concentrations of efavirenz (units = mg/L) were seen between the two genotypes. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment. p-value from univariate analysis with plasma concentration as the dependent variable.	Genotype CC is not associated with clearance of efavirenz in people with HIV Infections as compared to genotype CT.	CC	null	null	Is	Not associated with	null	clearance of	null	in people with	Disease:HIV infectious disease	null	CT	null
PMC4270923	G Protein-Coupled Receptor Kinase 5 Gene Polymorphisms Are Associated with Postoperative Atrial Fibrillation Following Coronary Artery Bypass Graft Surgery in Patients Receiving Beta-Blockers	articles/PMC4270923.md	null	1,451,843,520	rs10787959	GRK5	Beta Blocking Agents	25,049,040	Efficacy	yes	Single-nucleotide polymorphisms in 10 candidate genes were tested for association with atrial fibrillation after coronary artery bypass grafting despite perioperative beta blocker therapy.	Allele A is associated with decreased response to Beta Blocking Agents in people with Coronary Artery Disease as compared to allele G.	A	null	null	Is	Associated with	decreased	response to	null	in people with	Other:Coronary Artery Disease	null	G	null
PMC4557249	Association of serotonin transporter (SLC6A4) & receptor (5HTR1A, 5HTR2A) polymorphisms with response to treatment with escitalopram in patients with major depressive disorder: A preliminary study	articles/PMC4557249.md	null	1,452,040,220	SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)	SLC6A4	escitalopram	26,261,165	Efficacy	no	null	SLC6A4 HTTLPR long form (L allele) is not associated with response to escitalopram Depressive Disorder, Major as compared to SLC6A4 HTTLPR short form (S allele).	HTTLPR long form (L allele)	null	null	Is	Not associated with	null	response to	null	null	Other:Major Depressive Disorder	null	HTTLPR short form (S allele)	null
PMC4220464	Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins	articles/PMC4220464.md	null	1,184,997,431	rs646776	CELSR2	hmg coa reductase inhibitors	25,350,695	Efficacy	yes	Carriers of this SNP respond to statins with an additional 1.5% increase per allele in LDL-C lowering effect compared with non-carriers.	Allele C is associated with increased response to hmg coa reductase inhibitors as compared to allele T.	C	null	null	Is	Associated with	increased	response to	null	null	null	null	T	null
PMC4730664	The role of CYP3A5 polymorphism and dose adjustments following conversion of twice-daily to once-daily tacrolimus in renal transplant recipients	articles/PMC4730664.md	null	1,447,946,747	CYP3A51, CYP3A53	CYP3A5	tacrolimus	26,823,971	Dosage	yes	Patients converting from tacrolimus 2X daily (BID) to once daily (OD). A greater percentage of patients with the 1/1 or 1/3 genotype required some increase in dose following conversion as compared to those with the 3/3 genotype (69% vs 47%). Additionally, the mean dose increase for those with the 1/1 or 1/3 genotype was higher as compared to those with the 3/3 genotype (45.3% vs 26.6%).	CYP3A5 1/1 + 1/3 is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 3/3.	1/1 + 1/3	null	null	Is	Associated with	increased	dose of	null	in people with	Disease:Kidney Transplantation	null	3/3	null
PMC11531276	Pharmacogenomic Study of Selected Genes Affecting Amlodipine Blood Pressure Response in Patients with Hypertension	articles/PMC11531276.md	null	1,452,697,461	rs2239050	CACNA1C	amlodipine	39,492,848	Efficacy	yes	"A strong association between amlodipine response and the SNP rs2239050/CACNA1C was observed in the study participants. Participants carrying the GG genotype had better response/outcomes (P=0.004) when treated with amlodipine than carriers of CC or CG genotypes. After adjusting for confounding factors (age, sex, drug and diet compliance, etc)., no observable changes were noticed in the degree, level, or magnitude of the association. "	Genotype GG is associated with increased clinical benefit to amlodipine in people with Hypertension as compared to genotypes CC + CG.	GG	null	null	Is	Associated with	increased	clinical benefit to	null	in people with	Other:Hypertension	null	CC + CG	null
PMC6313513	Impact of Promoter Polymorphisms on the Transcriptional Regulation of the Organic Cation Transporter OCT1 (SLC22A1)	articles/PMC6313513.md	null	1,452,509,920	rs6935207	SLC22A1	metformin	30,544,975	Metabolism/PK	no	null	Allele A is not associated with clearance of metformin in healthy individuals as compared to allele G.	A	null	null	Is	Not associated with	null	clearance of	null	in healthy individuals	null	null	G	null
PMC3938989	A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS	articles/PMC3938989.md	null	1,183,680,170	rs295137	SPATS2L	salbutamol	23,992,748	Efficacy	no	GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation. This was assessed as a replication attempt for a previously reported association of a different SPATS2L SNP with response to bronchodilators. Bonferroni correction was performed according to the number of SNPs included that are within 50 kb up and downstream of SPATS2L.	Allele C is not associated with response to salbutamol in children with Asthma as compared to allele T.	C	Pediatric	null	Is	Not associated with	null	response to	null	in children with	Disease:Asthma	null	T	null
PMC3248257	The population pharmacokinetics of R- and S-warfarin: effect of genetic and clinical factors	articles/PMC3248257.md	null	827,863,693	CYP2C91, CYP2C93	CYP2C9	warfarin	21,692,828	Other, Metabolism/PK	not stated	For S-Warfarin in a model that included bodyweight, age and sex.	CYP2C9 3 is associated with decreased clearance of warfarin as compared to CYP2C9 1.	*3	null	null	Is	Associated with	decreased	clearance of	null	null	null	null	*1	null
PMC4693492	Personalizing initial calcineurin inhibitor dosing by adjusting to donor CYP3A‐status in liver transplant patients	articles/PMC4693492.md	null	1,446,899,553	rs776746	CYP3A5	cyclosporine, tacrolimus	26,271,661	Dosage, Metabolism/PK	yes	The genotype refers to the genotype of the donor liver. Patients who were recipients of a liver transplantation from a donor with the CC genotype AND low or intermediate CYP3A4 mRNA levels needed a significantly decreased dose of cyclosporine or tacrolimus as compared to patients who whose liver donors had the rs776746 CC genotype AND high CYP3A4 mRNA levels, or rs776746 CT/TT genotypes regardless of CYP3A4 mRNA levels.	Genotype CC is associated with decreased dose of cyclosporine or tacrolimus in people with liver transplantation as compared to genotypes CT + TT.	CC	null	null	Is	Associated with	decreased	dose of	or	in people with	Other:Liver transplantation	null	CT + TT	null
PMC4682920	Impact of IL28B, APOH and ITPA Polymorphisms on Efficacy and Safety of TVR- or BOC-Based Triple Therapy in Treatment-Experienced HCV-1 Patients with Compensated Cirrhosis from the ANRS CO20-CUPIC Study	articles/PMC4682920.md	null	1,447,682,467	rs1801690	APOH	boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir	26,670,100	Efficacy	no	This variant was not significantly associated with SVR to triple therapy including telaprevir or boceprevir in patients with compensated cirrhosis chronically infected with HCV-1.	Allele C is not associated with increased response to boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or telaprevir in people with Hepatitis C, Chronic as compared to allele G.	C	null	null	Is	Not associated with	increased	response to	or	in people with	Disease:Chronic hepatitis C virus infection	null	G	null
PMC3780966	Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide	articles/PMC3780966.md	null	1,183,634,307	rs13223171	CNTNAP2	"diuretics", "hydrochlorothiazide", "Thiazides, plain"	23,753,411	Efficacy	no	Significance was not attained. Observations: 2.89 mm Hg increased reduction of systolic blood pressure per T allele in PEAR + GERA, 1.12 mm Hg decreased reduction of systolic blood pressure per T allele in NORDIL, and 1.59 mm Hg increased reduction of systolic blood pressure per T allele in PEAR + GERA + NORDIL.	Allele T is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.	T	null	null	Is	Not associated with	null	response to	or	in people with	Disease:Hypertension	null	C	null
PMC3100476	Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance	articles/PMC3100476.md	null	981,479,744	rs11631682	null	olanzapine	21,519,338	Metabolism/PK	no	null	Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.	A	null	null	Is	Not associated with	null	clearance of	null	in people with	Disease:Schizophrenia	null	G	null
PMC5904201	Influence of APOA5 Locus on the Treatment Efficacy of Three Statins: Evidence From a Randomized Pilot Study in Chinese Subjects	articles/PMC5904201.md	null	1,449,311,045	rs662799	APOA5	atorvastatin, rosuvastatin, simvastatin	29,695,967	Other	yes	The correlation between APoB concentration and LDL cholesterol before and after treatment changed only slightly for the AG+GG genotypes (before rho = 0.55 p <0.001; after rho = 0.50 p<0.001) but decreased significantly for the AA genotype (before rho = 0.78 p<0.001; after rho 0.44 p<0.001) showing that the absolute reduction of ApoB was much smaller than the statin-induced reduction of LDLc. Please note: alleles have been complemented to the + chromosomal strand.	Genotype AA is associated with response to atorvastatin, rosuvastatin and simvastatin in people with Dyslipidaemia as compared to genotypes AG + GG.	AA	null	null	Is	Associated with	null	response to	and	in people with	Disease:Dyslipidaemia	null	AG + GG	null
PMC9974434	The influence of NUDT15 variants on 6-mercaptopurine-induced neutropenia in Vietnamese pediatric acute lymphoblastic leukemia	articles/PMC9974434.md	null	1,452,035,440	NUDT151, NUDT152, NUDT153, NUDT155, NUDT15*6	NUDT15	mercaptopurine	36,873,097	Dosage	yes	Median 6-MP adjusted dose (mg/m2/day) for IM was 48.7 and NM was 64.3	NUDT15 1/2 + 1/3 + 1/5 + 1/6 (assigned as intermediate metabolizer phenotype) is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to NUDT15 1/1 (assigned as normal metabolizer phenotype) .	1/2 + 1/3 + 1/5 + 1/6	Pediatric	intermediate metabolizer	Is	Associated with	decreased	dose of	null	in children with	Other:Acute lymphoblastic leukemia	null	1/1	normal metabolizer
PMC7308427	Polymorphisms of SLC19A1 80 G>A, MTHFR 677 C>T, and Tandem TS Repeats Influence Pharmacokinetics, Acute Liver Toxicity, and Vomiting in Children With Acute Lymphoblastic Leukemia Treated With High Doses of Methotrexate	articles/PMC7308427.md	null	1,451,552,723	rs1801133	MTHFR	methotrexate	32,612,964	Metabolism/PK	yes	SNP is referred to in the paper as 677 C>T and was mapped to rs1801133 by PharmGKB. Please note that alleles have been complemented to the positive strand.	Genotypes AG + GG are associated with increased steady-state concentration of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.	AG + GG	Pediatric	null	Are	Associated with	increased	steady-state concentration of	null	in children with	Other:Acute lymphoblastic leukemia	null	AA	null
PMC3461952	Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder	articles/PMC3461952.md	null	827,784,977	rs2071427	NR1D1, THRA	lithium	21,781,277	Efficacy	no	The authors describe this as a nominal association which did not survive correction for multiple testing.	Allele T is associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.	T	null	null	Is	Associated with	increased	response to	null	in people with	Disease:Bipolar Disorder	null	C	null
PMC2888980	A Candidate Gene Analysis of Methylphenidate Response in Attention-Deficit/Hyperactivity Disorder	articles/PMC2888980.md	null	1,450,376,375	rs4680	COMT	methylphenidate	19,858,760	Efficacy	no	Scales used to assess response: ADHD-RS-IV, SWAN, and Permanent product Measure of Performance (PERMP). A trend of effect was detected for the COMT variant. significance = p<0.025	Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.	G	Pediatric	null	Is	Not associated with	null	response to	null	in children with	Disease:Attention Deficit Disorder with Hyperactivity	null	A	null
PMC2364178	Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene	articles/PMC2364178.md	null	1,450,950,560	rs3918290	DPYD	fluorouracil	11,953,843	Metabolism/PK	yes	5-fluorouracil activity and DPD activity were compared between one patient with severe fluorouracil-induced toxicity and six control patients with normal 5-fluorouracil-related symptoms. All patients were being treated for colorectal cancer. The index patient was a 60-year-old white female who experienced leukopenia, thrombocytopenia, nausea, diarrhea, stomatitis, fever, hair loss. The control patients experienced mild nausea, vomiting, or grade 1 stomatitis. The clearance was 520 ml/min in the index patient vs 980-1780 mg/min in controls. The area under the curve from 0-3 hours in the index patient was 24.1 mgh/l vs 15.3 mgh/l as the highest value in controls. Sequence analysis revealed the index patient was heterozygous for the *2A (IVS14+1G>A) mutation. Sequence analysis of the six control patients revealed no mutations.	Genotype CT is associated with decreased clearance of fluorouracil in people with Colorectal Neoplasms as compared to genotype CC.	CT	null	null	Is	Associated with	decreased	clearance of	null	in people with	Disease:Colorectal Neoplasms	null	CC	null
PMC10154044	Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV	articles/PMC10154044.md	null	1,452,437,087	rs7570090	RPE	tenofovir	37,098,852	Metabolism/PK	no	Significance threshold was set at 6E-7.	Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.	T	null	null	Is	Not associated with	null	clearance of	null	in people with	Other:HIV infectious disease	null	C	null
PMC2042718	A novel mutant variant of the CYP2D6 gene (CYP2D6 17) common in a black African population: association with diminished debrisoquine hydroxylase activity	articles/PMC2042718.md	null	1,447,990,805	CYP2D61, CYP2D62	CYP2D6	debrisoquine	8,971,426	Metabolism/PK	no	MR of both diplotypes were similar, 1/1(n=12) =0.56 and 1/2 (n=13)=0.59.	CYP2D6 1/2 is not associated with decreased metabolism of debrisoquine in healthy individuals as compared to CYP2D6 1/1.	1/2	null	null	Is	Not associated with	decreased	metabolism of	null	in healthy individuals	null	null	1/1	null
PMC2888980	A Candidate Gene Analysis of Methylphenidate Response in Attention-Deficit/Hyperactivity Disorder	articles/PMC2888980.md	null	1,450,376,338	rs5569	SLC6A2	methylphenidate	19,858,760	Efficacy	no	Scales used to assess response: ADHD-RS-IV, SWAN, and Permanent productMeasure of Performance (PERMP).	Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.	G	Pediatric	null	Is	Not associated with	null	response to	null	in children with	Disease:Attention Deficit Disorder with Hyperactivity	null	A	null
PMC6595468	Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study	articles/PMC6595468.md	null	1,450,374,111	rs3745274	CYP2B6	(R)-methadone	30,907,440	Metabolism/PK	yes	Significance was lost following multivariate analysis.	Genotypes GT + TT are associated with increased concentrations of (R)-methadone in people with Opioid-Related Disorders as compared to genotype GG.	GT + TT	null	null	Are	Associated with	increased	concentrations of	null	in people with	Disease:Opioid-Related Disorders	null	GG	null
PMC2675161	The Pharmacokinetics and Pharmacogenomics of Efavirenz and Lopinavir/Ritonavir in HIV-Infected Persons Requiring Hemodialysis	articles/PMC2675161.md	null	1,448,997,679	rs3745274	CYP2B6	efavirenz	18,784,455	Metabolism/PK	yes	null	Genotypes GT + TT are associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotype GG.	GT + TT	null	null	Are	Associated with	increased	concentrations of	null	in people with	Disease:HIV infectious disease	null	GG	null
PMC3383686	Meta-Analysis on Pharmacogenetics of Platinum-Based Chemotherapy in Non Small Cell Lung Cancer (NSCLC) Patients	articles/PMC3383686.md	null	982,046,476	rs1045642	ABCB1	Platinum compounds	22,761,669	Efficacy	no	When stratified by race, this association was only significant in the Asian population, not in the Caucasian population.	Genotype GG is associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotypes AA + AG.	GG	null	null	Is	Associated with	increased	response to	null	in people with	Disease:Non-Small Cell Lung Carcinoma	null	AA + AG	null
PMC4500328	Physiologically based pharmacokinetic model for 6-mercpatopurine: exploring the role of genetic polymorphism in TPMT enzyme activity	articles/PMC4500328.md	null	1,444,695,511	TPMT poor metabolizer	TPMT	mercaptopurine	25,614,061	Metabolism/PK	not stated	The PK model predicted plasma and tissue concentrations of mercaptopurine and its metabolites, including 6-thioguanine nucleotide, which is responsible for its activity and toxicity, with the use of various factors, including TPMT phenotypes.	TPMT poor metabolizer is associated with increased concentrations of mercaptopurine as compared to TPMT normal metabolizer.	null	null	poor metabolizer	Is	Associated with	increased	concentrations of	null	null	null	null	null	normal metabolizer
PMC2733171	Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study	articles/PMC2733171.md	null	982,038,082	rs2854116	APOC3	fenofibrate	19,057,464	Efficacy	no	No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate. Please note alleles have been complemented to the plus chromosomal strand.	Genotypes CC + CT are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype TT.	CC + CT	null	null	Are	Not associated with	null	response to	null	in people with	Disease:Hypertriglyceridemia	null	TT	null
PMC4794377	Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy	articles/PMC4794377.md	null	1,447,677,231	rs1062033	CYP19A1	hdl cholesterol	26,463,708	Other	yes	when taking letrozole and lipid lowering agents (LLA), such as statins. Data are from a sub-analysis of the Exemestane and Letrozole Pharmacogenomics (ELPh) study, where post-menopausal women with early stage breast cancer were randomized to receive exemestane or letrozole. Of the 303 eligible women, 160 were randomized to the letrozole group, 52 of whom were also taking LLA. This SNP was associated with increases in HDL-cholesterol of 6.9 mg/dL (SE 1.5).	Allele G is associated with increased concentrations of hdl cholesterol in women with Breast Neoplasms and Menopause as compared to allele C.	G	null	null	Is	Associated with	increased	concentrations of	null	in women with	Disease:Breast Neoplasms, Disease:Menopause	and	C	null
PMC2853591	CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease	articles/PMC2853591.md	null	982,043,670	rs2740574	CYP3A4	amlodipine	19,907,160	Efficacy	no	No significant change in the likelihood of a patient reaching a target mean arterial pressure concentration of <= 92 mmHg or <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.	Genotypes CT + TT are not associated with response to amlodipine in people with Hypertension as compared to genotype CC.	CT + TT	null	null	Are	Not associated with	null	response to	null	in people with	Disease:Hypertension	null	CC	null
PMC3633658	Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration (AMD) in the Comparison of AMD Treatments Trials (CATT)	articles/PMC3633658.md	null	1,183,491,546	rs1061170	CFH	bevacizumab, ranibizumab	23,337,555	Efficacy	no	No significant differences in mean visual acuity (units = letters), mean visual acuity change from baseline (units = letters), >= 15-letter increase from baseline (%), mean number of injections, retinal thickness (%, units = um), mean change in total foveal thickness from baseline (units = um), dry on optical coherence tomography (%), leakage on fluorescein angiography (%) or mean change in lesion size from baseline (units = disc area) after 1 year of treatment were seen between genotypes. p <= 0.01 was considered statistically significant to adjust for multiple comparisons.	Genotype CC is not associated with response to bevacizumab or ranibizumab in people with Macular Degeneration as compared to genotypes CT + TT.	CC	null	null	Is	Not associated with	null	response to	or	in people with	Disease:Macular Degeneration	null	CT + TT	null
PMC6734474	CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA	articles/PMC6734474.md	null	1,451,104,838	rs4354668	SLC1A2	botulinum toxin type a	31,014,225	Efficacy	no	No significant difference in allele frequency between responders and non-responders.	Allele G is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele T.	G	null	null	Is	Not associated with	null	response to	null	in women with	Other:Migraine disorder	null	T	null
PMC7292331	Association between the rs7583431 single nucleotide polymorphism close to the activating transcription factor 2 gene and the analgesic effect of fentanyl in the cold pain test	articles/PMC7292331.md	null	1,449,716,020	rs268214	ATF2	fentanyl	30,106,255	Dosage	no	null	Allele C is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele T.	C	null	null	Is	Not associated with	null	dose of	null	in people with	Disease:Pain, Postoperative	null	T	null
PMC5074472	Pharmacokinetics of Bupropion and Its Pharmacologically Active Metabolites in Pregnancy	articles/PMC5074472.md	null	1,448,257,516	CYP2B61, CYP2B66	CYP2B6	bupropion	27,528,039	Metabolism/PK	no	The AUC of steady state was compared.	CYP2B6 6 is associated with increased steady-state concentration of bupropion in women with Pregnancy as compared to CYP2B6 1.	*6	null	null	Is	Associated with	increased	steady-state concentration of	null	in women with	Disease:Pregnancy	null	*1	null
PMC8915292	Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers	articles/PMC8915292.md	null	1,451,727,971	rs17847029	CYP2C9	AR-C124910XX, ticagrelor	35,280,252	Metabolism/PK	no	from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance	Genotype CT is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype CC.	CT	null	null	Is	Not associated with	decreased	concentrations of	or	in healthy individuals	null	null	CC	null
PMC6448146	Influence of Genetic Variants on Steady-State Etonogestrel Concentrations Among Contraceptive Implant Users	articles/PMC6448146.md	null	1,450,375,853	rs2461817	NR1I2	etonogestrel	30,870,275	Efficacy, Metabolism/PK	no	Corrected P-value cutoff of 5.0E-4 was not met.	Allele C is associated with increased steady-state concentration of etonogestrel in women as compared to allele A.	C	null	null	Is	Associated with	increased	steady-state concentration of	null	in women	null	null	A	null
PMC4612590	Pharmacogenetic Pathway Analysis of Docetaxel Elimination	articles/PMC4612590.md	null	1,448,107,849	rs776746	CYP3A5	docetaxel	18,509,327	Metabolism/PK	yes	The T allele corresponds with CYP3A51. The presence of the CYP3A51A allele was associated with a 49% (P = 0.020) increase in docetaxel clearance.	Allele T is associated with increased clearance of docetaxel in people with Neoplasms as compared to allele C.	T	null	null	Is	Associated with	increased	clearance of	null	in people with	Disease:Neoplasms	null	C	null
PMC4640545	Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients	articles/PMC4640545.md	null	1,447,678,311	rs2298771	SCN1A	carbamazepine	26,555,147	Metabolism/PK	no	In none of the measures that the authors used to measure exposure showed any association with the genotype. Please note: alleles have been complemented to the + chromosomal strand.	Genotype CC is not associated with metabolism of carbamazepine in people with Epilepsy as compared to genotypes CT + TT.	CC	null	null	Is	Not associated with	null	metabolism of	null	in people with	Disease:Epilepsy	null	CT + TT	null
PMC3769669	A published pharmacogenetic algorithm was poorly predictive of tacrolimus clearance in an independent cohort of renal transplant recipients	articles/PMC3769669.md	null	1,183,699,984	CYP3A51, CYP3A53	CYP3A5	tacrolimus	23,305,195	Metabolism/PK	yes	Genotype 1/3 vs 3/3 was reported. Clearance was estimated using the dose-normalized whole-blood trough concentration. The DeKAF algorithm was tested but it failed to predict tacrolimus clearance in this cohort.	CYP3A5 1/3 is associated with increased clearance of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 3/3.	1/3	null	null	Is	Associated with	increased	clearance of	null	in people with	Disease:Kidney Transplantation	null	3/3	null
PMC4928097	Association of HLA-DRB1 Haplotypes With Rheumatoid Arthritis Severity, Mortality, and Treatment Response	articles/PMC4928097.md	null	1,451,934,500	HLA-DRB1*04:01	HLA-DRB1	adalimumab, etanercept, infliximab	25,919,528	Efficacy	yes	Valine at position 11 (VKA haplotype is *04:01 based on table 1 in 22286218 with His at position 13 - position 13 not considered in this publication) was associated with better European League Against Rheumatism (EULAR) response to TNF inhibitor therapy (OR, 1.23 [95% CI, 1.06- 1.43]) 0.007.	HLA-DRB1 *04:01 is associated with increased response to adalimumab, etanercept or infliximab in people with Arthritis, Rheumatoid.	*04:01	null	null	Is	Associated with	increased	response to	or	in people with	Other:Rheumatoid arthritis	null	null	null
PMC4025175	The influence of CYP3A, PPARA, and POR genetic variants on the pharmacokinetics of tacrolimus and cyclosporine in renal transplant recipients	articles/PMC4025175.md	null	1,184,470,380	rs1057868	POR	tacrolimus	24,658,827	Metabolism/PK	yes	A single steady-state concentration of tacrolimus was collected for each patient 2-7 wks post-transplant and compared to dose of tacrolimus administered to patients at Oslo University Hospital. Reported concentrations are "steady-state dose-adjusted concentration" of tacrolimus. Steady-state is defined as at least 3 days after last dose adjustment for Tac and 4 days for cyclosporine.	Allele T is associated with increased metabolism of tacrolimus in people with Kidney Transplantation as compared to allele C.	T	null	null	Is	Associated with	increased	metabolism of	null	in people with	Other:Kidney Transplantation	null	C	null
PMC8915292	Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers	articles/PMC8915292.md	null	1,451,729,346	rs28371759	CYP3A4	AR-C124910XX, ticagrelor	35,280,252	Metabolism/PK	no	from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance	Genotype AG is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype AA.	AG	null	null	Is	Not associated with	decreased	concentrations of	or	in healthy individuals	null	null	AA	null
PMC2903324	Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741	articles/PMC2903324.md	null	1,451,155,365	rs10929302	UGT1A1	fluorouracil, irinotecan, oxaliplatin	20,530,282	Efficacy	no	Patients were taking either IFL (irinotecan + fluorouracil + leucovorin; n=114), FOLFOX (fluorouracil + oxaliplatin + leucovorin; n=299) or IROX (irinotecan + oxaliplatin; n=107). No significant association was seen between this variant and confirmed response rate in any of the treatment groups OR all treatment groups considered together. Significance level was set at 0.01. rs10929302 is reported as UGT1A193 (UGT1A1 93/93 is not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to UGT1A1 1/1 + 1/*93).	Genotype AA is not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to genotypes AG + GG.	AA	null	null	Is	Not associated with	null	response to	or	in people with	Disease:Colorectal Neoplasms	null	AG + GG	null
PMC10967865	Impact of Pharmacogenetic Testing on Clozapine Treatment Efficacy in Patients with Treatment-Resistant Schizophrenia	articles/PMC10967865.md	null	1,452,852,980	rs762551	CYP1A2	clozapine	38,540,209	Metabolism/PK	yes	"A significant difference in pharmacokinetic parameters was associated with the polymorphism of CYP1A2 gene encoding the main enzyme related to the metabolism of CLZ. Patient smokers (>7 cigarettes/day) with the 1F/1F genotype for the CYP1A2 gene had significant differences according to CLZ plasma levels and C/D CLZ (p = 0.029 and p = 0.034, respectively) versus 1/1F and 1/1 genotypes. Patients with 1F/1F (n = 49) showed lower values with significant differences between the smoker (n = 20) and non-smoker (n = 29) population according to CLZ dose, C/D total, C/D CLZ, and C/D NCLZ (p = 0.002, p = 0.035, p = 0.046, and p = 0.032, respectively)." Annotation done on rs762551 (-163C>A). PharmVar released an updated CYP1A2 nomenclature 12/2024. At this point, -163 C>A was included in 26 core alleles with *30 being the SNP by itself. The 25 other core alleles include the -163 C>A SNP in addition to amino acid changes.	Genotype AA is associated with decreased exposure to clozapine in people with Schizophrenia and Tobacco Use Disorder as compared to genotypes AC + CC.	AA	null	null	Is	Associated with	decreased	exposure to	null	in people with	Other:Schizophrenia, Other:Tobacco Use Disorder	and	AC + CC	null
PMC3657889	Cytochrome P450 (CYP2C92,3) & vitamin-K epoxide reductase complex (VKORC1 -1639G<A) gene polymorphisms & their effect on acenocoumarol dose in patients with mechanical heart valve replacement	articles/PMC3657889.md	null	1,444,705,544	CYP2C91, CYP2C93	CYP2C9	acenocoumarol	23,481,074	Dosage	yes	The CYP2C92, 3 and VKORC1 rs9923231 are analyzed together. Patients carrying any of the variant alleles was 34% among those receiving a low dose of =20 mg/wk while it was 13.8 per cent in those receiving >20 mg/wk (P=0.014).	CYP2C9 3 is associated with decreased dose of acenocoumarol as compared to CYP2C9 1.	*3	null	null	Is	Associated with	decreased	dose of	null	null	null	null	*1	null
PMC4484731	TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives	articles/PMC4484731.md	null	1,444,703,722	rs9590353	UGGT2	hydrochlorothiazide	25,695,618	Efficacy	no	The SNP was discovered in two independent cohorts, although no SNPs reached genome wide significance. The authors then considered P<1 x10^-5 as a threshold for significance (based on the results from a Q-Q plot distribution reference line). Using this revised threshold the authors reported that this SNP was associated with a lower decrease in diastolic blood pressure after hydrochlorothiazide treatment.	Allele G is associated with decreased response to hydrochlorothiazide in people with Essential hypertension as compared to allele T.	G	null	null	Is	Associated with	decreased	response to	null	in people with	Disease:Essential hypertension	null	T	null
PMC5980466	Population pharmacokinetics and pharmacogenomics of apixaban in Japanese adult patients with atrial fibrillation	articles/PMC5980466.md	null	1,449,191,990	rs1045642	ABCB1	apixaban	29,457,840	Metabolism/PK	no	null	Genotypes AA + AG are not associated with clearance of apixaban in people with Atrial Fibrillation as compared to genotype GG.	AA + AG	null	null	Are	Not associated with	null	clearance of	null	in people with	Disease:Atrial Fibrillation	null	GG	null
PMC4631184	In vivo assessment of the metabolic activity of CYP2D6 diplotypes and alleles	articles/PMC4631184.md	null	1,444,711,202	CYP2D6 intermediate metabolizers	CYP2D6	endoxifen	25,907,378	Metabolism/PK	yes	The patients of the cohort (83% White, 15% Black) were genotype with AmpliChip CYP450 test. The variations used to define the star alleles are not reported. The diplotypes of the patients are not reported. The alleles found in the cohort are not explicit reported but graphic 3 shows 1, 2, 35, 9, 10, 17, 29, and 41. The study included UMs and PM but no CYP2D6 star allele is reported for those phenotypes. 1, 2, 35 are grouped as active alleles and any combination of these defines the extensive metabolizer. 9, 10, 17, 29, and 41 are grouped as reduced function alleles. The article subgroups the IMs into EM/IM, EM/PM, IM/IM, IM/PM.	CYP2D6 intermediate metabolizer is associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 normal metabolizer.	null	null	intermediate metabolizer	Is	Associated with	decreased	concentrations of	null	in women with	Disease:Breast Neoplasms	null	null	normal metabolizer
PMC3922978	Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment	articles/PMC3922978.md	null	1,450,815,024	rs2636719	PPA2	risperidone	23,241,943	Efficacy	yes	The number of G alleles present in a patient was positively associated with CGI-S score. Please note that this variant is in high linkage disequilibrium with rs2636697.	Allele A is associated with decreased response to risperidone in people with Schizophrenia as compared to allele C.	A	null	null	Is	Associated with	decreased	response to	null	in people with	Other:Schizophrenia	null	C	null
PMC5583388	Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects	articles/PMC5583388.md	null	1,450,376,581	rs5569	SLC6A2	methylphenidate	28,871,191	Efficacy	no	Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).	Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.	G	Pediatric	null	Is	Not associated with	null	response to	null	in children with	Disease:Attention Deficit Disorder with Hyperactivity	null	A	null
PMC5423974	Pharmacokinetics and pharmacogenetics of the MEK1/2 inhibitor, selumetinib, in Asian and Western healthy subjects: a pooled analysis	articles/PMC5423974.md	null	1,448,613,426	rs2231142	ABCG2	selumetinib	28,283,692	Metabolism/PK	no	Not associated with AUC, AUC0-12 when allele was assessed within ethnic groups (Asian, White, Black) and when all ethnic groups were pooled together. Only P-values for AUC presented here.	Allele T is not associated with metabolism of selumetinib in healthy individuals as compared to allele G.	T	null	null	Is	Not associated with	null	metabolism of	null	in healthy individuals	null	null	G	null
PMC5600689	Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus	articles/PMC5600689.md	null	1,448,821,794	rs4149056	SLCO1B1	efavirenz	28,718,515	Metabolism/PK	no	null	Genotypes CC + CT are not associated with concentrations of efavirenz in children with HIV Infections as compared to genotype TT.	CC + CT	Pediatric	null	Are	Not associated with	null	concentrations of	null	in children with	Disease:HIV infectious disease	null	TT	null
PMC5538123	Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients	articles/PMC5538123.md	null	1,450,928,296	rs6311	HTR2A	risperidone	28,696,411	Efficacy	no	null	Allele C is not associated with response to risperidone in people with Schizophrenia as compared to allele T.	C	null	null	Is	Not associated with	null	response to	null	in people with	Other:Schizophrenia	null	T	null
PMC6612579	Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome‐Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2	articles/PMC6612579.md	null	1,450,807,049	rs28845026	null	anastrozole	30,648,747	Metabolism/PK	yes	The minor allele of this variant was associated with increased plasma concentrations of anastrozole in postmenopausal women with ER+ breast cancer.	Allele T is associated with increased concentrations of anastrozole in women with Breast Neoplasms as compared to allele C.	T	null	null	Is	Associated with	increased	concentrations of	null	in women with	Disease:Breast Neoplasms	null	C	null
PMC5583388	Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects	articles/PMC5583388.md	null	1,450,376,612	rs6551665	ADGRL3	methylphenidate	28,871,191	Efficacy	no	Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).	Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.	G	Pediatric	null	Is	Not associated with	null	response to	null	in children with	Disease:Attention Deficit Disorder with Hyperactivity	null	A	null
PMC5789875	Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder	articles/PMC5789875.md	null	1,449,166,088	rs4902333	CHURC1	methylphenidate	29,382,897	Efficacy	no	The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.	Allele T is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.	T	Pediatric	null	Is	Associated with	increased	response to	null	in people with	Disease:Attention Deficit Disorder with Hyperactivity	null	null	null
PMC3093392	Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response	articles/PMC3093392.md	null	1,451,161,642	CYP2C91, CYP2C92, CYP2C9*3	CYP2C9	methadone	21,589,866	Dosage	no	No significant difference in methadone dose between genotypes. No details about which specific variants/alleles were tested for.	CYP2C9 1/3 + 2/2 + 2/3 + 3/3 are not associated with dose of methadone in people with Opioid-Related Disorders as compared to CYP2C9 1/1 + 1/2.	1/3 + 2/2 + 2/3 + 3/3	null	null	Are	Not associated with	null	dose of	null	in people with	Other:Opioid-Related Disorders	null	1/1 + 1/2	null
PMC5943457	Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis	articles/PMC5943457.md	null	1,449,557,998	rs5836788	null	methotrexate	29,743,634	Efficacy	no	null	Allele del is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.	del	null	null	Is	Not associated with	null	response to	null	in people with	Disease:Rheumatoid arthritis	null	C	null
PMC5346878	Tacrolimus dose requirements in paediatric renal allograft recipients are characterized by a biphasic course determined by age and bone maturation	articles/PMC5346878.md	null	1,449,171,382	CYP3A71A, CYP3A71C	CYP3A7	tacrolimus	27,966,227	Metabolism/PK	yes	Dose-corrected tacrolimus exposure (AUC0-12/doseBW).	CYP3A7 1A/1A is associated with decreased concentrations of tacrolimus in children with Kidney Transplantation as compared to CYP3A7 1A/1C + 1C/1C.	1A/1A	Pediatric	null	Is	Associated with	decreased	concentrations of	null	in children with	Disease:Kidney Transplantation	null	1A/1C + 1C/1C	null
PMC5323433	Polymorphisms in drug-metabolizing enzymes and steady-state exemestane concentration in post-menopausal patients with breast cancer	articles/PMC5323433.md	null	1,448,489,015	CYP3A41, CYP3A422	CYP3A4	exemestane	27,549,341	Metabolism/PK	yes	The *22 allele was associated with a 54% greater exemestane concentration, and remained significant after adjustment for covariates.	CYP3A4 1/22 is associated with increased concentrations of exemestane in women with Breast Neoplasms as compared to CYP3A4 1/1.	1/22	null	null	Is	Associated with	increased	concentrations of	null	in women with	Disease:Breast Neoplasms	null	1/1	null
PMC10967865	Impact of Pharmacogenetic Testing on Clozapine Treatment Efficacy in Patients with Treatment-Resistant Schizophrenia	articles/PMC10967865.md	null	1,452,852,900	rs762551	CYP1A2	clozapine	38,540,209	Efficacy	yes	CYP1A2 1F/1F is associated with decreased clinical benefit to clozapine in people with Schizophrenia. "CYP1A2 rs7625521 also demonstrated a significant association with the Brief Negative Symptom Scale (BNSS) expression factor subscale (p = 0.007) between 1F and 1 allele. Patients with the 1F/1F genotype were associated with a significant worsening of expression factor subscale (p = 0.037). No association with BNSS overall score, BNSS Motivation and Pleasure Factor score, PANSS-positive score, Wellbeing (SWEMWBS) score, or Genal functioning (GAF) score." "...impaired emotional expressivity is more prominently observed in patients carrying the 1F/1F genotype as compared to patients with at least one wild type allele for CYP1A2 (1 allele), potentially associated with a reduction in metabolism, leading to a poorer response." The quote has a typo that is in the paper, the correct rs number should be rs762551. Annotation done on rs762551 (-163C>A). PharmVar released an updated CYP1A2 nomenclature 12/2024. At this point, -163 C>A was included in 26 core alleles with 30 being the SNP by itself. The 25 other core alleles include the -163 C>A SNP in addition to amino acid changes.	Genotype AA is associated with decreased clinical benefit to clozapine in people with Schizophrenia as compared to genotypes AC + CC.	AA	null	null	Is	Associated with	decreased	clinical benefit to	null	in people with	Other:Schizophrenia	null	AC + CC	null
PMC6179259	KIF6 gene as a pharmacogenetic marker for lipid-lowering effect in statin treatment	articles/PMC6179259.md	null	1,449,748,103	rs20455	KIF6	atorvastatin, simvastatin	30,304,062	Efficacy	yes	Please note that alleles have been complemented to the positive strand.	Genotype GG is associated with decreased response to atorvastatin or simvastatin in people with Hypercholesterolemia as compared to genotype AA.	GG	null	null	Is	Associated with	decreased	response to	or	in people with	Disease:Hypercholesterolemia	null	AA	null
PMC2715837	G-Protein-Coupled Receptor Kinase 4 Polymorphisms and Blood Pressure Response to Metoprolol Among African Americans: Sex-Specificity and Interactions	articles/PMC2715837.md	null	827,864,092	rs1801058	GRK4	metoprolol	19,119,263	Efficacy	no	Note; TT (V486) homozygotes were excluded. Response was measured by time to reach a mean arterial pressure of < or = 107 mm Hg.	Genotype CT is not associated with decreased response to metoprolol in men with hypertensive nephrosclerosis as compared to genotype CC.	CT	null	null	Is	Not associated with	decreased	response to	null	in men with	Disease:hypertensive nephrosclerosis	null	CC	null
PMC11512548	Effect of donor GSTM3 rs7483 genetic variant on tacrolimus elimination in the early period after liver transplantation	articles/PMC11512548.md	null	1,452,689,000	rs7483	GSTM3	tacrolimus	39,465,171	Metabolism/PK	yes	Alleles complemented. This was seen only for donor not recipient: For donor "Tac C/D ratios of donor GSTM3 rs7483 AA genotype were 231.0 ± 164.9, 127.3 ± 73.6, 120.4 ± 82.4 and 116.1 ± 71.1 at weeks 1, 2, 3 and 4 respectively. For AG and GG genotype carriers, the corresponding Tac C/D ratios at each time point were 328.2 ± 243.6, 195.1 ± 146.6, 213.4 ± 219.6 and 235.20 ± 180.3. The differences were significant (p = 0.035, 0.010, 0.035, 0.002, respectively)."	Genotype TT is associated with decreased concentrations of tacrolimus in people with Liver transplantation as compared to genotypes CC + CT.	TT	null	null	Is	Associated with	decreased	concentrations of	null	in people with	Other:Liver transplantation	null	CC + CT	null
PMC10085626	Novel and replicated clinical and genetic risk factors for toxicity from high-dose methotrexate in pediatric acute lymphoblastic leukemia	articles/PMC10085626.md	null	1,452,008,029	rs2306283	SLCO1B1	methotrexate	36,764,694	Metabolism/PK	not stated	"The G allele of rs2306283, which causes a missense mutation in SLCO1B1, demonstrated a; decreased risk for prolonged clearance"	Allele G is associated with increased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele A.	G	Pediatric	null	Is	Associated with	increased	clearance of	null	in children with	Other:Acute lymphoblastic leukemia	null	A	null
PMC2830602	The impact of SLCO1B1 polymorphisms on the plasma concentration of lopinavir and ritonavir in HIV-infected men	articles/PMC2830602.md	null	1,451,114,672	rs11045819	SLCO1B1	lopinavir, ritonavir	20,078,617	Metabolism/PK	no	No significant association between this variant and trough concentrations of lopinavir or ritonavir in HIV patients treated with lopinavir/ritonavir. Variant referred to in the paper as 463C>A.	Allele A is not associated with trough concentration of lopinavir or ritonavir in men with HIV Infections as compared to allele C.	A	null	null	Is	Not associated with	null	trough concentration of	or	in men with	Other:HIV infectious disease	null	C	null
PMC4171106	Genetic Variants in Transcription Factors Are Associated With the Pharmacokinetics and Pharmacodynamics of Metformin	articles/PMC4171106.md	null	1,444,668,331	rs784888	SP1	metformin	24,853,734	Metabolism/PK	yes	null	Allele G is associated with decreased clearance of metformin in healthy individuals as compared to allele C.	G	null	null	Is	Associated with	decreased	clearance of	null	in healthy individuals	null	null	C	null
PMC4541974	Impact of CYP2C19 polymorphism on the pharmacokinetics of nelfinavir in patients with pancreatic cancer	articles/PMC4541974.md	null	1,444,698,605	CYP2C191, CYP2C192	CYP2C19	nelfinavir	25,752,914	Metabolism/PK	yes	All patients were genotyped for CYP2C19 by RFLP analysis. Female and male patients were initially administered 750 or 900 mg/m2 gemcitabine IV over 30 min, 50 mg/m2 leucovorin IV over 30 min, and 2700 mg/m2 5-FU IV over 24 hours on day 1 weekly for 2 of 3 weeks for three cycles (day 1-63). Oral nelfinavir was given at 625 mg or 1250 mg twice daily for 3 weeks starting 2 weeks prior to initiation of radiation (days 56-75). 625 mg is better tolerated and preferred by patients. 1250 mg is the standard dose of nelfinavir when used to treat HIV patients. Differences in Cmax (mean) between genotype groups was only seen in the 1250 mg dose and not in the 650 mg dose. The AUC (0-12), terminal half-life, total body clearance (CLT/F) and apparent volume of distribution of nelfinavir (VD/F)did not significantly different between CYP2C19 genotype group.	CYP2C19 1/2 is associated with increased concentrations of nelfinavir in people with Pancreatic Neoplasms as compared to CYP2C19 1/1.	1/2	null	null	Is	Associated with	increased	concentrations of	null	in people with	Disease:Pancreatic Neoplasms	null	1/1	null
PMC10529681	Pharmacogenetics and Pharmacokinetics of Tamoxifen in a Zimbabwean breast cancer cohort	articles/PMC10529681.md	null	1,452,139,860	CYP2D6 intermediate metabolizer	CYP2D6	endoxifen	37,337,448	Metabolism/PK	yes	"The common phenotype; group was that of the normal metabolizers (NM), which was 67.5%. However, intermediate; metabolizers (IMs) had quite a significant frequency of 27.5%, while the frequency of; ultrarapid metabolizers (UMs) was 5%. There were no CYP2D6 poor metabolizers in this; study." Authors used CPIC phenotype classifications. "55.0% were post-menopausal women" "All the recruited; participants were female except 1 who was male." "Most of the breast cancer patients had a late diagnosis with at least; stage 3A breast cancer at diagnosis (64.9%)"	CYP2D6 intermediate metabolizer is associated with decreased concentrations of endoxifen in people with Breast Neoplasms as compared to CYP2D6 normal metabolizer.	null	null	intermediate metabolizer	Is	Associated with	decreased	concentrations of	null	in people with	Other:Breast Neoplasms	null	null	normal metabolizer
PMC3093079	Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients	articles/PMC3093079.md	null	1,444,710,945	CYP2C91, CYP2C93	CYP2C9	4-hydroxytamoxifen, endoxifen, N-desmethyltamoxifen, tamoxifen	21,480,951	Metabolism/PK	no	Patients (pre- (83%) and postmenopausal (17%)) with ER and/or PR positive breast tumors, which received 20 mg tamoxifen daily. Patients taking CYP2D6 inhibitors were excluded. DNA extracted from blood.	CYP2C9 3 is not associated with concentrations of 4-hydroxytamoxifen, endoxifen, n-desmethyltamoxifen and tamoxifen in women with Breast Neoplasms as compared to CYP2C9 1.	*3	null	null	Is	Not associated with	null	concentrations of	and	in women with	Disease:Breast Neoplasms	null	*1	null
PMC10951231	Individualized atomoxetine response and tolerability in children with ADHD receiving different dosage regimens: the need for CYP2D6 genotyping and therapeutic drug monitoring to dance together	articles/PMC10951231.md	null	1,452,428,860	CYP2D6*10	CYP2D6	atomoxetine	38,504,095	Metabolism/PK	yes	"CYP2D6 IMs exhibited significantly higher atomoxetine C/D values than EMs under the three dosing regimens" The regimens were qm (once morning), bid (twice daily) and qn (once nightly). Study measured CYP2D62, CYP2D610, and CYP2D614 and grouped 10/*10 as intermediate. There was only one PM that was excluded from analysis.	CYP2D6 10/10 (assigned as intermediate metabolizer phenotype) is associated with increased exposure to atomoxetine in children with Attention Deficit Disorder with Hyperactivity as compared to CYP2D6 normal metabolizer.	10/10	Pediatric	intermediate metabolizer	Is	Associated with	increased	exposure to	null	in children with	Other:Attention Deficit Disorder with Hyperactivity	null	null	normal metabolizer
PMC4669157	HLA-G 3’UTR Polymorphisms Impact the Prognosis of Stage II-III CRC Patients in Fluoropyrimidine-Based Treatment	articles/PMC4669157.md	null	1,447,678,780	rs17179108	HLA-G	capecitabine, fluorouracil	26,633,805	Efficacy	yes	The authors examined disease free survival (DFS) as well as overall survival (OS). The CT genotype was associated with improved DFS, but not OS.	Genotype CT is associated with increased response to capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotype CC.	CT	null	null	Is	Associated with	increased	response to	or	in people with	Disease:Colorectal Neoplasms	null	CC	null
PMC3291838	Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters	articles/PMC3291838.md	null	982,046,688	rs12714145	GGCX	phenprocoumon	21,110,013	Dosage, Metabolism/PK	no	Daily dose of phenprocoumon is not significantly associated with this SNP. Daily dose is negatively correlated with age. This study published an algorithm for daily dose that includes height, although height was not significant in univariate analysis. This SNP is also not significantly associated with phenprocoumon concentration.	Genotype CC is not associated with increased dose of phenprocoumon as compared to genotypes CT + TT.	CC	null	null	Is	Not associated with	increased	dose of	null	null	null	null	CT + TT	null
PMC3100476	Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance	articles/PMC3100476.md	null	981,479,862	rs17161981	CYP3A43	olanzapine	21,519,338	Metabolism/PK	no	null	Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.	A	null	null	Is	Not associated with	null	clearance of	null	in people with	Disease:Schizophrenia	null	G	null
PMC10557961	Influence of CYP450 Enzymes and ABCB1 Polymorphisms on Clopidogrel Response in Moroccan Patients with Acute Coronary Syndromes	articles/PMC10557961.md	null	1,452,272,060	CYP2C19 normal metabolizer	CYP2C19	clopidogrel	37,810,546	Efficacy	no	"Patients were subdivided into clopidogrel responder (PRU≤208) and clopidogrel non-responder group (PRU>208), 19 patients (34.55%) were clopidogrel non-responders, whereas 36 patients (65.45%) were clopidogrel responders. " "The tested alleles CYP2C93, Cyp2C192, Cyp2C193, CYP3A422, and CYP3A5*2 were not found in our study population"	CYP2C19 normal metabolizer is not associated with increased response to clopidogrel in people with Acute coronary syndrome as compared to CYP2C19 rapid metabolizer.	null	null	normal metabolizer	Is	Not associated with	increased	response to	null	in people with	Other:Acute coronary syndrome	null	null	rapid metabolizer
PMC11758033	Sodium channel mutation SCN1A T875M, D188V and associated dysfunction with drug resistant epilepsy	articles/PMC11758033.md	null	1,452,856,366	rs121917953	SCN1A	antiepileptics	39,974,498	Efficacy	yes	"The AT genotype exhibited significantly higher risk association with drug resistance with an odds ratio of 3.51 (95%CI = 1.256-3.826 and a P value = 0.017; Table 3)." AA also had increased risk but not significant. grouped p value not shown. Drug regimens not specified	Genotypes AA + AT is associated with increased resistance to antiepileptics in people with Epilepsy as compared to genotype TT.	AA + AT	null	null	Is	Associated with	increased	resistance to	null	in people with	Other:Epilepsy	null	TT	null
PMC10154044	Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV	articles/PMC10154044.md	null	1,452,437,097	rs7841320	null	tenofovir	37,098,852	Metabolism/PK	no	Significance threshold was set at 6E-7.	Allele A is not associated with clearance of tenofovir in people with HIV Infections as compared to allele G.	A	null	null	Is	Not associated with	null	clearance of	null	in people with	Other:HIV infectious disease	null	G	null
PMC6510382	VKORC1 and Novel CYP2C9 Variation Predict Warfarin Response in Alaska Native and American Indian People	articles/PMC6510382.md	null	1,450,370,787	CYP2C91, CYP2C93	CYP2C9	warfarin	30,821,933	Dosage	no	in Alaska Native and American Indian People.	CYP2C9 3 is not associated with decreased dose of warfarin as compared to CYP2C9 1/*1.	*3	null	null	Is	Not associated with	decreased	dose of	null	null	null	null	1/1	null
PMC2652833	A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose	articles/PMC2652833.md	null	827,641,885	rs2108622	CYP4F2	warfarin	19,300,499	Dosage	yes	null	Allele T is associated with increased dose of warfarin as compared to allele C.	T	null	null	Is	Associated with	increased	dose of	null	null	null	null	C	null
PMC5908314	Pharmacogenetics-based area-under-curve model can predict efficacy and adverse events from axitinib in individual patients with advanced renal cell carcinoma	articles/PMC5908314.md	null	1,449,310,602	rs2032582	ABCB1	axitinib	29,682,213	Metabolism/PK	yes	The authors develop a prediction model and calculated area under the concentration curve (AUC) using 6 SNPs (rs17868323, rs3832043, rs2231142, rs2032582, rs1045642, rs35305980) was compared with actual AUC in 16 patients prospectively which significantly correlated with the objective response rate (P = 0.0002), hand-foot syndrome, P = 0.0055 and hypothyroidism, P = 0.0381, and correlated with actual AUC (P < 0.0001) - the validation study, calculated AUC prior to axitinib treatment precisely predicted actual AUC after axitinib treatment (P = 0.0066).	Allele T is associated with concentrations of axitinib in people with Carcinoma, Renal Cell as compared to allele C.	T	null	null	Is	Associated with	null	concentrations of	null	in people with	Disease:Renal Cell Carcinoma	null	C	null
PMC7260086	OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study	articles/PMC7260086.md	null	1,451,407,809	rs16918875	OPRK1	butorphanol	31,806,881	Efficacy	no	Study-wide significance was set to p<0.017.	Allele A is not associated with response to butorphanol in healthy individuals as compared to allele G.	A	null	null	Is	Not associated with	null	response to	null	in healthy individuals	null	null	G	null
PMC5323433	Polymorphisms in drug-metabolizing enzymes and steady-state exemestane concentration in post-menopausal patients with breast cancer	articles/PMC5323433.md	null	1,448,496,262	rs10012	CYP1B1	exemestane	27,549,341	Metabolism/PK	no	No significant difference in exemestane concentrations were seen between the three genotypes. Please note that alleles have been complemented to the plus chromosomal strand.	Genotypes CC + CG are not associated with concentrations of exemestane in women with Breast Neoplasms as compared to genotype GG.	CC + CG	null	null	Are	Not associated with	null	concentrations of	null	in women with	Disease:Breast Neoplasms	null	GG	null
PMC3621996	Dramatic improvement of myotonia permanens with flecainide: a two-case report of a possible bench-to-bedside pharmacogenetics strategy	articles/PMC3621996.md	null	1,183,682,419	rs80338792	SCN4A	flecainide	23,052,413	Efficacy	not stated	This case study showed two patients (mother and son) who both had the same genetic variant (presented in the paper as SCN4A G1306E) causing myotonia permanens. After years of poor response to mexiletine, patients were switched to flecainide and saw huge improvements. This suggests that patients with this myotonia permanens causing variation may benefit more from treatment with flecainide than mexilitine.	Allele T is associated with increased response to flecainide in people with Myotonia as compared to allele C.	T	null	null	Is	Associated with	increased	response to	null	in people with	Disease:Myotonia	null	C	null
PMC11475898	Early CYP3A5 Genotype-Based Adjustment of Tacrolimus Dosage Reduces Risk of De Novo Donor-Specific HLA Antibodies and Rejection among CYP3A5-Expressing Renal Transplant Patients	articles/PMC11475898.md	null	1,452,648,018	CYP3A51, CYP3A53	CYP3A5	tacrolimus	39,410,605	Dosage	yes	"However, CYP3A5 expressers required tacrolimus dosages 2-fold higher during follow-up and exhibited significantly lower C/D ratios than did nonexpressers. We detected no significant differences between expressers and nonexpressers in the incidence of delayed graft function, rejection, CNI nephrotoxicity, and development of de novo anti-HLA antibodies and de novo DSAs after the follow-up period of 2 years. Renal allograft function was also well preserved in both groups during follow-up." Only *3 was measured.	CYP3A5 1/1 + 1/3 is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 3/3.	1/1 + 1/3	null	null	Is	Associated with	increased	dose of	null	in people with	Other:Kidney Transplantation	null	3/3	null
PMC7963143	Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial	articles/PMC7963143.md	null	1,451,113,980	rs9322447	OPRM1	naltrexone	31,206,155	Efficacy	no	No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.	Allele G is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele A.	G	null	null	Is	Not associated with	null	response to	null	in people with	Other:Tobacco Use Disorder	null	A	null
PMC2733171	Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study	articles/PMC2733171.md	null	982,038,126	rs11216158	APOA1	fenofibrate	19,057,464	Efficacy	no	No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate.	Genotypes AA + AG are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype GG.	AA + AG	null	null	Are	Not associated with	null	response to	null	in people with	Disease:Hypertriglyceridemia	null	GG	null
PMC4836090	Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway	articles/PMC4836090.md	null	1,447,983,326	rs2299267	PON2	antidepressants	27,091,189	Efficacy	yes	Identity of minor allele not specified, so minor allele of dbSNP used here (G). Response considered to be successful with a 50% reduction at discharge of the Hamilton Rating Scale for Depression (HRSD17). Patients measured at admission and discharge, 4-6 weeks later. Specific antidepressants not listed.	Allele G is associated with decreased response to antidepressants in people with Depressive Disorder, Major as compared to allele A.	G	null	null	Is	Associated with	decreased	response to	null	in people with	Disease:Major Depressive Disorder	null	A	null
PMC2830602	The impact of SLCO1B1 polymorphisms on the plasma concentration of lopinavir and ritonavir in HIV-infected men	articles/PMC2830602.md	null	1,451,114,660	rs4149056	SLCO1B1	ritonavir	20,078,617	Metabolism/PK	no	No significant association between this variant and trough concentrations of ritonavir in HIV patients treated with lopinavir/ritonavir. Variant referred to in the paper as 521T>C.	Allele C is not associated with trough concentration of ritonavir in men with HIV Infections as compared to allele T.	C	null	null	Is	Not associated with	null	trough concentration of	null	in men with	Other:HIV infectious disease	null	T	null
PMC6734474	CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA	articles/PMC6734474.md	null	1,451,104,967	rs1800497	DRD2	botulinum toxin type a	31,014,225	Efficacy	no	No significant difference in allele frequency between responders and non-responders. Please note that alleles have been complemented to the positive strand.	Allele A is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele G.	A	null	null	Is	Not associated with	null	response to	null	in women with	Other:Migraine disorder	null	G	null
PMC4833150	Genetic markers in CYP2C19 and CYP2B6 for prediction of cyclophosphamide's 4‐hydroxylation, efficacy and side effects in Chinese patients with systemic lupus erythematosus	articles/PMC4833150.md	null	1,446,907,717	rs13059232	NR1I2	cyclophosphamide	26,456,622	Metabolism/PK	no	This SNP had a small effect on cyclophosphamide (CPA) metabolite plasma concentrations (4-OH-CPA), but did not reach significance (Bonferroni corrected p-value= 0.0056).	Allele C is not associated with metabolism of cyclophosphamide in people with as compared to allele T.	C	null	null	Is	Not associated with	null	metabolism of	null	in people with	null	null	T	null
PMC3476140	Association study between clinical response to rizatriptan and some candidate genes	articles/PMC3476140.md	null	1,452,551,194	rs1799732	DRD2	rizatriptan	17,563,839	Efficacy	no	No significant difference in allele frequency between responders and non-responders to rizatriptan. Variant referred to in the paper as DRD2-BstNI and mapped to rs1799732 by PharmGKB.	Allele G is not associated with response to rizatriptan in people with Migraine without Aura as compared to allele del.	G	null	null	Is	Not associated with	null	response to	null	in people with	Other:Migraine without Aura	null	del	null
PMC11418302	CYP2C19 genotype and sodium channel blockers in lacosamide-treated children with epilepsy: two major determinants of trough lacosamide concentration or clinical response	articles/PMC11418302.md	null	1,452,616,160	CYP2C19 normal metabolizer	CYP2C19	lacosamide	39,314,259	Metabolism/PK	yes	"Patients with the NM phenotype exhibited lower drug exposure levels when compared to the IM and PM groups (β = −0.189, p < 0.001; Table 2). This pattern held true in the add-on therapy group as well, with NM individuals displaying lower exposure levels than IM and PM groups (β = −0.374, p < 0.001; Table 3)."	CYP2C19 normal metabolizer is associated with decreased exposure to lacosamide in children with Epilepsy as compared to CYP2C19 intermediate metabolizer and poor metabolizer.	null	Pediatric	normal metabolizer	Is	Associated with	decreased	exposure to	null	in children with	Other:Epilepsy	null	null	intermediate metabolizer and poor metabolizer
PMC4669157	HLA-G 3’UTR Polymorphisms Impact the Prognosis of Stage II-III CRC Patients in Fluoropyrimidine-Based Treatment	articles/PMC4669157.md	null	1,447,678,633	rs1710	HLA-G	capecitabine, fluorouracil	26,633,805	Efficacy	no	The authors examined disease free survival (DFS) as well as overall survival (OS). Neither were significantly associated with any genotype.	Genotype GG is not associated with response to capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotypes CC + CG.	GG	null	null	Is	Not associated with	null	response to	or	in people with	Disease:Colorectal Neoplasms	null	CC + CG	null
PMC10532907	Pharmacogenetic Variants Associated with Fluoxetine Pharmacokinetics from a Bioequivalence Study in Healthy Subjects	articles/PMC10532907.md	null	1,452,260,760	rs1065852	CYP2D6	fluoxetine	37,763,120	Metabolism/PK	yes	"The CYP2D6*10 haplotype, related to decreased CYP2D6 function (poor drug metabolism), was found in only one volunteer (subject 25), based on CYP2D6 rs1065852 (haplotype A/A) and rs11358490 (haplotype C/C). As shown in Table 2, t1/2 was three times higher (106.9 h) for this subject than the overall mean (31.02 h). AUCs and t1/2 were statistically different between genotypes of CYP2D6 rs1065852 (p < 0.001). Stratification of subjects based on CYP2D6 genotypes confirmed the difference in the PK profiles, based on the three SNVs found in this study (rs1065852, rs1135840, and rs28371703)"	Allele A is associated with increased half-life time of fluoxetine in healthy individuals as compared to allele G.	A	null	null	Is	Associated with	increased	half-life time of	null	in healthy individuals	null	null	G	null
PMC5505550	Efficacy of piroxicam for postoperative pain after lower third molar surgery associated with CYP2C8*3 and CYP2C9	articles/PMC5505550.md	null	1,448,820,083	rs1799853	CYP2C9	piroxicam	28,740,425	Efficacy	not stated	Subjects had at least one impacted lower third molar extracted. Measurements were taken of 1) postoperative mouth opening (millimeters) was measured pre- and post-op on days 2 & 7 2) and swelling measurements due to edema were recorded and 3) subjective measures of pain. None were associated with the genotype.	Allele T is not associated with response to piroxicam as compared to allele C.	T	null	null	Is	Not associated with	null	response to	null	null	null	null	C	null
PMC3978988	Lack of association between plasma levels of non-nucleoside reverse transcriptase inhibitors & virological outcomes during rifampicin co-administration in HIV-infected TB patients	articles/PMC3978988.md	null	1,448,993,476	rs3745274	CYP2B6	efavirenz	24,521,642	Metabolism/PK	yes	null	Genotype TT is associated with increased concentrations of efavirenz in people with HIV Infections and Tuberculosis as compared to genotypes GG + GT.	TT	null	null	Is	Associated with	increased	concentrations of	null	in people with	Disease:HIV infectious disease, Disease:Tuberculosis	and	GG + GT	null
PMC3780966	Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide	articles/PMC3780966.md	null	1,183,633,740	rs2432742	CSMD3	"diuretics", "hydrochlorothiazide", "Thiazides, plain"	23,753,411	Efficacy	no	There was a trend in results but significance was not attained. Observations: 2.52 mm Hg increased reduction of diastolic blood pressure per A allele in PEAR + GERA, 0.07 mm Hg decreased reduction of diastolic blood pressure per A allele in NORDIL (small, opposite direction effect), and 1.57 mm Hg increased reduction of diastolic blood pressure per A allele in PEAR + GERA + NORDIL.	Allele A is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele G.	A	null	null	Is	Not associated with	null	response to	or	in people with	Disease:Hypertension	null	G	null
PMC7393710	Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence	articles/PMC7393710.md	null	1,451,359,269	rs5320	DBH	heroin	32,736,537	Efficacy	no	No significant association between this variant and strength of euphoria on first heroin use.	Allele A is not associated with response to heroin as compared to allele G.	A	null	null	Is	Not associated with	null	response to	null	null	null	null	G	null
PMC3985268	Variation in P450 oxidoreductase (POR) A503V and flavin containing monooxygenase (FMO)-3 E158K is associated with minor alterations in nicotine metabolism but does not alter cigarette consumption	articles/PMC3985268.md	null	1,183,703,328	rs1057868	POR	nicotine	24,448,396	Metabolism/PK	yes	Participants received 4 mg oral nicotine. 3HC/COT was measured.	Genotypes CT + TT is associated with increased metabolism of nicotine in CYP2A6 normal, but not reduced, metabolizers as compared to genotype CC.	CT + TT	null	null	Is	Associated with	increased	metabolism of	null	in	PK:CYP2A6 normal, but not reduced, metabolizers	null	CC	null
PMC4585967	Pharmacogenetics of Complement Factor H Y402H Polymorphism and Treatment of Neovascular AMD with Anti-VEGF Agents: A Meta-Analysis	articles/PMC4585967.md	null	1,446,902,514	rs1061170	CFH	bevacizumab, ranibizumab	26,411,831	Efficacy	yes	Neovascular age-related macular degeneration. Meta-analysis with 13 studies. Anti-VEGF treatment was much less effective in patients with the CC genotype as compared to those with the CT or TT genotype. Significant results were also seen when considering exclusively Caucasians, though no significant results were seen when considering exclusively East Asians. 10 of the 13 studies defined a positive outcome from anti-VEGF therapy as improvement in visual function (visual acuity), while the remaining three define it as an improvement in retinal morphology (resolution of macular edema). A sub-analysis was done on studies only considering response as improvement in visual acuity, with significant results.	Genotype CC is associated with decreased response to bevacizumab and ranibizumab in people with Macular Degeneration as compared to genotypes CT + TT.	CC	null	null	Is	Associated with	decreased	response to	and	in people with	Disease:Macular Degeneration	null	CT + TT	null

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AutoGKB Annotation Benchmark

Dataset Description

The AutoGKB Annotation Benchmark is a comprehensive dataset designed to evaluate models' ability to extract pharmacogenomic variant-drug associations from scientific literature. This ground truth values for this data were compiled by reviewers from PharmGKB. This benchmark addresses the critical need for automated systems that can identify genetic variants, associated drugs, and their clinical relationships from biomedical texts.

Dataset Summary

This dataset contains 4,516 annotations extracted from 1,431 unique scientific papers (PMIDs), covering a wide range of pharmacogenomic relationships. Each annotation includes detailed information about genetic variants, drugs, phenotype categories, population specifics, and statistical associations. The goal of this dataset is to benchmark the process of extracting information a PubMed paper on pharmacogenomics. The annotation system should be able to understand and extract the key information that is represented in the dataset.

Languages

The dataset is in English (en).

Dataset Structure

Data Instances

Each example contains:

Core annotation fields: Variant, gene, drug, PMID, phenotype category
Association details: Significance, direction of effect, comparison data
Population information: Specialty populations, metabolizer types
Full text: Complete scientific article in markdown format

Example:

{
  "pmcid": "PMC6714673",
  "article_title": "Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients",
  "article_path": "articles/PMC6714673.md",
  "article_text": "# Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients\n\n## Abstract\n\nWarfarin is a commonly used anticoagulant...",
  "variant_annotation_id": 1449192282,
  "variant_haplotypes": "rs1799853",
  "gene": "CYP2C9",
  "drugs": "warfarin",
  "pmid": 28049362,
  "phenotype_category": "Dosage",
  "significance": "yes",
  "sentence": "Genotype CT is associated with decreased dose of warfarin as compared to genotype CC.",
  "alleles": "CT",
  "is_is_not_associated": "Associated with",
  "direction_of_effect": "decreased",
  "pd_pk_terms": "dose of",
  "comparison_alleles_or_genotypes": "CC"
}

Data Fields

Core Fields

pmcid: PubMed Central identifier of the source article
article_title: Title of the source scientific article
article_path: Relative path to the article file (markdown format)
article_text: Full text of the scientific article in markdown format
variant_annotation_id: Unique identifier for each annotation
variant_haplotypes: Genetic variant identifier (e.g., rs numbers, haplotypes)
gene: Gene symbol (e.g., CYP2D6, ABCB1)
drugs: Drug name(s) involved in the association
pmid: PubMed identifier of the source article

Phenotype Information

phenotype_category: Type of effect (Efficacy, Toxicity, Dosage, Metabolism/PK, etc.)
significance: Statistical significance (yes/no/not stated)
sentence: Key sentence describing the association
notes: Additional context or study details

Association Details

is_is_not_associated: Whether variant is associated with outcome
direction_of_effect: Direction of association (increased/decreased)
pd_pk_terms: Pharmacodynamic/pharmacokinetic terms
alleles: Specific alleles involved

Population Context

specialty_population: Specific patient populations
population_types: General population categories
population_phenotypes_or_diseases: Diseases or conditions
metabolizer_types: CYP metabolizer classifications

Comparison Data

comparison_alleles_or_genotypes: Reference genotypes for comparison
comparison_metabolizer_types: Reference metabolizer types

Data Splits

Split	Annotations	Unique Papers
Train	3,124	1,001
Validation	796	215
Test	596	215

Total: 4,516 annotations across 1,431 papers

Dataset Creation

Curation Rationale

This benchmark was created to address the growing need for automated pharmacogenomic knowledge extraction. With the rapid expansion of pharmacogenomic literature, manual curation becomes increasingly challenging. This dataset provides a standardized evaluation framework for developing and comparing automated extraction systems.

Source Data

Initial Data Collection and Normalization

The dataset is derived from peer-reviewed scientific publications in the pharmacogenomics domain. Articles were selected based on their content related to genetic variant-drug associations and clinical outcomes.

Who are the source language producers?

The source texts are scientific articles authored by researchers in pharmacogenomics, clinical pharmacology, and related biomedical fields, published in peer-reviewed journals.

Annotations

Annotation process

Annotations were created by domain experts following a comprehensive schema covering:

Genetic variant identification and standardization
Drug name normalization
Phenotype categorization using controlled vocabularies
Population and study context extraction
Statistical association characterization

Who are the annotators?

The annotations were created by experts in pharmacogenomics and biomedical informatics with specialized knowledge in genetic variant-drug associations.

Personal and Sensitive Information

The dataset contains only published scientific literature and does not include personal or sensitive information about individuals.

Considerations for Using the Data

Social Impact of Dataset

This dataset supports the development of automated systems for pharmacogenomic knowledge extraction, which can:

Accelerate precision medicine: Enable faster identification of clinically relevant variant-drug associations
Support clinical decision-making: Facilitate evidence-based prescribing decisions
Advance research: Enable large-scale analysis of pharmacogenomic literature

Discussion of Biases

Potential biases in the dataset may include:

Publication bias: Overrepresentation of statistically significant results
Population bias: Uneven representation of different ethnic populations in source studies
Drug bias: Focus on commonly studied drugs and variants
Temporal bias: Emphasis on more recent research publications

Other Known Limitations

Coverage: Represents approximately 33.6% of original pharmacogenomic annotations from the source database
Language: Limited to English-language publications
Domain scope: Focused specifically on pharmacogenomics, may not generalize to other biomedical domains
Text quality: Depends on the quality of PDF-to-text conversion for source articles

Additional Information

Dataset Curators

AutoGKB Team

Licensing Information

This dataset is released under the Apache License 2.0.

Citation Information

@misc{autogkb_annotation_benchmark_2025,
  title={AutoGKB Annotation Benchmark},
  author={Shlok Natarajan},
  year={2025},
  note={A benchmark for pharmacogenomic variant-drug annotation extraction from scientific literature}
}

Contributions

This dataset contributes to the biomedical NLP community by providing:

A standardized benchmark for pharmacogenomic information extraction
High-quality annotations with detailed schema
Full-text articles paired with structured annotations
Evaluation metrics and baseline models for comparison

Usage Examples

Loading the Dataset

from datasets import load_dataset

# Load the dataset from Hugging Face Hub
dataset = load_dataset("autogkb/autogkb-annotation-benchmark")

# Access different splits
train_data = dataset["train"]
val_data = dataset["validation"] 
test_data = dataset["test"]

# Example: Get all efficacy-related annotations
efficacy_examples = train_data.filter(
    lambda x: "Efficacy" in x["phenotype_category"]
)

# Example: Access article text for a specific annotation
first_example = train_data[0]
print(f"PMC ID: {first_example['pmcid']}")
print(f"Article Title: {first_example['article_title']}")
print(f"Gene: {first_example['gene']}")
print(f"Drug: {first_example['drugs']}")
print(f"Full Article Text: {first_example['article_text'][:500]}...")

Evaluation

The dataset includes evaluation scripts for measuring:

Field-level exact match accuracy
Overall accuracy across core fields
Phenotype-specific performance

# Run baseline model
python baseline_model.py val baseline_predictions.tsv

# Evaluate predictions
python evaluate.py baseline_predictions.tsv val/annotations.tsv --output results.json

File Structure

autogkb/
├── articles/             # Full article texts in markdown format
│   ├── PMC10038974.md
│   ├── PMC10085626.md
│   └── ...              # 1,431 articles total
├── train.jsonl          # Training annotations (3,124 examples)
├── val.jsonl            # Validation annotations (796 examples)
├── test.jsonl           # Test annotations (596 examples)
├── autogkb_annotation_benchmark.py  # HuggingFace dataset script
├── dataset_infos.json   # Dataset metadata
├── dataset_statistics.json  # Dataset statistics
├── LICENSE              # Apache 2.0 license
└── README.md           # This file

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