shlokn/autogkb huggingface dataset:
Article: Nephrotoxicity in a Patient With Inadequate Pain Control: Potential Role of Pharmacogenetic Testing for Cytochrome P450 2D6 and Apolipoprotein L1
Gene: CYP2D6
Variant/haplotype: CYP2D6*5, CYP2D6*17
Drug(s): hydrocodone, tramadol
Phenotype category: Efficacy
Significant: not stated
Association: CYP2D6 *5/*17 is associated with decreased response to hydrocodone or tramadol in women.
Notes: Case report of a patient with back pain who reported no analgesic effect of either hydrocodone or tramadol.
Article: UGT1A4*3 polymorphism influences serum concentration and therapeutic effect of lamotrigine for epilepsy treatment: A meta-analysis
Gene: UGT1A4
Variant/haplotype: UGT1A4*3b
Drug(s): lamotrigine
Phenotype category: Efficacy
Significant: yes
Association: UGT1A4 *3b is associated with decreased clinical benefit to lamotrigine.
Notes: "Only three studies [28, 29], involving 308 patients, reported the therapeutic efficacy of LTG based on UGT1A4*3 polymorphism. No statistical heterogeneity existed among the article results (I 2 = 0%). There was significant difference between individuals with TT genotype and the control group in the therapeutic effect of LTG (OR: 7.18, 95% [4.01, 12.83], P<0.00001) (Fig 4). The results indicated that the therapeutic effect of LTG with TT genotype was better than that with TG/GG." Mapped *3 to *3b since appears to be based on one SNP whereas 3a has 3 SNPs. *3b is rs2011425 G, with the reference T at that locus.
Article: Influence of NAT2 Polymorphisms on Sulfamethoxazole Pharmacokinetics in Renal Transplant Recipients
Gene: NAT2
Variant/haplotype: NAT2*4, NAT2*6, NAT2*7, NAT2*16
Drug(s): sulfamethoxazole
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 *4/*4 (assigned as rapid acetylator phenotype) is associated with increased metabolism of sulfamethoxazole in people with Kidney Transplantation as compared to NAT2 *16/*6 + *6/*6 + *6/*7 + *7/*7 (assigned as slow acetylator phenotype) .
Notes: As measured by plasma sulfamethoxazole AUC 0-24. Originally annotated as "compared to NAT2 *5D/*6B + *6B/*6B + *6B/*7A + *7A/*7A (assigned as slow acetylator phenotype)". Please note; this was combined analysis of rapid acetylators vs slow acetylators. Slow acetylators; genotype *5/*6, *6/*6, *6/*7, *7/*7). Rapid acetylators; genotype *4/*4. There was no significant difference with intermediate acetylators. Genotyped 3 SNPs; *5 (T341C, rs1801280), *6  (G590A, rs1799930), *7 (G857A, rs1799931).; The arylamine N-acetyltransferases (NATs) database was transitioned into the PharmVar database in March 2024. The alleles in this annotation are mapped as following: NAT2*5D under the *16 core allele; NAT2*6B under the *6 core allele; NAT2*7A under the *7 core allele.
Article: Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins
Gene: LPA
Variant/haplotype: rs10455872
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to hmg coa reductase inhibitors as compared to allele A.
Notes: Carriers of this variant respond to statins with a 5.9% smaller LDL-C lowering per minor allele compared with non-carriers.
Article: Genome-wide study of methotrexate clearance replicates SLCO1B1
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): methotrexate
Phenotype category: Efficacy, Toxicity, Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele G.
Notes: This association was found in patients already stratified for rs4149056 genotype.
Article: Pharmacogenetic interactions between antiretroviral drugs and vaginally-administered hormonal contraceptives
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype TT is associated with decreased metabolism of efavirenz in women with HIV Infections as compared to genotype GG.
Notes: Analysis was done as CYP2B6 slow metabolizer genotypes grouping (15582CC-516TT-983TT; 9: 15582CC-516GT- 983CT; or 10: 15582CC-516GG-983CC), which  were associated with higher plasma efavirenz log10 AUC0–8 hours, log10 maximum concentration (Cmax), and log10 minimum concentration (Cmin) values at days 0 and 21.
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: P2RX7
Variant/haplotype: rs1718119
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele G.
Notes: No significant difference in allele frequency between responders and non-responders. Please note that alleles have been complemented to the positive strand.
Article: Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus
Gene: SLC22A2
Variant/haplotype: rs316019
Drug(s): sulfonamides, urea derivatives
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to sulfonamides, urea derivatives in people with Diabetes Mellitus as compared to allele C.
Article: A phase I/II pharmacokinetic and pharmacogenomic study of calcitriol in combination with cisplatin and docetaxel in advanced non-small-cell lung cancer
Gene: CYP24A1
Variant/haplotype: rs3787554
Drug(s): calcitriol, cisplatin, docetaxel
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to calcitriol, cisplatin and docetaxel in people with Carcinoma, Non-Small-Cell Lung as compared to allele A.
Notes: No association was seen with overall survival or progression-free survival. Please note alleles have been complemented to the plus chromosomal strand.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: NR1I2
Variant/haplotype: rs7643645
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype GG.
Notes: Genotypes of AA, AG and GG did not influence donepezil clearance in a covariate model.
Article: Large‐Scale Gene‐Centric Analysis Identifies Polymorphisms for Resistant Hypertension
Gene: ATP2B1
Variant/haplotype: rs12817819
Drug(s): Antihypertensives
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased resistance to Antihypertensives in people with Coronary Artery Disease or Hypertension as compared to genotype CC.
Notes: 45,573 SNPs included in association analysis with resistant hypertension (RHTN) in European Americans and Hispanics from the INVEST cohort. Statistical threshold of p=2.6 x 10^-6 used. No SNP achieved this threshold, but the top signal from a meta-analysis of the European American and Hispanic INVEST cohorts was rs12817819. There was a 57% to 76% increase in risk for RHTN for each additional copy of the T allele. To replicate this association, it was tested in a different cohort (Women's Ischemia Syndrome Evaluation (WISE)); there was a consistent trend for this SNP and RHTN, though it did not achieve statistical significance. However, chip-wide significance was achieved in a meta-analysis of both INVEST cohorts and the WISE cohort. No evidence of heterogeneity was seen across the 3 studies. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: NR1I2
Variant/haplotype: rs3814055
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased clearance of carbamazepine in people with Epilepsy as compared to allele C.
Notes: This association was only significant in the African American patients and not in Caucasian patients.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: GGCX
Variant/haplotype: rs699664
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotypes CT + TT are not associated with dose of warfarin in people with heart valve replacement as compared to genotype CC.
Notes: 158/220 patients had the target INR (1.5–2.5). The comparison of weekly warfarin maintenance dose was among patients of different genotypes. Differences in maintenance dose were not observed in patients with variant genotypes of GGCX rs699664.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs142155704
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of vancomycin as compared to allele A.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Outcomes of methotrexate therapy for psoriasis and relationship to genetic polymorphisms
Gene: ATIC
Variant/haplotype: rs2372536
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in people with Psoriasis as compared to allele G.
Notes: 250 responders; 80 non-responders. Bonferroni-corrected p > 0.05
Article: Genetic variants in NECTIN4 encoding an adhesion molecule are associated with continued opioid use
Gene: NECTIN4
Variant/haplotype: rs11265549
Drug(s): methadone
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with decreased dose of methadone in people with Opioid-Related Disorders as compared to genotypes AG + GG.
Notes: rs11265549 was found to be in high linkage disequilibrium with rs3892375 and rs12116949 and was selected to be the tag SNP for all three variants.
Article: Race/ethnicity difference in the pharmacogenetics of bilirubin-related atazanavir discontinuation
Gene: UGT1A1
Variant/haplotype: rs887829
Drug(s): atazanavir
Phenotype category: Toxicity
Significant: no
Association: Genotype TT is not associated with increased discontinuation of atazanavir as compared to genotype CC.
Notes: risk to for bilirubin-related atazanavir discontinuation
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: OSMR
Variant/haplotype: rs74378198
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele A.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Capability of Utilizing CYP3A5 Polymorphisms to Predict Therapeutic Dosage of Tacrolimus at Early Stage Post-Renal Transplantation
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: Those with the CT and TT genotypes ("extensive metabolizers") had a higher body weight-adjusted dose of tacrolimus on day 28 after transplant as compared to those with the CC genotype ("poor metabolizers"; p<0.001). However, no significant result was seen when considering trough concentrations (p=0.481). Additionally, in multiple linear regression analysis, CYP3A5 genotype was significantly associated with dose on days 14, 21 and 28 post-transplant. The contribution of CYP3A5 genotype increased from 7.2% on day 14 to 18.4% and 20.4% on days 21 and 28 respectively. Lastly, patients with the extensive metabolizer genotype had a lower achievement rate of trough concentrations in the target range on days 7 and 14 post-transplant (p=0.011 and p=0.001, respectively). More specifically, extensive metabolizers had trough concentrations lower than the target range on days 7 and 14.
Article: Novel SNP in CYP2C9 is associated with changes in warfarin clearance and CYP2C9 expression levels in African Americans
Gene: CYP2C9
Variant/haplotype: rs7089580
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AT is associated with increased dose of warfarin as compared to genotype AA.
Article: No significant influence of OCT1 genotypes on the pharmacokinetics of morphine in adult surgical patients
Gene: SLC22A1
Variant/haplotype: rs34059508
Drug(s): morphine
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of morphine in people with Pain, Postoperative as compared to allele G.
Notes: Analyzed as part of haplotypes with rs12208357, rs72552763 and rs34130495. No significant association between haplotypes and PCA doses of morphine.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DDC
Variant/haplotype: rs12666409
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to heroin as compared to allele T.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: Pharmacogenetics of Naltrexone And Disulfiram in Alcohol Dependent, Dually Diagnosed Veterans
Gene: DBH
Variant/haplotype: rs1611115
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to naltrexone in men with Alcoholism as compared to genotype CC.
Notes: Veterans. Two-thirds had a lifetime history of major depressive disorder, 37% had a lifetime history of post-traumatic stress disorder. 65% took SSRIs and 39% took anticonvulsants. 84-day treatment period. Patients who carried the T allele had more abstinence from heavy drinking days as compared to those with the CC genotype. Note that heavy drinking days was defined as more than four standard drinks in a day.
Article: Effects of CYP2C19 Loss-of-Function Variants on the Eradication of H. pylori Infection in Patients Treated with Proton Pump Inhibitor-Based Triple Therapy Regimens: A Meta-Analysis of Randomized Clinical Trials
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): esomeprazole, lansoprazole, omeprazole, rabeprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 are associated with decreased response to esomeprazole, lansoprazole, omeprazole or rabeprazole in people with Helicobacter Infections as compared to CYP2C19 *2/*2 + *2/*3 + *3/*3.
Notes: Subjects with the *1/*2 or *1/*3 genotype had a significantly lower eradication rate of Helicobacter pylori (H. pylori), as compared to those with the *2/*2, *2/*3 or *3/*3 genotype. This was a meta-analysis and included 16 studies. Patients were treated with the drugs anywhere from 7-14 days, and also received antibiotics as part of triple therapy: either amoxicillin and clarithromycin, amoxicillin and metronidazole, or amoxicillin and levofloxacin.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: AQP2
Variant/haplotype: rs3759125
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: COMT Val158Met, BDNF Val66Met, and OPRM1 Asn40Asp and Methamphetamine Dependence Treatment Response: Preliminary Investigation
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): modafinil
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to modafinil in people with methamphetamine dependence as compared to allele A.
Notes: No significant association between this variant and Treatment Effectiveness Scores following modafinil treatment compared to placebo.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs129882
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of heroin in people with Heroin Dependence as compared to allele C.
Article: CYP2B6 G516T Polymorphism but Not Rifampin Coadministration Influences Steady-State Pharmacokinetics of Efavirenz in Human Immunodeficiency Virus-Infected Patients in South India
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotypes GG + GT.
Article: Combinatorial Pharmacogenetic Interactions of Bucindolol and β1, α2C Adrenergic Receptor Polymorphisms
Gene: ADRB1
Variant/haplotype: rs1801253
Drug(s): bucindolol
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to bucindolol in people with Heart Failure as compared to genotypes CG + GG.
Notes: This SNP was mainly referred to as an Arg>Gly amino acid change at position 389, with the Arg amino acid resulting in better patient outcome. This study was interested in the effect of this SNP in tandem with rs61767072. Patients homozygous for the Arg amino acid showed significantly less occurrences of all cause mortality, cardiac transplant, or heart failure hospitalizations as compared to other patients. Patients carrying the Gly amino acid but were homozygous for the wildtype allele at rs61767072 responded worse than those that were homozygous for wildtype allele at this SNP, but much better than patients carrying the variant allele at both SNPs. Patients carrying the variant allele at both SNPs and were treated with bucindolol had worse outcomes than those that were given a placebo.
Article: Allelic Variant in the Glucagon-Like Peptide 1 Receptor Gene Associated with Greater Effect of Liraglutide and Exenatide on Gastric Emptying: A Pilot Pharmacogenetics Study
Gene: GLP1R
Variant/haplotype: rs6923761
Drug(s): exenatide, liraglutide
Phenotype category: PD
Significant: no
Association: Genotypes AA + AG is associated with increased response to exenatide or liraglutide in people with Obesity as compared to genotype GG.
Notes: "A allele of GLP1R (rs6923761) is associated with a greater delay in gastric emptying in response to treatment with GLP-1 agonists."
Article: No major role of norepinephrine transporter gene variations in the cardiostimulant effects of MDMA
Gene: SLC6A2
Variant/haplotype: rs47958
Drug(s): 3,4-methylenedioxymethamphetamine
Phenotype category: Other
Significant: no
Association: Allele C is not associated with response to 3,4-methylenedioxymethamphetamine as compared to allele A.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: COMT
Variant/haplotype: rs4680
Drug(s): morphine
Phenotype category: Efficacy
Significant: not stated
Association: Genotype AA is associated with decreased response to morphine in healthy individuals as compared to genotypes AG + GG.
Notes: Nominally significant difference in ischemic pain threshold between genotype groups, but this association was not seen in other pain modalities. Study-wide significance was set to p<0.017.
Article: Nuclear receptor gene polymorphisms and warfarin dose requirements in the Quebec Warfarin Cohort
Gene: VDR
Variant/haplotype: rs4760658
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of warfarin as compared to genotypes AA + AG.
Notes: This SNP is in very tight linkage disequilibrium with rs11168293 and rs11168292 (r2>0.97). Mean dose (in mg) of warfarin according to genotype was: GG>AG>AA. p-value adjusted for CYP2C9 metabolizer status and VKORC1 activity status phenotypes, among other factors. Warfarin dose requirement was defined as the reported daily dose at 3 months following treatment initiation.
Article: Disposition of debrisoquine and nortriptyline in Korean subjects in relation to CYP2D6 genotypes, and comparison with Caucasians
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*10
Drug(s): debrisoquine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *1/*10 is associated with decreased metabolism of debrisoquine in healthy individuals as compared to CYP2D6 *1/*1.
Notes: There was a difference found between AUC (0-8) of 4-hydroxydebrisoquine, which was significantly lower in *1/*10 than in *1/*1, but no other differences were found for debrisoquine and none were found for nortriptyline in this sample.
Article: Multiple regulatory variants modulate expression of 5-hydroxytryptamine 2A receptors in human cortex
Variant/haplotype: rs585719
Drug(s): citalopram
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to citalopram in people with Depression as compared to genotype CC.
Notes: This was only true in African Americans and was attributed to LD with rs76665058.  No TT were seen in this cohort.
Article: The largest prospective warfarin-treated cohort supports genetic forecasting
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with dose of warfarin.
Notes: This SNP explained 30% (P = 9.82 x 10(-100)) of the variation in warfarin dose. The direction of the allele:dose relationship is not stated.
Article: Effects of rs958804 and rs7858836 single‐nucleotide polymorphisms of the ASTN2 gene on pain‐related phenotypes in patients who underwent laparoscopic colectomy and mandibular sagittal split ramus osteotomy
Gene: ASTN2
Variant/haplotype: rs7858836
Drug(s): fentanyl
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT are associated with decreased dose of fentanyl in people with Pain, Postoperative as compared to genotype CC.
Notes: This variant was found to be in moderate LD with rs958804. p<0.025 was considered to be statistically significant.
Article: Pharmacodynamic and kinetic effect of rabeprazole on serum gastrin level in relation to CYP2C19 polymorphism in Chinese Hans
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): rabeprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*2 + *1/*3 is not associated with response to rabeprazole in healthy individuals as compared to CYP2C19 *2/*2.
Notes: No significant differences in median 24 hour intragastric pH or serum gastrin area under the concentration-time curve from 0-24 hours (AUC0-24) were seen between the two genotype groups. Subjects were given rabeprazole for 8 days; 24 hour intragastric pH and serum gastrin AUC were measured on day 1 and day 8 after rabeprazole administration. Please note that the *2 and *3 alleles were referred to by their previous designations (CYP2C19*m1 and *m2, respectively).