shlokn/autogkb huggingface dataset:
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ALDH1L1
Variant/haplotype: rs2886059
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: 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.
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: rs2762939
Drug(s): calcitriol, cisplatin, docetaxel
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is associated with increased response to calcitriol, cisplatin and docetaxel in people with Carcinoma, Non-Small-Cell Lung as compared to genotypes CC + CG.
Notes: The GG genotype was correlated with stable disease and partial response.
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1A
Variant/haplotype: rs2276332
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: Pharmacokinetic-Pharmacodynamic interaction associated with venlafaxine-XR remission in patients with major depressive disorder with history of citalopram / escitalopram treatment failure
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): duloxetine
Phenotype category: Efficacy
Significant: no
Association: SLC6A4 HTTLPR long form (L allele) is not associated with response to duloxetine in people with Depressive Disorder, Major as compared to SLC6A4 HTTLPR short form (S allele).
Notes: The 5-HTTLPR was not associated with significant differences in remission (QIDS-C16) in patients receiving duloxetine (duloxetine after SSRI failure).
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: CHST3
Variant/haplotype: rs4148950
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele G.
Notes: (allele inferred by frequency comparison with dbSNP, actual base not listed in paper)
Article: Sex Differences in the Blood Concentration of Tacrolimus in Systemic Lupus Erythematosus and Rheumatoid Arthritis Patients with CYP3A5*3/*3
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Arthritis, Rheumatoid or Lupus Erythematosus, Systemic as compared to CYP3A5 *1/*1 + *1/*3.
Notes: The dose-adjusted concentration of tacrolimus was significantly higher in patients with the *3/*3 genotype as compared to those with the *1/*1 or *1/*3 genotypes. The authors note that within those with the *3/*3 genotype, tacrolimus concentration was higher in men than woman (p<0.05) and higher in women over 50 than women under 50 (p<0.05).
Article: Exploration of CYP450 and drug transporter genotypes and correlations with nevirapine exposure in Malawians
Gene: CYP2D6
Variant/haplotype: rs28371706
Drug(s): nevirapine
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with decreased clearance of nevirapine in children with HIV Infections as compared to genotype GG.
Notes: This association was not observed in adults, only in children. The A allele was referred to as CYP2D6*17 in this study. This variant was not a significant factor in a multiple regression model for determining nevirapine AUC but age was. [stat_test: linear regression]
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs529520
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methadone in people with Opioid-Related Disorders as compared to allele A.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment.; Please note that alleles have been complemented to the positive strand.
Article: Effects of genetic polymorphisms on methotrexate levels and toxicity in Chinese patients with acute lymphoblastic leukemia
Gene: MTRR
Variant/haplotype: rs1801394
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with increased concentrations of methotrexate in people with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.
Notes: at 48 hours.
Article: Genetic Polymorphisms in Aquaporin 1 as Risk Factors for Malignant Mesothelioma and Biomarkers of Response to Cisplatin Treatment
Gene: AQP1
Variant/haplotype: rs1049305
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CG are not associated with response to cisplatin in people with Mesothelioma as compared to genotype GG.
Notes: No significant association between genotype and progress-free survival, overall survival or chemotherapy response in patients with malignant mesothelioma who were treated with cisplatin-based chemotherapy.
Article: TOLLIP, MUC5B, and the Response to N-Acetylcysteine among Individuals with Idiopathic Pulmonary Fibrosis
Gene: TOLLIP
Variant/haplotype: rs3750920
Drug(s): acetylcysteine
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to acetylcysteine in people with Pulmonary Fibrosis as compared to genotypes CC + CT.
Notes: Clinical endpoints included death, transplant, hospitalization, or FVC decline,  and risk was adjusted for age, sex, prednisone use, azathioprine use, FVC, diffusion capacity of the lung, and trial/center.
Article: Pharmacogenetics of unboosted atazanavir in HIV-infected individuals in resource-limited settings: a sub-study of the AIDS Clinical Trials Group (ACTG) PEARLS study (NWCS 342)
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG (assigned as deficiency phenotype) is not associated with concentrations of atazanavir in people with HIV Infections as compared to genotypes AA + AG.
Notes: Looked at CL/F, Concentration at 24 hours, ratios of metabolites 1 and 2 to atazanavir.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: LYN
Variant/haplotype: rs1546519
Drug(s): ziprasidone
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with response to ziprasidone in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. Please note: reported allele was C, this has been complemented to the plus chromosomal strand. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Clinic and genetic predictors in response to erenumab
Gene: RAMP1
Variant/haplotype: rs7590387
Drug(s): erenumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with decreased clinical benefit to erenumab in people with Migraine NOS as compared to allele C.
Notes: "RAMP1 rs7590387 was found to confer a lower probability of being 75‐RESP compared to the rs7590387C allele (for each G allele, OR [95% CI]: 0.53 [0.29–0.99], p = 0.048, Table 4). However, the nominal association of RAMP1 rs7590387 with 75‐RESP was lost after adjustments for clinical confounders (OR [95% CI] 0.55 [0.28–1.10], p = 0.09, Table 4)" 75-RESP is a 75% reduction in monthly migraine days after 3 months treatment.
Article: Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population
Gene: GGCX
Variant/haplotype: rs11676382
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin as compared to allele G.
Notes: Neither the addition of race, number of concurrent medications nor the number of concurrent medications interacting with warfarin enhanced algorithm performance. Similarly, consideration of CYP4F2, CALU or GGCX variant genotypes did not improve algorithms.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: ATF3
Variant/haplotype: rs11811628
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: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Variant/haplotype: rs17010902
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele G.
Notes: Significance was not attained. Observations: 7.35 mm Hg increased reduction of systolic blood pressure per A allele in PEAR + GERA, 1.28 mm Hg decreased reduction of systolic blood pressure per A allele in NORDIL, and 4.34 mm Hg increased reduction of systolic blood pressure per A allele in PEAR + GERA + NORDIL.
Article: Response to citalopram is not associated with SLC6A4 genotype in African-Americans and Caucasians with major depression
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: SLC6A4 HTTLPR long form (L allele) is not associated with response to citalopram in people with Depressive Disorder, Major as compared to SLC6A4 HTTLPR short form (S allele).
Notes: The 5-HTTLPR was not associated with significant differences in response (HAMD) in patients receiving citalopram.
Article: Genetic Determinants of Response to Warfarin during Initial Anticoagulation
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with decreased dose of warfarin as compared to genotype GG.
Notes: With *1/*2 (AG) requiring intermediate dose. This was most marked at day 28 to end of follow-up with average doses of 3.66mg/day for *2*2 (HaplotypeA/HaplotypeA"), 4.45mg/day for HaplotypeA/nonA and 5.68mg/day for nonA/nonA. Authors also used rs9923231, rs2884737, rs9934438, and rs8050894 to define HaplotypeA.
Article: TBX21: A functional variant predicts improvement in asthma with the use of inhaled corticosteroids
Gene: TBX21
Variant/haplotype: rs2240017
Drug(s): corticosteroids
Phenotype category: Efficacy
Significant: yes
Association: Genotype CG is associated with increased response to corticosteroids in children with Asthma as compared to genotype CC.
Notes: There were no GG individuals.
Article: Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus
Gene: SLC22A1
Variant/haplotype: rs72552763
Drug(s): sulfonamides, urea derivatives
Phenotype category: Efficacy
Significant: no
Association: Allele del is not associated with response to sulfonamides, urea derivatives in people with Diabetes Mellitus as compared to allele GAT.
Notes: described as Met420Del in paper.
Article: Genome wide association study identifies the common variants in CYP3A4 and CYP3A5 responsible for variation in tacrolimus trough concentration in Caucasian kidney transplant recipients
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to allele G.
Notes: GWAS in patients with two CYP3A5 loss-of-function alleles. Loss-of-function alleles were *3, *6, or *7. Genotype composition in the population was 1342 with *3/*3, 2 with *3/*6 and 1 with *3/*7. The association of the variant with TAC concentration was significant in the GWAS analysis P=2.21E-17. The distribution of the dose-normalized TAC concentration for all three genotypes is shown in Supplementary Figure S2 with the AA (*22/*22) and AG (*1/*22) genotypes having higher dose-adjusted concentrations as compared to the GG (*1/*1) genotype. However, no statistical analysis was preformed with regards to the individual genotypes.
Article: Therapeutic Dosing of Acenocoumarol: Proposal of a Population Specific Pharmacogenetic Dosing Algorithm and Its Validation in North Indians
Gene: CYP2C9
Variant/haplotype: CYP2C9*1
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: no
Association: CYP2C9 *1 is not associated with increased dose of acenocoumarol as compared to CYP2C9 *2 + *3.
Notes: No significant difference was seen between the daily dose for CYP2C9 wildtype patients and the daily dose for CYP2C9 variant carriers. This study provides an algorithm for predicting the maintenance dose of acenocoumarol using genotypes as well as clinical factors as predictive variables.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs6356
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: Pharmacokinetics of lamotrigine and its metabolite N‐2‐glucuronide: Influence of polymorphism of UDP‐glucuronosyltransferases and drug transporters
Gene: SLC22A1
Variant/haplotype: rs628031
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is associated with increased dose of lamotrigine in people with Epilepsy as compared to genotypes AA + AG.
Notes: This study was conducted in 100 patients -- 54 receiving monotherapy for lamotrigine, and 46 receiving combination therapy with carbamazepine, oxcarbazepine, valproic acid, phenytoin, phenobarbital, levetiracetam, topiramate, lacosamide, zonisamide, pregabalin, clonazepam, or clobazam. All patients were on stable therapy for at least 2 months.
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Hepatitis C, HIV Infections and HIV Infections as compared to genotypes GG + GT.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Pharmacogenomic Study of Selected Genes Affecting Amlodipine Blood Pressure Response in Patients with Hypertension
Gene: CACNA1D
Variant/haplotype: rs312481
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased clinical benefit to amlodipine in people with Hypertension as compared to genotypes AA + AG.
Notes: "Individuals with the GG genotype demonstrated a significant independent reduction in blood pressure (unadjusted odds ratio (95% CI)=2.91(1.34–4.97), p=0.021). After adjusting for confounding variables, the association between SNP rs312481 and blood pressure regulation by amlodipine remained consistent (adjusted odds ratio (95% CI)= 2.01 (1.12–5.01), P=0.024). "
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP2B6
Variant/haplotype: rs2279343
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele A.
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA3
Variant/haplotype: rs3743077
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele T is not associated with exposure to nicotine in men as compared to allele C.
Notes: No significant association between this allele and status as a smoker or non-smoker.
Article: Effect of Genetic Variability in the CYP4F2, CYP4F11, and CYP4F12 Genes on Liver mRNA Levels and Warfarin Response
Gene: CYP4F11
Variant/haplotype: rs1060467
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with decreased dose of warfarin as compared to allele A.
Notes: The G allele was associated with a decrease in stable warfarin dose and accounted for  2.6% of the variance. AA= 4.6 ± 0.2, AG = 3.9 ± 0.1 GG = 3.8 ± 0.2. The addition of rs1060467 to PGx algorithm (included CYP2C9, VKORC1) explained a further 0.5–0.7% of variability. When conditioned on rs1060467, the association w/ rs2108622 & warfarin dose decreased (beta initial = 0.078, beta conditional = 0.063, initial P-value = 0.003, conditional P-value = 0.05). Alleles have been complemented to the positive strand.
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP3A5
Variant/haplotype: CYP3A5 poor metabolizer and intermediate metabolizer genotypes
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of endoxifen in women with Breast Neoplasms.
Article: Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients
Gene: CALU
Variant/haplotype: rs339097
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotypes AG + GG are associated with increased dose of warfarin as compared to genotype AA.
Notes: A p value of 0.04 was given for  dose- genotype association, but the authors stated that this association did not reach significanc in multiple regression testing (p = 0.066), and that was likely due to insufficient power.Variant allele carriers required 14.1 mg/week more warfarin than AA.
Article: Genetic polymorphisms in key methotrexate pathway genes are associated with response to treatment in rheumatoid arthritis patients
Gene: SHMT1
Variant/haplotype: rs1979277
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid.
Article: Effects of CYP2C19 genetic polymorphisms on the cure rates of H. pylori in patients treated with the proton pump inhibitors: An updated meta-analysis
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizer and intermediate metabolizer genotypes
Drug(s): Proton pump inhibitors
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 intermediate metabolizer and poor metabolizer is associated with increased clinical benefit to Proton pump inhibitors in people with Helicobacter Infections as compared to CYP2C19 normal metabolizer.
Notes: in meta-analysis of cure rates of H. pylori in triple therapy.
Article: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway
Gene: RAPGEF5
Variant/haplotype: rs16873129
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to antidepressants in people with Depressive Disorder, Major as compared to allele T.
Notes: Identity of minor allele not specified, so minor allele of dbSNP used here (C). 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.
Article: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *28/*28 is not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to UGT1A1 *1/*1 + *1/*28.
Notes: 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.
Article: Pharmacotherapy Effects on Smoking Cessation Vary with Nicotine Metabolism Gene (CYP2A6)
Gene: CYP2A6
Variant/haplotype: CYP2A6 high activity
Drug(s): bupropion
Phenotype category: Efficacy
Significant: no
Association: CYP2A6 high activity is not associated with response to bupropion in people with Tobacco Use Disorder as compared to CYP2A6 low activity.
Notes: Patients with a predicted CYP2A6 "fast metabolizer" or "slow metabolizer" phenotype were equally likely to respond to bupropion as smoking cessation treatment.
Article: Influence of ABCB1 polymorphisms on aripiprazole and dehydroaripiprazole plasma concentrations
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): aripiprazole, dehydroaripiprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of aripiprazole and dehydroaripiprazole as compared to genotype AA.
Notes: Alleles complemented. "Regarding ARI/DHA ratio, significant differences between the different variants were observed in the three SNPs analyzed. Specifically, for C3434T it was obtained an ARI/DHA ratio 37.4% higher for CC (2.35) compared to the TT variant (1.71), for G2677T 93% higher for GG (3.27) vs TT (1.69) and for C1236T 64.2% higher for CC (2.93) vs TT (1.78) (Fig. 1A). Comparing Non-T carriers vs. T carriers variants as a whole, yielded 22.3%, 70.07% and 47.43% more respectively, maintaining statistical significance (Fig. 1B)." "For ABCB1, the following variants were analyzed: C3435T (rs1045642), C2677 T/A (rs2032582) and C1236T (rs1128503)."