shlokn/autogkb huggingface dataset:
Article: The Relationship Between Single Nucleotide Polymorphisms in 5-HT2A Signal Transduction-Related Genes and the Response Efficacy to Selective Serotonin Reuptake Inhibitor Treatments in Chinese Patients with Major Depressive Disorder
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): citalopram, paroxetine, sertraline
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to citalopram, paroxetine or sertraline in people with Depressive Disorder, Major as compared to allele C.
Notes: Response measure with HAMD.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs2291834
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of vancomycin as compared to allele C.
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: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: EPHX1
Variant/haplotype: rs2234922
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with clearance of carbamazepine in people with Epilepsy as compared to genotypes AA + AG.
Article: Race-specific influence of CYP4F2 on dose and risk of hemorrhage among warfarin users
Variant/haplotype: rs12777823
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG are associated with decreased dose of warfarin as compared to genotype GG.
Notes: in African americans, but not European americans.
Article: Incidence and predictors of regimen-modification from first-line antiretroviral therapy in Thailand: a cohort study
Gene: HLA-B
Variant/haplotype: HLA-B*40:01
Drug(s): lamivudine, nevirapine, stavudine
Phenotype category: Efficacy
Significant: yes
Association: HLA-B *40:01 is associated with response to lamivudine, nevirapine and stavudine in people with HIV Infections.
Notes: HLA-B*40:01 was a significant predictor of regimen modification due to treatment failure, with presence of the *40:01 allele leading to a decreased risk of regimen modification due to treatment failure.
Article: Impact of polymorphisms in CYP and UGT enzymes and ABC and SLCO1B1 transporters on the pharmacokinetics and safety of desvenlafaxine
Gene: CYP2C19
Variant/haplotype: CYP2C19 rapid metabolizer
Drug(s): desvenlafaxine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 rapid metabolizer is associated with decreased concentrations of desvenlafaxine in healthy individuals as compared to CYP2C19 normal metabolizer and intermediate metabolizer and poor metabolizer.
Notes: as measured by increased Cmax. UM were not grouped with RM and had similar Cmax to NM+IM+PM but there were only 2 individuals. Also genotyping only included rs4244285(*2), rs4986893 (*3) and rs12248560 (*17) and did not rule out *4 which is in linkage with *17 in some populations.  "However, none of these associations; remained significant after Bonferroni correction for multiple; comparisons. "
Article: IL28B gene polymorphisms and viral kinetics in HIV/hepatitis C virus-coinfected patients treated with pegylated interferon and ribavirin
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CT + TT.
Notes: These patients were also HIV infected.  Treatment was with ribavirin plus peginterferon alfa- 2a or -2b.  The increased response was significant for Hepatitis C types 1 and 4 (pooled after no significant differences were found between the two) and was marginal for types 2 and 3.  The effect was mainly due to increased viral clearance during the first 12 weeks of treatment. 86 CC; 110 CT or TT.
Article: 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
Gene: APOC3
Variant/haplotype: rs2854117
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype CC.
Notes: 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.
Article: CBR1 and CBR3 pharmacogenetics and their influence on doxorubicin disposition in Asian breast cancer patients
Gene: CBR1
Variant/haplotype: rs20572
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased clearance of doxorubicin in people with Breast Neoplasms as compared to genotype CT.
Article: Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with decreased dose of warfarin as compared to genotype CT.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AG is not associated with metabolism of carbamazepine in people with Epilepsy as compared to genotypes AA + GG.
Notes: 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.
Article: Genome-wide study of methotrexate clearance replicates SLCO1B1
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): methotrexate
Phenotype category: Efficacy, Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
Notes: Average clearance was about 13% lower in CC than in TT patients.
Article: A randomized placebo-controlled trial of ataluren for the treatment of nonsense mutation cystic fibrosis
Gene: CFTR
Variant/haplotype: rs77010898
Drug(s): ataluren
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to ataluren in people with Cystic Fibrosis as compared to allele G.
Notes: Outcomes assessed for all nonsense mutations together (W1282X, G542X, R1162X, and R553X). Case-control study with placebo. Endpoint measured was change in Forced Expiratory Volume in 1 second. A difference was seen in the subset of patients on tobramycin.
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: SLCO1B1
Variant/haplotype: rs10841753
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with decreased concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype CC.
Notes: There is an association between selected SNPs and methotrexate plasma level at 48 h between the first dose of methotrexate infusion. med. MTX concentration: CT+TT (0.47 (0.09–41.63)) vs. CC 0.32 (0.14–5.50)).
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Gene: ADRA2A
Variant/haplotype: rs1800544
Drug(s): dexmedetomidine
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with decreased dose of dexmedetomidine in people with surgery as compared to genotypes CC + CG.
Notes: "In this research, homozygous carriers of the major allele (GG) required less DXM than carriers of the minor allele (GC/CC) (35.49 ± 7.46 vs. 40.08 ± 12.99, p = 0.038). Thus, homozygosity for the major allele G) of ADRA2A rs1800544 may be involved in a higher sensitivity to DXM."
Article: Th2 Cytokines (Interleukin-5 and -9) Polymorphism Affects the Response to Anti-TNF Treatment in Polish Patients with Ankylosing Spondylitis
Gene: IL5
Variant/haplotype: rs2069812
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Spondylitis, Ankylosing as compared to genotype GG.
Notes: as measured by reduction in Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) after 12 weeks treatment. Also as measured by reductions in CRP and VAS scores.
Article: Influence of APOA5 Locus on the Treatment Efficacy of Three Statins: Evidence From a Randomized Pilot Study in Chinese Subjects
Gene: APOA5
Variant/haplotype: rs662799
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to atorvastatin in people with Dyslipidaemia as compared to genotypes AG + GG.
Notes: Subjects were randomized to receive one of three dose-adjusted statins (N = 65 rosuvastatin, N= 65 atorvastatin, N= 65 simvastatin) and cholesterol (HDL, LDL), triglycerides and free-fatty acids (FFA) were compared between groups before and after statin treatment. Please note: alleles have been complemented to the + chromosomal strand.
Article: Association of BDNF, HTR2A, TPH1, SLC6A4, and COMT polymorphisms with tDCS and escitalopram efficacy: ancillary analysis of a double-blind, placebo-controlled trial
Gene: BDNF
Variant/haplotype: rs6265
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to escitalopram in people with Depression as compared to allele C.
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: rs6269
Drug(s): butorphanol
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to butorphanol in healthy individuals as compared to genotypes AA + AG.
Notes: Significant difference in pressure pain at the ulna between genotype groups, but this association was not seen in other pain modalities. Study-wide significance was set to p<0.017.
Article: A genotype-directed phase I–IV dose-finding study of irinotecan in combination with fluorouracil/leucovorin as first-line treatment in advanced colorectal cancer
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Dosage
Significant: not stated
Association: UGT1A1 *1/*28 + *28/*28 are associated with decreased dose of irinotecan in people with Colorectal Neoplasms as compared to UGT1A1 *1/*1.
Notes: This study provided maximum tolerated doses of irinotecan for the *1/*1, *1/*28 and *28/*28 genotypes. The maximum tolerated doses for *1/*1 and *1/*28 were found to be considerably higher than the recommended irinotecan dose of 180 mg/m2, though the maximum tolerated dose for *28/*28 was considerable lower than the recommended dose. Those who received an irinotecan dose of >=260 mg/m2 had a significantly higher response rate as compared to patients who received a dose of <260mg/m2.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of warfarin in people with heart valve replacement as compared to genotype AC.
Notes: 130 plasma samples were obtained 12 hours after the last dose of warfarin. The plasma warfarin concentrations of these samples were comparing plasma concentration within a group of patients with INR between 1.5–2.5 (n = 92) between genotype groups. The relationship between plasma concentration and maintenance dose was evaluated to explore the effect of rs1057910 (CYP2C9) on the pharmacokinetics of warfarin. Within both the low-dosage group (<17.5 mg/w) and the middle-dosage group (17.5–26.25 mg/w) the AC genotypes required higher plasma concentration as compared to the AA genotypes although the differences were not statistically significant.
Article: CYP2B6*6 Genotype Specific Differences in Artemether‐Lumefantrine Disposition in Healthy Volunteers
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): artemether
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6/*6 is associated with decreased metabolism of artemether in healthy individuals as compared to CYP2B6 *1/*1.
Notes: Subjects with the *6/*6 genotype had a significantly increased metabolic ratio of artemether:dihydroatmemisnin copmared to subjects with the *1/*1 genotype. However, there were no significant differences in any other PK parameters assessed.
Article: Influence of (ATP)-Binding Cassette Transporter Subfamily B Member 1 (ABCB1) Gene Polymorphism on the Efficacy of Remifentanil
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): remifentanil
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to remifentanil as compared to genotype AA.
Notes: Patients with the GG genotype had significantly longer analepsia time, longer autonomous respiratory recovery time and longer orientation recovery time than patients with the AA genotype.
Article: CYP2B6 Variants and Plasma Efavirenz Concentrations during Antiretroviral Therapy in Port-au-Prince, Haiti
Gene: CYP2A6
Variant/haplotype: rs28399433
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AC is associated with decreased metabolism of efavirenz in people with HIV Infections as compared to genotype AA.
Notes: As determined by higher plasma levels. Although this association was not statistically significant after Bonferroni correction for multiple comparisons. This polymorphism was described as being in the cyp2a6 promoter region.
Article: Polymorphisms in the ABCB1 gene and effect on outcome and toxicity in childhood acute lymphoblastic leukemia
Gene: ABCB1
Variant/haplotype: rs2229109
Drug(s): doxorubicin, methotrexate, prednisolone, vincristine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased resistance to doxorubicin, methotrexate, prednisolone and vincristine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype CC.
Notes: In children with high-risk acute lymphoblastic leukemia (ALL; see paper for definition of high risk); no significant results seen for children with low-risk ALL. Risk of relapse was approximately 4-fold greater for those with the CT genotype as compared to those with the CC genotype. Multivariate analysis adjusted for protocol, gender and immunophenotype. Please note that alleles have been complemented to the plus chromosomal strand.
Article: PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients
Gene: NR1I2
Variant/haplotype: rs1464602
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with metabolism of efavirenz in people with HIV Infections as compared to genotype AA.
Notes: Plasma levels of efavirenz were not statistically significantly different between the GG, AG, AA genotypes of this SNP. Alleles have been complemented to the plus chromosomal strand.
Article: No significant influence of OCT1 genotypes on the pharmacokinetics of morphine in adult surgical patients
Gene: SLC22A1
Variant/haplotype: rs12208357
Drug(s): morphine
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of morphine in people with Pain, Postoperative as compared to allele C.
Notes: Analyzed as part of haplotypes with rs34059508, rs72552763 and rs34130495. No significant association between haplotypes and PCA doses of morphine.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs3823010
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele G.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.
Article: Combined Effects of 2 Interleukin 28B Polymorphisms on the Therapeutic Outcome of Hepatitis C Patients With Circulating Cryoglobulins
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): interferons, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to interferons and ribavirin in people with Hepatitis C as compared to genotypes GT + TT.
Notes: Measured according to impact on sustained virological response. Significant only in non-cryoglobulinemic patients. Not significant in cryoglobulinemic patients. GG to TT p = 0.049.
Article: Population Pharmacokinetics, Pharmacodynamics, and Pharmacogenetics Modeling of Oxypurinol in Hmong Adults with Gout and/or Hyperuricemia
Gene: PDZK1
Variant/haplotype: rs12129861
Drug(s): allopurinol
Phenotype category: Dosage
Significant: not stated
Association: Allele C is associated with increased dose of allopurinol in people with Gout as compared to allele T.
Notes: "Most individuals with both PDZK1 rs12129861 AA and SLC22A12 rs505802 CC genotypes achieve target SU (with at least 75% success rate) with allopurinol below the maximum dose, regardless of renal function and body mass. In contrast, individuals with both PDZK1 rs12129861 GG and SLC22A12 rs505802 TT genotypes would require more than the maximum dose, thus selecting alternative medications."
Article: Impact of Promoter Polymorphisms on the Transcriptional Regulation of the Organic Cation Transporter OCT1 (SLC22A1)
Gene: SLC22A1
Variant/haplotype: rs6935207
Drug(s): cycloguanil, fenoterol, sumatriptan
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with exposure to cycloguanil, fenoterol or sumatriptan in healthy individuals as compared to allele G.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs10485057
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele A.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.
Article: Atazanavir pharmacokinetics in genetically determined CYP3A5 expressors versus non-expressors
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3, CYP3A5*6, CYP3A5*7
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3 + *6 + *7 are associated with decreased metabolism of atazanavir in healthy individuals as compared to CYP3A5 *1.
Notes: in individuals who are co-administered ritonavir as a booster. In this two-phase study, healthy participants were given atazanavir only for 7 days and then were co-administered ritonavir as a booster for days 8-14. The results here are for day 8-14 (atazanavir and ritonavir). Non-expressor status was assigned to CYP3A5 homozygous variants (*3, *6 or *7) and expressor status was assigned to those carrying at least one *1 allele. After the first phase of the study 1 expresser and 4 non-expressers withdrew from, but did not indicate why. There were no significant differences in ritonavir boosted atazanavir oral clearance comparing between CYP3A5 expressers and non-expressers. The only significant differences emerged when comparing within the non-African-American group: the CYP3A5 expresser group had faster CL vs. non-expressers. Note: the authors do not specify which *3 allele patients had and so *3a here represents all *3 alleles.
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/*1 is 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/*1 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: Genetic and environmental factors determining clinical outcomes and cost of warfarin therapy: a prospective study
Gene: CYP2C9
Variant/haplotype: rs2860905
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with decreased dose of warfarin as compared to allele G.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: SLC24A4
Variant/haplotype: rs77441273
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to salbutamol in children with Asthma as compared to genotype GG.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  This association was significant in the initial GWAS (in GALA II).  In an attempted replication by imputation in silico in GALA I, there was a consistent direction of effect in Puerto Ricans, but the result was not significant.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.
Article: Interpatient variability in the pharmacokinetics of the HIV non-nucleoside reverse transcriptase inhibitor efavirenz: the effect of gender, race, and CYP2B6 polymorphism
Gene: CYP2B6
Variant/haplotype: rs3211371
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype TT is not associated with metabolism of efavirenz in people with HIV Infections as compared to genotype CC.
Notes: Efavirenz plasma concentrations were not significantly different between the CC genotype and CT or the CC genotype and the TT genotype. The T allele was at a significantly lower frequency in Black and Asian patients compared to Caucasian patients.
Article: Tacrolimus Elimination in Four Patients With a CYP3A5*3/*3 CYP3A4*22/*22 Genotype Combination
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype TT is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to genotypes CC + CT.
Notes: The TT genotype at rs776746 (CYP3A5 *3/*3) was found along with the AA genotype at rs35599367 (CYP3A4 *22/*22) in 4/1366 kidney transplant recipients. Individuals who were homozygous for both had the highest dose-adjusted trough concentrations of tacrolimus (3.05 ng/ml/mg) and the lowest concentrations of tacrolimus (2.5 mg/day) as compared to patients who carried the  rs776746 CC and rs35599367 GG genotypes.