shlokn/autogkb huggingface dataset:
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): simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to simvastatin 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: Genetic Polymorphisms in ERCC1 Gene and Their Association with Response to Radiotherapy in Moroccan Patients with Nasopharyngeal Carcinoma
Gene: ERCC1
Variant/haplotype: rs3212986
Drug(s): radiotherapy
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with resistance to radiotherapy in people with Nasopharyngeal Neoplasms as compared to allele C.
Notes: . Statistical analyses showed no significant; association between the radio-resistance status and,; C8092A genotypes (p=0.81) and allelic frequencies; (p=0.56).
Article: Systematic Review and Meta-Analysis of the Moderating Effect of rs1799971 in OPRM1, the Mu-opioid Receptor Gene, on Response to Naltrexone Treatment of Alcohol Use Disorder
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to naltrexone in people with Alcoholism as compared to allele A.
Notes: No significant association between the variant and drinking outcomes following correction for multiple comparisons. A meta-analysis combined all outcomes measured also found no significant association with the variant.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs2241767
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotype AA are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotypes AG + GG.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: STMN2
Variant/haplotype: rs113889867
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
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: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Gene: SLC6A3
Variant/haplotype: rs2550948
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT are associated with increased response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype TT.
Notes: For the genetic component, in the CGI-S model, a dominant effect in SLC6A3 rs2550948 was found with a significant improvement in the symptoms. Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: CYP2B6*6, CYP2B6*18, Body weight and sex are predictors of efavirenz pharmacokinetics and treatment response: population pharmacokinetic modeling in an HIV/AIDS and TB cohort in Zimbabwe
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT are associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotype TT.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: AKT1
Variant/haplotype: rs2494732
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to risperidone in people with Schizophrenia as compared to allele C.
Article: Effect of the Most Relevant CYP3A4 and CYP3A5 Polymorphisms on the Pharmacokinetic Parameters of 10 CYP3A Substrates
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): ambrisentan, aripiprazole, atorvastatin, donepezil, olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with metabolism of ambrisentan, aripiprazole, atorvastatin, donepezil or olanzapine in healthy individuals as compared to allele T.
Notes: No significant changes in PK parameters in the presence of the C allele. The C allele is also referred to in the paper as the CYP3A5*3 allele.
Article: PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients
Gene: NR1I3
Variant/haplotype: rs3003596
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased metabolism of efavirenz in people with HIV Infections as compared to genotype AA.
Notes: Plasma levels of efavirenz were significantly lower in patients with the GG genotype compared to the AA genotype, and in patients with the AG genotype compared to the AA genotype. Alleles have been complemented to the plus chromosomal strand.
Article: Genome‐Wide Meta‐Analysis of Blood Pressure Response to β1‐Blockers: Results From ICAPS (International Consortium of Antihypertensive Pharmacogenomics Studies)
Gene: BST1
Variant/haplotype: rs28404156
Drug(s): Beta blocking agents, selective
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to Beta blocking agents, selective in people with Hypertension as compared to allele G.
Notes: The A allele was associated with an improved systolic blood pressure response. This variant met the suggestive level of significance in the discovery meta-analysis and was successfully replicated. However, it did not reach genome-wide significance in a meta-analysis of the discovery and replication data.
Article: Avoiding Tacrolimus Underexposure and Overexposure with a Dosing Algorithm for Renal Transplant Recipients: A Single Arm Prospective Intervention Trial
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: not stated
Association: CYP3A5 *1/*1 + *1/*3 is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: see Rx annotation for algorithm.
Article: Association between opioid receptor mu 1 (OPRM1) gene polymorphisms and tobacco and alcohol consumption in a Spanish population
Gene: OPRM1
Variant/haplotype: rs10485057
Drug(s): nicotine
Phenotype category: Dosage
Significant: no
Association: Genotype AA is associated with increased dose of nicotine as compared to genotypes AG + GG.
Notes: Subjects with the AA genotype had increased tobacco consumption, but this association failed to meet statistical significance.
Article: Genetic determinants of serum bilirubin using inferred native American gene variants in Chilean adolescents
Gene: SLCO1B1, SLCO1B3, SLCO1B7
Variant/haplotype: rs1910167
Drug(s): bilirubin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of bilirubin in children as compared to allele T.
Notes: "Among the suggestive variants, we found the rs1910167 variant, effect allele C, in the solute carrier organic anion transporter family member 1B3 (SLCO1B3), 1B7 (SLCO1B7), and upstream of 1B1 (SLCO1B1), beta = 0.16 mg/dL total bilirubin, p = 1.26 × 10−6. This variant masked 368 other significant variants in the vicinity in high linkage disequilibrium and has a frequency of 8.3% in GOCS (Supplementary Table S4)." "The variant rs887829 near UGT1A1 explained 34.98% of the variation in total bilirubin levels, while the rs1910167 variant near SLCO1B1 only explained 4.61%. "
Article: Characterizing variability in warfarin dose requirements in children using modelling and simulation
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype CC is associated with increased dose of warfarin in children with Heart Diseases as compared to genotype TT.
Notes: A model was created to predict maintenance doses for children of different ages, all with a baseline INR of 1 and a target INR of 2.5, based on longitudinal data from children taking warfarin. A two-fold difference in dose between children with the CC and TT genotype was found. A table predicting warfarin dose for children of 2, 8 and 14 years old with different rs9923231 genotype and CYP2C9 genotype is presented in the paper. CYP2C9 genotype, VKORC1 genotype, bodyweight, age, baseline INR, target INR and time since initiation of therapy were all found to be significant causes of warfarin dose variability in children. Note: alleles have been complemented to the plus chromosomal strand.
Article: Methadone Dosage and Plasma Levels, SNPs of OPRM1 Gene and Age of First Drug Use Were Associated With Outcomes of Methadone Maintenance Treatment
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methadone in people with Heroin Dependence as compared to allele T.
Notes: This SNP was not significantly associated with compliance with methadone maintenance therapy or 'negative rate of morphine urine test'.
Article: Translesion Polymerase Genes Polymorphisms and Haplotypes Influence Survival of Osteosarcoma Patients
Gene: REV1
Variant/haplotype: rs3087399
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CT are not associated with increased response to cisplatin in people with Osteosarcoma as compared to genotype TT.
Notes: This SNP was not associated with event-free survival (p = 0.458) or overall survival (p = 0.707), as determined by recurrence or death, with a mean follow-up time of 143 months.
Article: Effectiveness of clopidogrel dose escalation to normalize active metabolite exposure and antiplatelet effects in CYP2C19 poor metabolizers
Gene: CYP2C19
Variant/haplotype: rs4244285
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A (assigned as poor metabolizer phenotype) is associated with increased dose of clopidogrel in healthy individuals as compared to allele G (assigned as normal metabolizer phenotype) .
Notes: Assays done in blood samples of six each of *1/*1 (EM/GG),*1/*2(IM/AG) and *2/*2(PM/AA) [based on only assaying for *2; 2 EMs were *1/*17 and one IM was a *2/*17] were compared for MPA4 (maximal platelet aggregation 4 hrs post-dose) and for active metabolite area under the curve. For the EMs, this result was significant for both the 150 and 300 mg/day doses; for the IMs and PMs, it was significant for the 300 mg/day dose.  At day 8, PMs needed 300 mg/day and IMs needed 150 mg/day to attain a similar MPA4 as EMs on the 75 mg/day dose.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: PROC
Variant/haplotype: rs1799809
Drug(s): phenprocoumon
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotype AA is not associated with increased dose of phenprocoumon as compared to genotypes AG + GG.
Notes: 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.
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): tamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of tamoxifen in women with Breast Neoplasms.
Article: Effect of apolipoprotein E (APOE) gene polymorphisms on the lipid profile of children being treated for acute lymphoblastic leukemia
Gene: APOE
Variant/haplotype: rs429358
Drug(s): cholesterol
Phenotype category: Toxicity
Significant: yes
Association: Genotype TT is associated with increased concentrations of cholesterol in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes CC + CT.
Notes: "Specifically, children with the TT genotype presented significantly higher total cholesterol and LDL cholesterol και apoB-100 levels compared to children with the TC + CC genotypes (p = 0.033, p = 0.009, and p = 0.012, respectively). The same applies to ε3/ε3 isoforms."
Article: Impact of CYP2C9, VKORC1 and CYP4F2 genetic polymorphisms on maintenance warfarin dosage in Han-Chinese patients: A systematic review and meta-analysis
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin as compared to allele A.
Article: Pharmacogenetics predictors of methylphenidate efficacy in childhood ADHD
Gene: SLC6A2
Variant/haplotype: rs28386840
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AT + TT are associated with increased response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype AA.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC22A2
Variant/haplotype: rs316019
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with exposure to metformin as compared to allele A.
Article: The Effect of CYP2D6 polymorphisms on the Response to Pain Treatment for Pediatric Sickle Cell Pain Crisis
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*5
Drug(s): codeine
Phenotype category: Efficacy
Significant: yes
Association: CYP2D6 *5 is associated with decreased response to codeine in children with Anemia, Sickle Cell as compared to CYP2D6 *1.
Notes: Pediatric patients with severe sickle cell disease who have failed codeine therapy for a pain crisis while taking hydroxyurea were found to be more likely to have a reduced function allele (including *4, *5, *6, *17, *40) as compared to those with mild disease, likely due to a decreased conversion of codeine to morphine. Allele frequencies were not reported. Reduced function alleles were grouped for analysis.
Article: A genetic variant in NRP1 is associated with worse response to ranibizumab treatment in neovascular age-related macular degeneration
Gene: NRP1
Variant/haplotype: rs2247383
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to ranibizumab in people with Macular Degeneration as compared to allele A.
Notes: Response was measured as change in visual acuity after 3 months of treatment in patients who received three monthly ranibizumab injections.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Variant/haplotype: rs6064463
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele T.
Article: Genetic variation in the Catechol-O-Methyltransferase (COMT) gene and morphine requirements in cancer patients with pain
Gene: COMT
Variant/haplotype: rs4818
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele C is associated with decreased dose of morphine in people with Neoplasms as compared to allele G.
Notes: This was for alleviation of pain from cancer.  The association was as part of a haplotype consisting of 11 rsIDs (the other rsIDs are rs2075507,rs7287550, rs5746849, rs737866, rs6269, rs2239393, rs740603, rs4680, rs174699, rs165728).  The haplotype was associated with a dose reduction factor of 0.71 .  Authors state that because the SNPs are linked, a strict Bonferroni correction is too conservative; however, that is what has been done here for p value.  Also noted was that the carriers of haplotype 1 have had the cancer diagnosis longer than have carriers of other haplotypes, and so the true difference in morphine requirements may be even greater than observed here. Since this is a G/C SNP,  there is ambiguity regarding which is the associated allele.  C is reported to be part of the haplotype associated with decreased dose, and this gene is on the positive chromosomal strand.
Article: Association between CXCL10 and DPP4 Gene Polymorphisms and a Complementary Role for Unfavorable IL28B Genotype in Prediction of Treatment Response in Thai Patients with Chronic Hepatitis C Virus Infection
Gene: CXCL10
Variant/haplotype: rs56061981
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased response to peginterferon alfa-2a or peginterferon alfa-2b in people with Hepatitis C, Chronic as compared to genotype CC.
Notes: PEG-interferon alfa (2a and b) was co-adminstered with ribavirin. Response was assessed by sustained virological response (SVR) percent by genotype. When assessed alone, the polymorphism was not significantly associated with SVR. However, in patients infected with hepatitis C- genotype I (N=266), who also carried the rs12979860 CT or TT genotypes, the CT+TT genotypes of rs56061981 became associated with increased rats of SVR when compared to patients with the CC genotype (CC+CT genotype 66.7% vs. CC genotype 33.0%, P = 0.004). Please note, alleles have been complemented to the + chromosomal strand.
Article: Pharmacogenetic Predictors of Statin-Mediated Low-Density Lipoprotein Cholesterol Reduction and Dose Response
Gene: APOE
Variant/haplotype: rs7412
Drug(s): atorvastatin, pravastatin, simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to atorvastatin, pravastatin or simvastatin in people with Hyperlipidemias as compared to allele T.
Notes: As measured by reduction in LDLc. Association was significant only at high doses.
Article: Pharmacogenetics of Asthma Controller Treatment
Gene: CRHR1
Variant/haplotype: rs1876829
Drug(s): fluticasone propionate
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to fluticasone propionate in people with Asthma as compared to allele T.
Notes: The minor allele is reported to be associated with increased response.  dbSNP lists C as the minor allele in a CEU panel.
Article: Angiotensin-converting enzyme gene polymorphism predicts the time-course of blood pressure response to angiotensin converting enzyme inhibition in the AASK trial
Gene: ACE
Variant/haplotype: rs4359
Drug(s): ramipril
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + TT are associated with increased response to ramipril in people with Hypertension as compared to genotype CT.
Notes: This SNP was also reported as ACE C17888T. This SNP was in linkage disequilibrium with rs4344, D' = .88. Patients homozygous for this SNP (CC or TT) responded to ACE inhibitor treatment (reached target blood pressure) faster than patients heterozygous (CT) for this SNP.
Article: A novel UGT1 marker associated with better tolerance against irinotecan-induced severe neutropenia in metastatic colorectal cancer patients
Gene: UGT1A
Variant/haplotype: rs11563250
Drug(s): bilirubin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with decreased concentrations of bilirubin in people with Colorectal Neoplasms as compared to genotype AA.
Notes: Carriers of the G allele had a 17.5% decrease in total bilirubin as compared to those with the AA genotype. This suggests that carriers of the G allele may have elevated activity of UGT1A1 (the sole UGT1A enzyme responsible for bilirubin glucuronidation and subsequent elimination).
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C19
Variant/haplotype: rs140278421
Drug(s): mephenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of mephenytoin as compared to allele G.
Notes: In vitro analysis showed that intrinsic clearance of S-mephenytoin by CYP2C19 protein containing the A allele was 6.5% of that of the WT protein. Variant referred to as 557G>A in the paper.
Article: Association of Pharmacogenetic Markers with Premature Discontinuation of First-line Anti-HIV Therapy: An Observational Cohort Study
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): atazanavir / ritonavir
Phenotype category: Toxicity
Significant: no
Association: UGT1A1 *1/*28 is not associated with increased discontinuation of atazanavir / ritonavir in people with HIV Infections as compared to UGT1A1 *1/*1.
Notes: even though *28/*28 was significant (see annotation on homozygote).
Article: Influence of SLCO1B1 and CYP2C8 gene polymorphisms on rosiglitazone pharmacokinetics in healthy volunteers
Gene: SLCO1B1
Variant/haplotype: SLCO1B1*1, SLCO1B1*5, SLCO1B1*15, SLCO1B1*16
Drug(s): rosiglitazone
Phenotype category: Metabolism/PK
Significant: no
Association: SLCO1B1 *5 + *15 + *16 are not associated with concentrations of rosiglitazone in healthy individuals as compared to SLCO1B1 *1/*1.
Notes: There were no significant differences in rosiglitazone pharmacokinetic parameters between SLCO1B1 diplotype groups. Note *17 was listed in the original publication. *17 was merged with *15 due to PharmVar 2021 update.
Article: Genome-Wide Pharmacogenomic Study on Methadone Maintenance Treatment Identifies SNP rs17180299 and Multiple Haplotypes on CYP2B6, SPON1, and GSG1L Associated with Plasma Concentrations of Methadone R- and S-enantiomers in Heroin-Dependent Patients
Variant/haplotype: rs17180299
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG are associated with increased concentrations of methadone in people with Opioid-Related Disorders as compared to genotype AA.
Notes: This study specifically found an association with R-methadone enantiomer concentration. The association with the G allele was a dose effect, with patients with the GG genotyping having higher concentrations than patients with AG genotype. Patients included were heroin-dependent.
Article: Glycine and a Glycine Dehydrogenase (GLDC) SNP as Citalopram/Escitalopram Response Biomarkers in Depression: Pharmacometabolomics-informed Pharmacogenomics
Gene: GLDC
Variant/haplotype: rs10975641
Drug(s): citalopram, escitalopram
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to citalopram and escitalopram in people with Depressive Disorder, Major as compared to allele C.
Notes: Be careful- GC SNP.  The paper states that the minor allele was assoc with decreased odds for remission(in the original cohort), and from dbSNP freq/orientation of fastA compared to Golden path, I believe G on the + chr strand to be the minor allele.  For the STAR*D study, remission was not found to be significantly associated; the significant association was with "the binary phenotype "response"".