shlokn/autogkb huggingface dataset:
Article: Associations between P2RY12 gene polymorphisms and risks of clopidogrel resistance and adverse cardiovascular events after PCI in patients with acute coronary syndrome
Gene: P2RY12
Variant/haplotype: rs6785930
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased resistance to clopidogrel as compared to genotype GG.
Notes: in Chinese patients with acute coronary syndrome undergoing PCI. This variant is also called P2RY12 C34T.
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: GSTP1
Variant/haplotype: rs1695
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is not associated with response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms.
Article: High imatinib dose overcomes insufficient response associated with ABCG2 haplotype in chronic myelogenous leukemia patients
Gene: ABCG2
Variant/haplotype: rs12505410
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to allele T.
Notes: As part of a haplotype with rs2725252. Where response was defined as BCR-ABL/ABL standardized ratio (BCR-ABL^IS) of <=10% at 3 months, <=1% at 12 months and <=0.1% at 18 months. Patients were either taking 400mg/day or 600mg/day dose of imatinib. Those with the G-C haplotype (rs12505410-rs2725252) taking a 400mg/day dose had a significantly better response (under all definitions of response), as compared to those with any other haplotype (i.e. G-A, T-C, T-A). Results were NOT significant for those taking a 600mg/day dose (p=0.209, 0.316 and 0.209, respectively for the different response definitions). Please note that alleles for rs2725252 have been complemented to the plus chromosomal strand.
Article: Genetic markers for the efficacy of tumour necrosis factor blocking therapy in rheumatoid arthritis
Gene: TGFB1
Variant/haplotype: rs1800471
Drug(s): etanercept
Phenotype category: Efficacy
Significant: yes
Association: Genotype CG is associated with decreased response to etanercept in people with Arthritis, Rheumatoid as compared to genotype GG.
Notes: When combined with the IL1RN VNTR in intron 2, A2 allele (no rsID available). Those with the CG-A2 positive combined genotype were more likely to be non-responders to treatment, as compared to those with any other combination of genotypes. However, no significant difference in genotype frequencies was seen between responders and non-responders when considering the rs1800471 SNP or IL1RN VNTR alone. Responders defined using the American College of Rheumatology (ACR) response criteria and response criteria based on the modified disease activity score (DAS)28 index. Non-responders failed to fulfill both these criteria.
Article: Lack of tacrolimus circadian pharmacokinetics and CYP3A5 pharmacogenetics in the early and maintenance stages in Japanese renal transplant recipients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): tacrolimus
Phenotype category: Toxicity, Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of tacrolimus in people with Kidney Transplantation as compared to allele A.
Notes: No significant differences in dose-adjusted area under the concentration-time curve from 0-12 hours (AUC0-12/D), dose-adjusted trough level (C0/D), dose-adjusted maximum plasma concentration (Cmax/D), body weight-adjusted clearance or AUC0-12 were seen between any of the GG, AG or AA genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs2218603
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: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: BDNF
Variant/haplotype: rs6265
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to risperidone in people with Schizophrenia as compared to allele T.
Notes: Please note that alleles have been complemented to the positive strand.
Article: SLC28A3 genotype and gemcitabine rate of infusion affect dFdCTP metabolite disposition in patients with solid tumours
Gene: SLC28A3
Variant/haplotype: rs4877831
Drug(s): gemcitabine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with metabolism of gemcitabine as compared to genotypes CC + CG.
Notes: Gemcitabine, dFdCTP, and dFdU plasma concentrations were measured before (5, 15, 30, 45 min) and after gemcitabine infusion (1, 1.25, 1.5, 2, 6, 24, 48, 72 hrs). Population pharmacokinetic analysis of gemcitabine and metabolites (dFdU, dFdCTP) were performed by non-linear mixed effects modeling. rs4877831 is not associated with metabolism of gemcitabine.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs10070381
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of vancomycin as compared to allele T.
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: Carriers of HLA-DRB1*04:05 have a better clinical response to abatacept in rheumatoid arthritis
Gene: HLA-DRB1
Variant/haplotype: HLA-DRB1*04:05
Drug(s): abatacept
Phenotype category: Efficacy
Significant: yes
Association: HLA-DRB1 *04:05 is associated with increased clinical benefit to abatacept in people with Arthritis, Rheumatoid.
Notes: as measured by percent change in SDAI after 3 months. "Of all the HLA-DRB1 alleles, the only one that showed a significant difference in percent change in SDAI after 3 months was HLA-DRB1*04:05, one of the SE alleles in ABT use (28.5% SDAI improvement in HLA-DRB1*04:05 allele non-carriers and 59.8% SDAI improvement in HLA-DRB1*04:05 allele carriers, p = 0.003, false discovery rate = 0.039). " Not significant for tocilizumab, or TNF inhibitors.
Article: Polymorphisms of the Proinflammatory Cytokine Genes Modulate the Response to NSAIDs but Not to Triptans in Migraine Attacks
Gene: IL1B
Variant/haplotype: rs1143634
Drug(s): almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan, zolmitriptan
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with clinical benefit to almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan or zolmitriptan in people with Migraine without Aura as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Influence of IL-18 and IL-10 Polymorphisms on Tacrolimus Elimination in Chinese Lung Transplant Patients
Gene: IL18
Variant/haplotype: rs5744247
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CG is associated with increased dose-adjusted trough concentrations of tacrolimus in people with lung transplantation as compared to genotype GG.
Notes: Patients with the CC or CG genotypes had higher dose-adjusted trough concentrations of tacrolimus at weeks 1 (p=0.002), 2 (p=0.004), 3 (p=0.005) and 4 (p=0.026) post-transplant as compared to those with the GG genotype. This variant was also analyzed in combination with rs1946518 - patients with <=1 allele (Group 1), patients with 2 alleles (Group 2) and patients with >= 3 alleles (Group 3) were compared. Group 3 had lower dose-adjusted trough concentrations as compared to Groups 1 + 2 (p<0.05); no significant difference was seen between Groups 1 and 2. Additionally, note that this polymorphism had a significant impact among CYP3A5 expressers (rs776746 CT+TT) but NOT among nonexpressers (CC). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ABCC1
Variant/haplotype: rs35592
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: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: EPHX1
Variant/haplotype: rs1051740
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased metabolism of carbamazepine in people with Epilepsy as compared to genotypes CC + CT.
Notes: as measured by a lower carbamazepine-10,11-transdihydrodiol:carbamazepine-10-11 epoxide metabolite ratio. This association was only significant in the African American patients and not in Caucasian patients.
Article: RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients
Gene: RRM1
Variant/haplotype: rs1561876
Drug(s): cladribine, cytarabine
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to cladribine and cytarabine in children with Leukemia, Myeloid, Acute as compared to genotypes AA + AG.
Notes: The GG genotype (reported as CC in the paper) was associated with lower intracellular cytarabine levels at day 1 of therapy, inferior response after the first course of remission induction therapy, poor event-free survival and a greater risk of relapse. No multiple testing adjustments were performed: 7 SNPs were investigated.
Article: Th2 Cytokines (Interleukin-5 and -9) Polymorphism Affects the Response to Anti-TNF Treatment in Polish Patients with Ankylosing Spondylitis
Gene: IL9
Variant/haplotype: rs2069885
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: Valproic acid levels in neurodevelopmental disorders: correlation with CYP and SULT genes using LC-MS/MS
Gene: CYP2C19
Variant/haplotype: CYP2C19*2
Drug(s): valproic acid
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *2 is not associated with increased concentrations of valproic acid in people with Autism or Intellectual Disability.
Notes: "No significant correlation was observed between VPA plasma concentrations and genotypes of SULT1A1 (p = 0.522), CYP2C192 (p = 0.288), CYP2D64 (p = 0.895), or CYP2D6*10 (p = 0.067)." "Sample numbers (2 and 8) have heterozygous abnormal CYP 2C19*2; sample number (2) has a therapeutic VPA level, but sample number (8) has a toxic level of VPA. "
Article: Personalized CFTR Modulator Therapy for G85E and N1303K Homozygous Patients with Cystic Fibrosis
Gene: CFTR
Variant/haplotype: rs80034486
Drug(s): elexacaftor / tezacaftor / ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Genotype GG is associated with increased clinical benefit to elexacaftor / tezacaftor / ivacaftor in people with Cystic Fibrosis.
Notes: "Elexacaftor/tezacaftor/ivacaftor (ETI) therapy improves clinical outcomes in the N1303K/N1303K patient."
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: NTRK2
Variant/haplotype: rs2378676
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotype AA is associated with decreased dose of methadone in people with Heroin Dependence as compared to genotypes AC + CC.
Notes: This association was statistically significant after permutation analysis based on 40,000 replicates, but not statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction). Note; this SNP was in LD with rs4358872, rs1948308, and rs4877900 (r^2>0.7).  Alleles were reported as T/G, here they are complemented with A representing T and C representing G.
Article: Genetic polymorphisms in key methotrexate pathway genes are associated with response to treatment in rheumatoid arthritis patients
Gene: MTHFD1
Variant/haplotype: rs2236225
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid.
Notes: This was considered a proxy SNP to compare with rs17850560 (MTHFD1:1958G>A) that has previously been shown to be involved in methotrexate efficacy.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs571335587
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele A is associated with decreased metabolism of nicotine as compared to allele C.
Notes: Assigned as loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments. Please note that alleles have been complemented to the positive strand.
Article: Effects of genetic variation in H3K79 methylation regulatory genes on clinical blood pressure and blood pressure response to hydrochlorothiazide
Gene: DOT1L
Variant/haplotype: rs2269879
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype CC.
Notes: More than 90% of participants were receiving 25 mg/day HCTZ (the rest received 12.5 mg/day). The direction of association in GERA Whites was the same as in PEAR Whites, but in GERA, the association was not significant.  [stat_test:linear regression].
Article: A single tumour necrosis factor haplotype influences the response to adalimumab in rheumatoid arthritis
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to adalimumab in people with Arthritis, Rheumatoid as compared to genotypes AA + AG.
Notes: No significant difference in genotype frequencies was seen between those who were responders to treatment and those who were non-responders. Response defined as a 50% percent response to adalimumab therapy according to the American College of Rheumatology criteria (ACR50 responders) at week 12 after treatment initiation.
Article: A proposal for an individualized pharmacogenetic-guided isoniazid dosage regimen for patients with tuberculosis
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): isoniazid
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 slow acetylator is associated with decreased concentrations of isoniazid in people with Tuberculosis as compared to NAT2 rapid acetylator.
Notes: Serum concentrations of isoniazid were significantly lower in NAT2 rapid acetylators (2.55 mg/L) as compared to slow acetylators (6.78 mg/L). Slow acetylators were defined as those with any two slow alleles. Intermediate and rapid acetylators were defined as those with one or two wild-type NAT*4 alleles, respectively. The authors also provided suggested doses for individuals based on NAT2 acetylator status and weight. Those with genotype-based dosing were more frequently in the therapeutic range as compared to those given standard dosing.
Article: Investigation of candidate polymorphisms and disease activity in rheumatoid arthritis patients on methotrexate
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele G.
Article: FSH receptor gene polymorphisms have a role for different ovarian response to stimulation in patients entering IVF/ICSI-ET programs
Gene: FSHR
Variant/haplotype: rs6166
Drug(s): gonadotropin,chorionic
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with increased dose of gonadotropin,chorionic in women as compared to genotype CT.
Notes: In patients with ovarian dysfunction. SNP referred to as Ser680Asn in the paper and mapped to rs6166 by PharmGKB.
Article: Effect of NLRP3 inflammasome genes polymorphism on disease susceptibility and response to TNF-α inhibitors in Iraqi patients with rheumatoid arthritis
Gene: NLRP3
Variant/haplotype: rs4612666
Drug(s): etanercept, infliximab
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to etanercept or infliximab in people with Arthritis, Rheumatoid as compared to genotypes CC + CT.
Notes: Responders = ΔDAS-28 ≥ 1.2 and DAS-28 ≤ 3.2, Non-responders = ΔDAS-28 ≤ 1.2 and DAS28 ≤ 5.1 (Table 1)
Article: Genetic Variants Influencing Plasma Renin Activity in Hypertensive Patients from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Variant/haplotype: rs7184292
Drug(s): atenolol
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with decreased dose of atenolol in people with Hypertension as compared to genotypes AA + AG.
Article: PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis
Gene: ILF3
Variant/haplotype: rs76966440
Drug(s): apremilast
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased clinical benefit to apremilast in people with Psoriasis as compared to allele C.
Notes: "Allele-based association tests detected 64 SNPs displaying nominal p values < 0.05 (Table 2) including 10 SNPs with p values ≤ 0.01. " Table 2 shows frequency of minor allele is responders and non-responders. Responder status maybe defined by PASI score improvement greater than 75% after 24–36 weeks of treatment.
Article: Investigation of CYP 3A5 and ABCB1 gene polymorphisms in the long-term following renal transplantation: Effects on tacrolimus exposure and kidney function
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*3 is associated with decreased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: Patients with the *1/*3 genotype had decreased dose-adjusted trough concentrations of tacrolimus at 6, 12 and 24 months post-transplant. Results were also significant in multivariate analysis (p<0.01). They also had increased dose requirements at 6 and 12 months post-transplant; no significant results were seen at 24 months post-transplant. Additionally, no significant results were seen at any of these three months for trough concentrations.
Article: Genome-wide association study of warfarin maintenance dose in a Brazilian sample
Gene: CYP2C9
Variant/haplotype: rs9332238
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with increased dose of warfarin as compared to allele A.
Notes: The G allele was strongly associated with high warfarin dose (G allele, OR: 6.8 [5.0–9.1]; p = 4.4 × 10-13) in Brazilian patients. This variant is in virtually perfect LD with CYP2C9*2 (rs1799853) and CYP2C9*3 (rs1057910).
Article: Nuclear receptor gene polymorphisms and warfarin dose requirements in the Quebec Warfarin Cohort
Gene: GATA4
Variant/haplotype: rs2645400
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of warfarin as compared to allele T.
Notes: Warfarin dose requirement was defined as the reported daily dose at 3 months following treatment initiation.
Article: Serotonin transporter 5-HTTLPR polymorphism and escitalopram treatment response in patients with major depressive disorder
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizer
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 poor metabolizer is not associated with decreased response to escitalopram in people with Major Depressive Disorder as compared to CYP2C19 normal metabolizer.
Notes: "No significant differences were observed in the distribution of predicted CYP2C19 and CYP2D6 metabolizer phenotypes between responder and non-responder groups."
Article: Influence of SLCO1B3 haplotype-tag SNPs on docetaxel disposition in Chinese nasopharyngeal cancer patients
Gene: SLCO1B3
Variant/haplotype: rs4149118
Drug(s): docetaxel
Phenotype category: Other, Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased clearance of docetaxel in people with Nasopharyngeal Neoplasms.
Notes: Significance as part of a haplotype with rs7311358, rs11045585 and rs3834935.
Article: Interaction between ABCG2 421C>A polymorphism and valproate in their effects on steady‐state disposition of lamotrigine in adults with epilepsy
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of lamotrigine in people with Epilepsy as compared to allele G.
Notes: In patients with the AA and AG genotype, steady-state measured and dose-adjusted lamotrigine trough concentration was higher in those administered lamotrigine as compared to the GG genotype and lower in those administered lamotrigine only as compared to the GG genotype.
Article: Impact of NFIB and CYP1A variants on clozapine serum concentration—A retrospective naturalistic cohort study on 526 patients with known smoking habits
Gene: CYP1A1
Variant/haplotype: rs2472297
Drug(s): clozapine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype CT is associated with decreased dose-adjusted trough concentrations of clozapine as compared to genotype CC.
Notes: significance is only given for combination of both CYP1A rs2472297 C>T and NFIB rs28379954 T>C genotypes
Article: The impact of SLCO1B1 polymorphisms on the plasma concentration of lopinavir and ritonavir in HIV-infected men
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT are associated with increased trough concentration of lopinavir in men with HIV Infections as compared to genotype TT.
Notes: Trough concentrations of lopinavir were significantly increased in patients with the CT genotype compared to TT and in the CC genotype compared to CT. Patients were treated with lopinavir/ritonavir, but no corresponding increase in trough concentrations was observed with ritonavir. Variant referred to in the paper as 521T>C.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: APBB1IP
Variant/haplotype: rs11015149
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AC is associated with increased resistance to clopidogrel in people with Coronary Disease as compared to genotype CC.
Notes: was significant in dominant and co-dominant models in discovery. This was not replicated.