shlokn/autogkb huggingface dataset:
Article: High imatinib dose overcomes insufficient response associated with ABCG2 haplotype in chronic myelogenous leukemia patients
Gene: ABCG2
Variant/haplotype: rs2725252
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to allele A.
Notes: As part of a haplotype with rs12505410. 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: The association between serotonin-related gene polymorphisms and susceptibility and early sertraline response in patients with panic disorder
Gene: SLC6A4
Variant/haplotype: rs57098334
Drug(s): sertraline
Phenotype category: Efficacy
Significant: no
Association: Genotype (AGCCCACCC)10/(AGCCCACCC)10 is not associated with response to sertraline in people with Panic Disorder as compared to genotype (AGCCCACCC)12/(AGCCCACCC)12.
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: CYP1A2
Variant/haplotype: rs762551
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with concentrations of efavirenz in people with HIV Infections as compared to genotypes AA + AC.
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Variant/haplotype: rs141294036
Drug(s): dexmedetomidine
Phenotype category: Toxicity
Significant: yes
Association: Genotype CC is associated with increased response to dexmedetomidine in people with surgery as compared to genotypes CT + TT.
Notes: as measured by decreased in mean arterial pressure. "KATP rs141294036 In our study, homozygous carriers of the major allele (CC) produced a bigger absolute value for the percent changes in MAP than those either heterozygous (CT) or homozygous for the minor allele (TT) (−9.80 ± 9.40 vs. −2.94 ± 9.33, p = 0.032). Homozygosity for the major allele C) of KATP rs141294036 can be inferred to be associated with greater susceptibility to the cardiovascular impact of DXM."
Article: Effects of SLCO1B1 polymorphisms on plasma estrogen concentrations in women with breast cancer receiving aromatase inhibitors exemestane and letrozole
Gene: SLCO1B1
Variant/haplotype: rs10841753
Drug(s): estrone sulfate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased estrone sulfate in women with Breast Neoplasms as compared to allele T.
Notes: prior to treatment with aromatase inhibitors.
Article: Genetic Variants Influencing Plasma Renin Activity in Hypertensive Patients from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Variant/haplotype: rs16872401
Drug(s): atenolol
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of atenolol in people with Hypertension as compared to allele T.
Article: An expanded pharmacogenomics warfarin dosing table with utility in generalised dosing guidance
Gene: CYP2C9
Variant/haplotype: rs72558189
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele A is associated with dose of warfarin as compared to allele G.
Notes: This variant annotation is part of a dosing algorithm table based on 8 genetic variants.
Article: Effect of CYP2B6 Gene Polymorphisms on Efavirenz Plasma Concentrations in Chinese Patients with HIV Infection
Gene: CYP2B6
Variant/haplotype: rs2279343
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG are associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotype AA.
Article: Association of ABCC2 polymorphism with clopidogrel response in Chinese patients undergoing percutaneous coronary intervention
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with decreased response to clopidogrel in people with Coronary Artery Disease as compared to genotypes CC + CT.
Notes: "neither ABCC2 rs2273697 nor ABCC2 rs3740066 polymorphisms affected PAIR% values "
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs3211371
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of methadone as compared to genotypes CC + CT.
Article: Polymorphisms of the Proinflammatory Cytokine Genes Modulate the Response to NSAIDs but Not to Triptans in Migraine Attacks
Gene: IL1B
Variant/haplotype: rs16944
Drug(s): almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan, zolmitriptan
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with clinical benefit to almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan or zolmitriptan in people with Migraine without Aura as compared to allele A.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype GG.
Notes: from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance
Article: Influence of ABCC2 and ABCC4 Polymorphisms on Tenofovir Plasma Concentrations in Thai HIV-Infected Patients
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG is not associated with concentrations of tenofovir in people with HIV Infections as compared to genotype GG.
Article: VEGF-A polymorphisms predict progression-free survival among advanced castration-resistant prostate cancer patients treated with metronomic cyclophosphamide
Gene: VEGFA
Variant/haplotype: rs699947
Drug(s): cyclophosphamide
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with decreased response to cyclophosphamide in people with Prostatic Neoplasms as compared to genotypes AA + AC.
Notes: Not significant by Bonferroni's correction (p-value set at <0.017). Patients with advanced prostate cancer undergoing metronomic chemotherapy who have the CC genotype were more frequently non-responders to chemotherapy. Responders were classified as patients who had a decrease in prostrate-specific antigen (PSA) of >= 50% and a PSA stabilization of >= 6 months. Patients also received celecoxib and dexamethasone, and some patients received docetaxel-, mitoxantrone-, and vinorelbine-based chemotherapeutic regimens.
Article: Effects of UGT1A1 Genotype on the Pharmacokinetics, Pharmacodynamics, and Toxicities of Belinostat Administered by 48-Hour Continuous Infusion in Patients With Cancer
Gene: UGT1A1
Variant/haplotype: UGT1A1*28
Drug(s): belinostat
Phenotype category: Metabolism/PK
Significant: no
Association: UGT1A1 *28 is not associated with metabolism of Belinostat in people with Neoplasms.
Notes: No significant difference in AUC, Cmax, clearance or half-life was seen between the *1/*1 (n=11), *1/*28 (n=11) or *28/*28 (n=3) genotypes, either when considering all patients (n=25) or only those who received a belinostat dose greater than 400 mg/m2/24h (n=15).
Article: Effect of Factor XIII-A G185T Polymorphism on Visual Prognosis after Photodynamic Therapy for Neovascular Macular Degeneration
Gene: F13A1
Variant/haplotype: rs5985
Drug(s): Photodynamic therapy
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC are associated with decreased response to photodynamic therapy in people with Choroidal Neovascularization as compared to genotype CC.
Notes: Alleles given as reverse strand T and G. Change in measured best-correct visual acuity after 2 years of treatment.
Article: Escitalopram and sertraline population pharmacokinetic analysis in pediatric patients
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizer
Drug(s): escitalopram
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 intermediate metabolizer and poor metabolizer is associated with decreased clearance of escitalopram in children as compared to CYP2C19 normal metabolizer.
Notes: "On average, poor and intermediate metabolizers had 69% and 20%; slower CL/F relative to normal metabolizers, respectively,; whereas rapid and ultrarapid metabolizers had 18% and; 23% faster CL/F, respectively"
Article: Apple juice greatly reduces systemic exposure to atenolol
Gene: SLCO2B1
Variant/haplotype: rs2306168
Drug(s): atenolol
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype TT is not associated with increased exposure to atenolol in healthy individuals as compared to genotype CC.
Notes: both *1/*1 and *3/*3 had similar Cmax and AUC and both were reduced significantly by apple juice.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP2C19
Variant/haplotype: rs4244285
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype GG.
Notes: from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance
Article: Effect of MDR1 C3435T and CYP2C19 genetic polymorphisms on the outcome of Helicobacter pylori eradication treatment in children with gastritis and peptic ulcer, Vietnam
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): Antibiotics, esomeprazole
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased clinical benefit to Antibiotics and esomeprazole in children with Helicobacter Infections as compared to genotypes AG + GG.
Notes: " In the MDR1; C3435T polymorphism analysis, the cure rates for MDR1; 3435T/T were lowest with 68,6%, C/T, and T/T genotypes were 85.4%, and 86.7%, respectively (p=0.02). The; patients with MDR1 3435T/T genotype were 3 times; more likely to fail treatment than MDR1 3435  C/C and; C/T." Alleles complemented.
Article: Effects of CYP2D6 gene polymorphism on plasma concentration and therapeutic effect of olanzapine
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10, CYP2D6*34, CYP2D6*39, CYP2D6*65
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *10/*65 is associated with decreased concentrations of olanzapine in people with Schizophrenia as compared to CYP2D6 *1/*1 + *1/*34 + *1/*39 + *2/*2 + *2/*34 + *2/*39 + *10/*39 + *39/*39 (assigned as normal metabolizer phenotype) .
Notes: *10/*65 was labeled as "Unknowns" for metabolizer phenotype. "The EMs group showed a trend of lower olanzapine plasma concentrations and C/D ratios than the IMs group at different time points (Fig. 1A and B). Interestingly, the olanzapine concentration in the Unknowns group exhibited a noticeable decrease at 8 weeks, leading to a lower trend of concentrations compared to the other two groups (Fig. 1A and B). However, the difference was not statistically significant.""The results showed no significant differences in plasma olanzapine concentrations, treatment response, or the occurrence of adverse effects among different CYP2D6 genotypes"
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs9306356
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele T.
Article: Pharmacogenetic analysis of high-dose methotrexate treatment in children with osteosarcoma
Gene: NR1I2
Variant/haplotype: rs7643038
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased metabolism of methotrexate in children with Osteosarcoma as compared to allele A.
Notes: The G allele is associated with longer half-life of methotrexate.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to risperidone in people with Schizophrenia as compared to allele A.
Notes: Please note that alleles have been complemented to the positive strand.
Article: IL28B, HLA-C, and KIR Variants Additively Predict Response to Therapy in Chronic Hepatitis C Virus Infection in a European Cohort: A Cross-Sectional Study
Gene: HLA-C
Variant/haplotype: HLA-C*01:02, HLA-C*02:02, HLA-C*03:02, HLA-C*04:01, HLA-C*05:01, HLA-C*06:02, HLA-C*07:01, HLA-C*08:01, HLA-C*12:02, HLA-C*14:02, HLA-C*15:02, HLA-C*16:01, HLA-C*17:01
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: HLA-C *02:02 + *04:01 + *05:01 + *06:02 + *15:02 + *17:01 is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to HLA-C *01:02:01 + *03:02 + *07:01:01 + *08:01 + *12:02:01 + *14:02:01 + *16:01:01.
Notes: HLA-C alleles are grouped in the paper as C1 and C2. C1 alleles are written as Cw*01, Cw*03, Cw*07, Cw*08, Cw*12, Cw*14 and Cw*16. C2 alleles are written as Cw*02, Cw*04, Cw*05, Cw*06, Cw*15 and Cw*17. The authors state that patients who are homozygous for HLA-C2 (i.e. they have two alleles from group C2) are less likely to clear hepatitis C virus upon treatment than patients who are HLA-C1 homozygous or are HLA-C1/C2 heterozygous.
Article: Potential role of polymorphisms in the transporter genes ENT1 and MATE1/OCT2 in predicting TAS-102 efficacy and toxicity in patients with refractory metastatic colorectal cancer
Gene: SLC29A1
Variant/haplotype: rs9394992
Drug(s): tipiracil hydrochloride, trifluridine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to tipiracil hydrochloride and trifluridine in people with Colorectal Neoplasms as compared to genotype CC.
Notes: The SNP was tested for association alone and with three other SNPs after univariate and multivariate analysis in a training (N= 52, Japan) and testing cohorts (N = 127, Italy). Although it remained significantly associated with progression-free and overall survival in univariate and multivariate analysis in the training cohort, it was not significant in the testing cohort.
Article: Determination of the Most Influential Sources of Variability in Tacrolimus Trough Blood Concentrations in Adult Liver Transplant Recipients: A Bottom-Up Approach
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*3 is associated with increased clearance of tacrolimus in people with liver transplantation as compared to CYP3A5 *3/*3.
Notes: Liver DONOR genotype.
Article: CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*3
Drug(s): paclitaxel
Phenotype category: Efficacy
Significant: yes
Association: CYP2C8 *1/*3 + *3/*3 is associated with increased response to paclitaxel in women with Breast Neoplasms as compared to CYP2C8 *1/*1.
Notes: Response = complete clinical response (cCR).  55% cCR vs 23%.  Some patients who had HER2 overexpressing tumors received trastuzumab at the same time as the paclitaxel.
Article: Combined Effects of 2 Interleukin 28B Polymorphisms on the Therapeutic Outcome of Hepatitis C Patients With Circulating Cryoglobulins
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): interferons, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to interferons and ribavirin in people with Hepatitis C as compared to genotypes CT + TT.
Notes: Measured according to impact on sustained virological response. Significant only in non-cryoglobulinemic patients. Not significant in cryoglobulinemic patients. CC to CT p = 0.023; CC to TT p = 0.017.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: CAP2
Variant/haplotype: rs910039
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: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs72772787
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele T.
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: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: OPRD1
Variant/haplotype: rs678849
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to oxycodone as compared to allele C.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test, subjective effects of oxycodone.
Article: Pharmacogenetic Predictors of Cannabidiol Response and Tolerability in Treatment‐Resistant Epilepsy
Gene: SLC15A1
Variant/haplotype: rs1339067
Drug(s): cannabidiol
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to cannabidiol in people with Epilepsy as compared to genotypes AA + AT.
Article: Impact of ABCC2 1249G>A and −24C>T Polymorphisms on Lacosamide Efficacy and Plasma Concentrations in Uygur Pediatric Patients With Epilepsy in China
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): lacosamide
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased resistance to lacosamide in children with Epilepsy as compared to allele G.
Notes: "the proportion of patients with the ABCC2 1249G>A (rs2273697) A; allele and ABCC2 -24C>T (rs717620) T allele in the drug-resistant group was; significantly higher than that in the drug-responsive group"
Article: ABCC2 Polymorphisms and Haplotype are Associated with Drug Resistance in Chinese Epileptic Patients
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased resistance to antiepileptics in people with Epilepsy as compared to allele A.
Notes: However, a haplotype of TGT (ABCC2 -24C>T/ABCC2 1249G>A/ABCC2 3972C>T) was found at significantly higher frequencies in resistant patients compared to responsive patients.
Article: ABC Transporter Polymorphisms are Associated with Irinotecan Pharmacokinetics and Neutropenia
Gene: ABCC1
Variant/haplotype: rs6498588
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AT + TT are associated with increased exposure to SN-38 in people with Colorectal Neoplasms as compared to genotype AA.
Notes: AUC of SN-38 was adjusted for irinotecan dose.
Article: Correlation of N-Acetyltransferase 2 Genotype with Isoniazid Acetylation in Polish Tuberculosis Patients
Gene: NAT2
Variant/haplotype: NAT2*4, NAT2*6, NAT2*7, NAT2*16
Drug(s): isoniazid
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 *16/*16 + *16/*6 + *6/*6 + *6/*7 + *7/*7 (assigned as slow acetylator phenotype) is associated with decreased metabolism of isoniazid in people with Tuberculosis as compared to NAT2 *4/*4 (assigned as rapid acetylator phenotype) .
Notes: Originally annotated as NAT2 *5A/*5A + *5A/*6B + *6B/*6B + *6B/*7A + *7A/*7A (assigned as slow acetylator phenotype). Slow acetylators (a combination of two slow alleles NAT2*5, *6 or *7) had higher isoniazid plasma concentrations and bioavailability compared to rapid (*4/*4) and intermediate acetylators (*4 allele combined with *5, *6 or *7). Patients with *7/*7 genotype had the highest levels. Authors report "To identify the three NAT2* mutations, C481T (NAT2*5), G590A (NAT2*6), and G857A (NAT2*7)"; The arylamine N-acetyltransferases (NATs) database was transitioned into the PharmVar database in March 2024. The alleles in this annotation is mapped as following: NAT2*5A under the *16 core allele; NAT2*6B under the *6 core allele; NAT2*7A under the *7 core allele.
Article: Nuclear receptor gene polymorphisms and warfarin dose requirements in the Quebec Warfarin Cohort
Gene: VKORC1
Variant/haplotype: VKORC1 low activity
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: VKORC1 low activity is associated with decreased dose of warfarin.
Notes: Mean dose (in mg) of warfarin according to activity phenotype was: High Activity (HA)>Intermediate Activity (IA)>Poor Activity (PA). Activity phenotype was based on presence of VKORC1*2, *3 and *4. Warfarin dose requirement was defined as the reported daily dose at 3 months following treatment initiation.
Article: MMP-2 and MMP-9 gene polymorphisms act as biological indicators for ulinastatin efficacy in patients with severe acute pancreatitis
Gene: MMP2
Variant/haplotype: rs243865
Drug(s): ulinastatin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to ulinastatin in people with Pancreatitis as compared to allele C.