shlokn/autogkb huggingface dataset:
Article: Probing Conformational Rescue Induced by a Chemical Corrector of F508del-Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutant
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele del is associated with increased response to ivacaftor.
Notes: in vitro assays using cells expressing a F508del-KXK-CFTR: CFTR with the F508del mutation (rs113993960 del) and mutations of arginines at positions 553 and 555 (these increased protein processing and function). Cells were activated (forskolin, IBMX) then treated with ivacator and a corrector compound VRT-325.
Article: Impact of GGCX, STX1B and FPGS Polymorphisms on Warfarin Dose Requirements in European‐Americans and Egyptians
Gene: STX1B
Variant/haplotype: rs4889606
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AG + GG are associated with decreased dose of warfarin as compared to genotype AA.
Notes: in both European-Americans, and Egyptians.  "However, STX1B rs4889606 was in high linkage disequilibrium with VKORC1-1639 G>A, and was no longer significant after including VKORC1-1639 G>A in the regression model. Based on these data, the polymorphisms do not appear to influence, in a clinically important way, warfarin dose requirements in European-Americans and Egyptians. "
Article: Genetic Variation in CYP2D6, UGT1A4, SLC6A2 and SLCO1B1 Alters the Pharmacokinetics and Safety of Mirabegron
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): mirabegron
Phenotype category: Metabolism/PK
Significant: no
Association: NAT2 slow acetylator is associated with decreased dose-adjusted trough concentrations of mirabegron in healthy individuals as compared to NAT2 intermediate acetylator and rapid acetylator.
Notes: "The Cmax/DW was significantly lower in NAT2 slow acetilators (SAs) compared to intermediate (IAs) and rapid acetilators (RAs) (puv = 0.046). Even though differences disappeared in pair comparison, the observed lower Cmax/DW in NAT2 SAs was maintained when IAs and RAs were merged in a unique group (puv = 0.016), accompanied by a tendency towards a lower AUC/DW (puv = 0.089) and higher tmax and CL/F in SAs (puv = 0.083 and puv = 0.076, respectively)."
Article: Genetic Variation at the LDL Receptor and HMG CoA Reductase Gene Loci, Lipid Levels, Statin Response, and Cardiovascular Disease Incidence in PROSPER
Gene: LDLR
Variant/haplotype: rs2738466
Drug(s): pravastatin
Phenotype category: Efficacy
Significant: not stated
Association: Genotype GG is associated with increased response to pravastatin in people with Vascular Diseases as compared to genotype AA.
Notes: PROSPER study.Baseline Lipid Values, LDL-C lowering response,trial CHD and CVD outcomes were measured.  40 mg/day pravastatin.
Article: Genetic-based dosing in orthopedic patients beginning warfarin therapy
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin in people with total knee or hip arthroplasty as compared to allele A.
Notes: C (*3) was associated with 38.1 %(95% CI 29.3 -45.7%) reduction in therapeutic dose (defined as the dose that gave an INR in the target therapeutic range after 7 consecutive days) per copy.
Article: A genetic variant in NRP1 is associated with worse response to ranibizumab treatment in neovascular age-related macular degeneration
Gene: NRP1
Variant/haplotype: rs2070296
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to ranibizumab in people with Macular Degeneration as compared to genotype CC.
Notes: Associated with change in visual acuity after 3 months of treatment in patients who received three monthly ranibizumab injections.
Article: The Correlation of Il28B Genotype With Sustained Virologic Response In Romanian patients With Chronic Hepatitis C
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CT + TT.
Notes: This genotype is associated with increased sustained virological response (SVR; 73.1%[19 of 26] vs. 43.7%[35 of 80], P=0.0126) as well as increased occurrence of complete early virological response (cEVR; 80.8%[21 of 26] vs. 51.2%[41 of 80], P=0.011) when compared to patients with non-CC genotypes.
Article: Pharmacogenetic association with early response to intravitreal ranibizumab for age-related macular degeneration in a Korean population
Gene: HTRA1
Variant/haplotype: rs11200638
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to ranibizumab in people with Macular Degeneration as compared to allele G.
Notes: Age-related macular degeneration. No significant differences in best-corrected visual acuity (BCVA) changes or central subfield macular thickness (CSMT) changes were seen between baseline and 3 or 6 months of treatment between any of the genotypes.
Article: A Common 5′-UTR Variant in MATE2-K Is Associated With Poor Response to Metformin
Gene: SLC47A2
Variant/haplotype: rs12943590
Drug(s): metformin
Phenotype category: Efficacy, Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased response to metformin in people with Diabetes Mellitus as compared to genotypes AG + GG.
Article: Association between single nucleotide polymorphisms in the mu opioid receptor gene (OPRM1) and self-reported responses to alcohol in American Indians
Gene: OPRM1
Variant/haplotype: rs648007
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to ethanol as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand. The A allele was associated with increased scores in the dizzy and nausea traits on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: IL28B polymorphism genotyping as predictor of rapid virologic response during interferon plus ribavirin treatment in hepatitis C virus genotype 1 patients
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GG + GT is associated with decreased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to genotype TT.
Notes: Carriage of the G allele was the best predictor of null-R (not achieving a hepatitis C virus (HCV) RNA drop of >= 1 log at week 4) within logistic regression analysis.
Article: Interleukin-6 (IL-6) haplotypes and the response to therapy of chronic hepatitis C virus infection
Gene: IL6
Variant/haplotype: rs1800797
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to peginterferon alfa-2a in people with Hepatitis C, Chronic as compared to allele A.
Notes: This association is as part of a haplotype which also includes rs1800796G and rs1800795G.
Article: Impact of Sex and Genetic Variation in Relevant Pharmacogenes on the Pharmacokinetics and Safety of Valsartan, Olmesartan and Hydrochlorothiazide
Gene: SLC22A1
Variant/haplotype: rs34059508
Drug(s): hydrochlorothiazide, olmesartan
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased dose-adjusted trough concentrations of hydrochlorothiazide null olmesartan in healthy individuals as compared to genotype GG.
Notes: There were no AA homozygotes. "Higher hydrochlorothiazide AUC∞/DW was observed in SLC22A1 rs34059508 G/A volunteers compared to G/G volunteers"
Article: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Gene: ADRA2A
Variant/haplotype: rs1800544
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele C.
Notes: Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: MTHFR and MTRR Genetic Polymorphism of Methotrexate Therapy Outcomes in Early Rheumatoid Arthritis
Gene: MTHFR
Variant/haplotype: rs1801131
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Genotype GT is associated with increased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotype TT.
Notes: alleles complemented to plus chromosomal strand. Response measured by ESR, erythrocyte sedimentation rate; TJC, tender joints counts; SJC, swollen joints counts; DAS28, Disease Activity Score in 28 joints. "DAS28 was decreased after the post-treatment in 677TT and 1298AC, but was not statistically significant." No  homozygotes were observed for the minor allele.
Article: Bleeding Events Associated with Rivaroxaban Therapy in Naive Patients with Nonvalvular Atrial Fibrillation: A Longitudinal Study from a Genetic Perspective with INR Follow-Up
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): rivaroxaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with decreased concentrations of rivaroxaban in people with Atrial Fibrillation as compared to genotype AA.
Notes: "In our study, we found that for ABCB1-related rs4148738 and rs2032582, there was a statistically significant difference between the wild and mutant genotypes and a decrease in the CDR max values of rivaroxaban, while CDRss was statistically significant between the wild and homozygous mutant genotypes. For rs1045642 and rs1128503 of ABCB1, the decreased CDR max and Css levels of rivaroxaban were statistically significant between the wild (AA) and mutant (AG, GG) genotypes. Our findings suggest that polymorphism in the P-glycoprotein expressed by the ABCB1 gene can affect the peak plasma levels of rivaroxaban."
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: ABCB1
Variant/haplotype: rs2235048
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele G.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients. This is a proxy for rs1045642 (3435C>T).
Article: Folate metabolic pathway single nucleotide polymorphisms: a predictive pharmacogenetic marker of methotrexate response in Indian (Asian) patients with rheumatoid arthritis
Gene: SLC19A1
Variant/haplotype: rs1051266
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotype CC.
Article: NUDT15 Polymorphisms Alter Thiopurine Metabolism and Hematopoietic Toxicity
Gene: NUDT15
Variant/haplotype: NUDT15*1, NUDT15*2, NUDT15*3, NUDT15*4, NUDT15*5
Drug(s): mercaptopurine
Phenotype category: Dosage
Significant: yes
Association: NUDT15 *1/*1 (assigned as high activity phenotype) is associated with increased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to NUDT15 *1/*2 + *1/*3 + *1/*4 + *1/*5 + *3/*3 + *3/*5 + *2/*3 (assigned as intermediate and low activity phenotype) .
Notes: Patients were classified into three diplotypic groups: normal activity (*1/*1), intermediate activity (*1/*2, *1/*3, *1/*4, *1/*5) and low activity (*2/*3, *3/*3, *3/*5). Across three cohorts (Guatemalan, Singaporean, Japanese), and in a meta-analysis of the three cohorts, the tolerated mercaptopurine dose (mg/m2) was highest in those with normal activity, followed by intermediate activity and low activity. Note that those with the *1/*2 and *1/*3 diplotypes had similar degree of mercaptopurine tolerance, and compound-heterozygous genotypes had a similar degree of tolerance compared to homozygotes (*3/*3).
Article: ABCB1 and ABCC2 and the risk of distant metastasis in Thai breast cancer patients treated with tamoxifen
Gene: ABCC2
Variant/haplotype: rs717620
Drug(s): tamoxifen
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to tamoxifen in women Breast Neoplasms as compared to genotype CC.
Notes: Efficacy was measured as disease-free survival in breast cancer patients with distant metastasis of bone, lung, or liver. No patients had the TT genotype.
Article: The influence of COMT and ABCB1 gene polymorphisms on sufentanil analgesic effect for postoperative pain in children with fracture
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): sufentanil
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of sufentanil in children with Pain, Postoperative as compared to genotypes AA + AG.
Notes: "Pediatric patients in the CC group of ABCB1 had higher pain scores and total consumption of sufentanil at awakening, as well as at 2 and 6 hours postoperatively, compared to the TT and CT groups (P < .05). However, there was no statistically significant difference between the TT and CT groups (P > .05)."
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs362726
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele T.
Notes: Response was assessed by changes in PANSS score. A reduction of 50% or more in PANSS score was classified as a good response.
Article: TRAF1/C5 but Not PTPRC Variants Are Potential Predictors of Rheumatoid Arthritis Response to Anti-Tumor Necrosis Factor Therapy
Gene: REL
Variant/haplotype: rs13031237
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with decreased response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: using either the absolute change in DAS28 or the proportion of good responders and non-responders as outcomes.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: SLC28A1
Variant/haplotype: rs2242048
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype GG is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AA + AG.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
Article: Effect of the Most Relevant CYP3A4 and CYP3A5 Polymorphisms on the Pharmacokinetic Parameters of 10 CYP3A Substrates
Gene: CYP3A5
Variant/haplotype: rs41303343
Drug(s): ambrisentan, aripiprazole, atorvastatin, donepezil, olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with metabolism of ambrisentan, aripiprazole, atorvastatin, donepezil or olanzapine in healthy individuals as compared to allele del.
Notes: No significant changes in PK parameters in the presence of the A allele. The A allele is also referred to in the paper as the CYP3A5*7 allele.
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: rs3821799
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotype CC.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).  The TT genotype was associated with a greater decrease in waist circumference as compared to the TC and CC genotypes after pioglitazone therapy (p=0.033).
Article: A genetic variant in GLP1R is associated with response to DPP-4 inhibitors in patients with type 2 diabetes
Gene: GLP1R
Variant/haplotype: rs3765467
Drug(s): gemigliptin, linagliptin, saxagliptin, sitagliptin, vildagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased clinical benefit to gemigliptin, linagliptin, saxagliptin, sitagliptin or vildagliptin in people with Diabetes Mellitus, Type 2 as compared to genotype GG.
Notes: "The proportion of DPP-4 inhibitor responders with GG genotype (52.7%) was significantly lower than that of responders with GA/AA genotype (68.8%, P = 0.018). " "No significant differences in baseline fasting blood glucose and HbA1c were found between patients with GA/AA genotype and those with GG genotype. However, patients with GA/AA genotype were associated with a significantly greater reduction of HbA1c levels after DPP-4 inhibitor treatment (variation: 1.3 ± 1.1% vs 0.9 ± 1.2%; P = 0.022) (Table 2)."
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: DPP4
Variant/haplotype: rs17574
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to peginterferon alfa-2a or peginterferon alfa-2b in people with Hepatitis C, Chronic as compared to genotype AG.
Notes: PEG-interferon alfa (2a and b) was co-adminstered with ribavirin. Response was assessed by sustained virological response (SVR) percent by genotype. Please note, alleles have been complemented to the + chromosomal strand.
Article: Variants in the CYP2B6 3′UTR alter in vitro and in vivo CYP2B6 activity: potential role of microRNAs
Gene: CYP2B6
Variant/haplotype: rs707265
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with increased metabolism of efavirenz in healthy individuals as compared to genotype GG.
Notes: "An increase in CYP2B6 activity was also seen among volunteers carrying the variant allele G/G vs. G/A [34.2% increase; p<0.05] and A/A [72.4% increase; p<0.0001]".
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: PPARD
Variant/haplotype: rs3734254
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele C.
Notes: (allele inferred by frequency comparison with data in pgkb, actual base not listed in paper)
Article: UGT1A1*28 genotype and irinotecan dosage in patients with metastatic colorectal cancer: a Dutch Colorectal Cancer Group study
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *1/*28 + *28/*28 is not associated with response to irinotecan in people with Colorectal Neoplasms as compared to UGT1A1 *1/*1.
Notes: Response was defined as complete or partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria. Non-response was defined as stable or progressive disease, also according to RECIST. Patients were treated with irinotecan monotherapy or capecitabine plus irinotecan.
Article: A genetic variant in Rassf1a predicts outcome in mCRC patients treated with cetuximab plus chemotherapy: results from FIRE-3 and JACCRO 05 and 06 trials
Gene: LATS2
Variant/haplotype: rs558614
Drug(s): cetuximab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to cetuximab in people with Colorectal Neoplasms as compared to allele G.
Notes: No significant difference in tumor response, progression-free survival or overall survival was seen between the genotype groups. Patients also receiving treatment with fluorouracil, leucovorin and irinotecan (FOLFIRI).
Article: Polymorphisms in CYP2C9 are associated with response to indomethacin among neonates with patent ductus arteriosus
Gene: CYP2C9
Variant/haplotype: rs2153628
Drug(s): indomethacin
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to indomethacin as compared to allele A.
Notes: among neonates with patent ductus arteriosus (PDA).
Article: Genotype-guided new approach for dose optimisation of hydroxychloroquine administration in Chinese patients with SLE
Gene: CYP2D6
Variant/haplotype: rs1065852
Drug(s): desethylchloroquine, hydroxychloroquine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased concentrations of desethylchloroquine and hydroxychloroquine in people with Lupus Erythematosus, Systemic as compared to genotypes AG + GG.
Notes: "In addition, polymorphism of CYP2D6*10 (rs1065852) was significantly correlated with the DHCQ:HCQ ratio in both dose groups (p=0.032 and p=0.036, respectively), and the DHCQ:HCQ ratio was lower in patients with the AA genotype compared with the GG and AG genotypes."
Article: Single nucleotide polymorphisms in the apolipoprotein B and low density lipoprotein receptor genes affect response to antihypertensive treatment
Gene: LDLR
Variant/haplotype: rs688
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is associated with response to atenolol in people with Hypertension.
Notes: The presence of a C allele MAY be associated with BP reduction.  Not significant.; 50 mg/ atenolol for twelve weeks.
Article: Relationship between Genotypes Sult1a2 and Cyp2d6 and Tamoxifen Metabolism in Breast Cancer Patients
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*9, CYP2D6*10, CYP2D6*17, CYP2D6*41
Drug(s): 4-hydroxytamoxifen, N-desmethyltamoxifen, tamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *3/*9 + *4/*4 + *4/*5 + *4/*10 + *4/*41 + *5/*17 + *5/*41 + *41/*41 are not associated with decreased concentrations of 4-hydroxytamoxifen, n-desmethyltamoxifen or tamoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*1 + *1/*3 + *1/*4 + *1/*5 + *1/*6 + *1/*9 + *1/*17 + *1/*41.
Notes: Please note: article provides diplotypes as wt/wt or wt/*3 etc. CYP2D6 wt includes *1, *2, *35 but the individual diplotypes concerning wt alleles are not included so  compared to diplotypes are examples with *1 could be *2 or *35. Pre and postmenopausal woman with estrogen receptor-positive breast cancer undergoing tam treatment after surgery and chemotherapy/radiation. Patients were excluded if tamoxifen therapy was started with either chemotherapy or radiation, SSRI treatment was allowed. Roche-AmpliChip® CYP450 Test was used. Genotypes were classified into the three groups: wt/wt, patients with 2 or more copies of any functional allele; wt/v, patients carrying one functional allele and one variant -intermediate or null- allele; v/v, patients featuring intermediate or null alleles. [pre-menopausal][post-menopausal] [adjuvant] [DNA source: blood] [HWE: yes]