shlokn/autogkb huggingface dataset:
Article: IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic.
Notes: This genotype is associated with decreased incidence of sustained virological response (SVR; OR: 0.37, 95%CI:[0.23–0.59], P=2.47E-5, multivariate analysis) when compared to CT/CC genotypes. However, when rs368234815 and  rs12979860 were introduced in the same logistic model, the TT genotype was associated with increased incidence of SVR (OR: 3.41, 95%CI:[1.01–11.4], P=0.0477). Hence, the polarity of the association between rs12979860-TT genotype and SVR is questionable.
Article: Genetic Variation of the Mu Opioid Receptor (OPRM1) and Dopamine D2 Receptor (DRD2) is Related to Smoking Differences in Patients with Schizophrenia but not Bipolar Disorder
Gene: DRD2
Variant/haplotype: rs1800497
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Genotypes AA + AG are not associated with exposure to nicotine in people with Schizophrenia as compared to genotype GG.
Notes: Subgroup analysis of schizophrenia patients only found no significant difference in the number of cigarettes smoked per day between the genotype groups. However, the authors noted that female schizophrenia patients with the GG genotype reported smoking significantly more cigarettes per day than male schizophrenia patients carrying the A allele (p=0.28)
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: WFS1
Variant/haplotype: rs734312
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele A.
Notes: No significant difference in allele frequency between responders and non-responders.
Article: Estimation of the Warfarin Dose with Clinical and Pharmacogenetic Data
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is associated with decreased dose of warfarin.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with decreased dose of warfarin in people with as compared to genotype CT.
Notes: 58/220 patients had the target INR (1.5–2.5). The comparison of weekly warfarin maintenance dose was among patients of different genotypes. The AA  genotype of rs9923231 required a significantly lower maintenance dose than the AG genotype (rs9923231: 19.21±5.66 mg/w vs 28.62±8.02 mg/w, p < 0.001; ANOVA). rs9923231 and rs1057910 had significant effects on maintenance dose (rs9923231: coefficient was 1.398, p < 0.001; rs1057910: coefficient was-0.994, p < 0.001) and together explained apx. 32.0% of warfarin maintenance dose variability.
Article: β2-Adrenergic Receptor Gene Affects the Heart Rate Response of β-Blockers: Evidence From 3 Clinical Studies
Gene: ADRB1
Variant/haplotype: rs1801252
Drug(s): atenolol, metoprolol
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to atenolol or metoprolol in people with Tachycardia as compared to allele A.
Notes: No significant association between this variant and response to atenolol or metoprolol, as measured by changes in heart rate, in black or white patients.
Article: Polymorphisms in CYP2C9 are associated with response to indomethacin among neonates with patent ductus arteriosus
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): indomethacin
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to indomethacin as compared to allele C.
Notes: among neonates with patent ductus arteriosus (PDA).
Article: Pharmacogenetic Study of Serotonin Transporter and 5HT2A Genotypes in Autism
Gene: HTR2A
Variant/haplotype: rs7997012
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased response to escitalopram in people with Autistic Disorder as compared to allele G.
Notes: Participants were enrolled in a 6 week, forced titration, open label examination. Doses started at 2.5 mg/day up to a possible dose of 20 mg/ day. The study compared AA to AG to GG genotypes and found no significant association.
Article: NCCTG N0543 (Alliance): A Phase II Trial of Pharmacogenetic-Based Dosing of Irinotecan, Oxaliplatin, and Capecitabine as First-Line Therapy for Advanced Small Bowel Adenocarcinoma
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Dosage
Significant: not stated
Association: UGT1A1 *28 is associated with decreased dose of irinotecan in people with Adenocarcinoma and Gastrointestinal Neoplasms as compared to UGT1A1 *1.
Notes: Patients were genotyped and dosed according to genotype. Study then examined if this reduced severe toxicities.
Article: Polymorphisms in the Drug Transporter Gene ABCB1 Are Associated with Drug Response in Saudi Epileptic Pediatric Patients
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased clinical benefit to antiepileptics in children with Epilepsy as compared to genotypes AC + CC.
Notes: Alleles complemented to plus chromosomal strand. "good responders were classified as those who were totally free from seizures for at least 1 year during treatment with ASMs as a monotherapy or in combination at optimal tolerated therapeutic doses." "good responders were significantly more likely to have the TT genotypes at rs1045642 and rs2032582 SNPs compared to poor responders." Specific antiseizure medications not mentioned.
Article: Genotype-Dependent Effects of Dalcetrapib on Cholesterol Efflux and Inflammation: Concordance With Clinical Outcomes
Gene: ADCY9
Variant/haplotype: rs1967309
Drug(s): dalcetrapib
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to dalcetrapib in people with as compared to genotype GG.
Notes: Part of the dal-OUTCOMES and dal-PLAQUE-2 studies. Outcome was mean change in cholesterol efflux. Patients with the AG genotype had intermediate response.
Article: Methadone dose in heroin-dependent patients: role of clinical factors, comedications, genetic polymorphisms and enzyme activity
Gene: CYP2C19
Variant/haplotype: rs12248560
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of methadone in people with Opioid-Related Disorders as compared to allele C.
Notes: Methadone maintenance dose was not associated with genotype of the SNP but it was correlated to the highest dose ever used. Multiple doses versus single dose, body weight, history of cocaine dependence and ethnicity (Asian>Caucasian>African) were independently associated with methadone dose in multiple regression analysis. Please note: alleles have been complemented to the + chromosomal strand.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype AA.
Notes: Genotypes of GG, AG and AA did not influence donepezil clearance in a covariate model. Alleles have been complemented to the plus chromosomal strand.
Article: IFNL4 ss469415590 Variant Shows Similar Performance to rs12979860 as Predictor of Response to Treatment against Hepatitis C Virus Genotype 1 or 4 in Caucasians
Gene: IFNL4
Variant/haplotype: rs11322783
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT/TT is associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C as compared to genotypes G/TT + GG.
Notes: Patients were infected with HCV genotype 1 or 4. Sustained viral response (SVR) was defined as undetectable plasma HCV RNA 24 weeks after the completion of treatment. The two SNPs rs12979860 (IL28B) and rs368234815 (IFNL4) are in strong LD (r squared of 0.82). The -G allele of rs368234815 causes a frame shift in the DNA sequence (TT-> -G) which has been shown, in vitro, to induce expression of IFNL4, possibly affecting HCV clearance.; The SNPs were also tested by HCV genotype (1 or 4) and were both equally predictive.; The AUROC model that included rs368234815 was 0.756 (95% CI: 0.687-0.826)
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ARHGAP12
Variant/haplotype: rs2799018
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.
Article: Effect of UGT2B10, UGT2B17, FMO3, and OCT2 Genetic Variation on Nicotine and Cotinine Pharmacokinetics and Smoking in African Americans
Gene: UGT2B10
Variant/haplotype: rs2942857
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with increased clearance of nicotine in people with Tobacco Use Disorder as compared to genotypes AA + AC.
Notes: This annotation was on rs116294140, but dbSNP has merged these two rs IDs.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): phenprocoumon
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with increased dose of phenprocoumon as compared to genotypes CT + TT.
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: 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: rs548646
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to ethanol as compared to allele C.
Notes: The T allele was associated with increased scores in the buzzed, clumsy and dizzy traits as well as increased total score on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: Effects of captopril administration on pulmonary haemodynamics and tissue oxygenation during exercise in ACE gene subtypes in patients with COPD: a preliminary study
Gene: ACE
Variant/haplotype: rs1799752
Drug(s): captopril
Phenotype category: Efficacy
Significant: yes
Association: Genotype del/del is associated with decreased response to captopril in men with Pulmonary Disease, Chronic Obstructive as compared to genotypes ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC + ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del.
Notes: The del/del genotype is associated with a increased mean pulmonary arterial pressure (mPAP; units = mmHg) and increased pulmonary vascular resistance (PVR; units = mmHg/l/min/m2) after exercise, as compared to the remaining genotypes. This indicates a decreased response to captopril.
Article: Prediction Formulas for Individual Opioid Analgesic Requirements Based on Genetic Polymorphism Analyses
Gene: CACNA1E
Variant/haplotype: rs3845446
Drug(s): fentanyl
Phenotype category: Dosage, Efficacy
Significant: no
Association: Genotype TT is not associated with dose of fentanyl in people with Pain, Postoperative as compared to genotypes CC + CT.
Notes: A formula was developed to predict individual opioid use during the first 24-h post-operative period for patients who underwent craniofacial surgery. The post-operative period R squared values were higher when genotype information was included. In the first group fentanyl was administered by IV, on demand, with a bolus dose of 20 micrograms and a 10 minute lockout period 24-h post-op.
Article: Polymorphisms in STAT4, PTPN2, PSORS1C1 and TRAF3IP2 Genes Are Associated with the Response to TNF Inhibitors in Patients with Rheumatoid Arthritis
Gene: STAT4
Variant/haplotype: rs7574865
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to adalimumab in people with Arthritis, Rheumatoid as compared to allele G.
Notes: No significant associations were seen at either six months or two years after the beginning of treatment when response was measured as number of patients in remission or with low disease activity or by EULAR score.
Article: Comparative efficacy and safety of sitagliptin or gliclazide combined with metformin in treatment-naive patients with type 2 diabetes: A single-center, prospective, randomized, controlled, noninferiority study with genetic polymorphism analysis
Gene: DPP4
Variant/haplotype: rs4664443
Drug(s): sitagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to sitagliptin in people with Diabetes Mellitus, Type 2.
Notes: "Similarly, for the rs4664443 GG genotype, the median HbA1c improvement in the study group was 0.69 (IQR, 0.48–0.91) compared with 1.25 (IQR, 1.00–1.46) in the control group (P < .001), indicating lower efficacy of sitagliptin."
Article: Pharmacogenetic analysis of high-dose methotrexate treatment in children with osteosarcoma
Gene: NR1I2
Variant/haplotype: rs3814055
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased metabolism of methotrexate in children with Osteosarcoma as compared to allele C.
Notes: The T allele is associated with longer half-life of methotrexate.
Article: Susceptibility to thiopurine toxicity by TPMT and NUDT15 variants in Colombian children with acute lymphoblastic leukemia
Gene: NUDT15
Variant/haplotype: rs116855232
Drug(s): mercaptopurine
Phenotype category: Dosage
Significant: no
Association: Genotype CT is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype CC.
Notes: Authors stated "Although no statistically significant associations were identified, two of the four patients; heterozygous for NUDT15 required a decrease in 6-MP during the follow-up period. " No TT homozygotes were observed. "Studies with a larger population size are needed"
Article: No association between IFNL3 (IL28B) genotype and response to peginterferon alfa-2a in HBeAg-positive or -negative chronic hepatitis B
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to peginterferon alfa-2a in people with Hepatitis B, Chronic as compared to genotypes CT + TT.
Notes: The authors found no association between IFNL3 genotype and peginterferon 2a response in either HBeAg-positive or HBeAg-negative chronic hepatitis B patients, in both Asian and White patients.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: EPHX1
Variant/haplotype: rs2234922
Drug(s): carbamazepine
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with resistance to carbamazepine in people with Epilepsy as compared to genotypes AG + GG.
Notes: The authors evaluated the distribution of genotypes between individuals who developed resistance to carbamazepine (CBZ) and those who did not. There were no significant differences in genotype distributions between the two groups.
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: ABCG2
Variant/haplotype: rs2231137
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CC + CT are not associated with concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype TT.
Notes: There is no association between selected SNPs and methotrexate plasma level at 48 h between the first dose of methotrexate infusion. med. MTX concentration: CC +TC (0.45 (0.09–41.63)) vs. TT(0.46 (0.15–10.29)). Please note: alleles have been complemented to the + chromosomal strand.
Article: DRD2, DRD3, and HTR2A Single-Nucleotide Polymorphisms Involvement in High Treatment Resistance to Atypical Antipsychotic Drugs
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: no
Association: Genotype CT is associated with decreased resistance to antipsychotics in people with Mood Disorders or Schizophrenia as compared to genotype CC.
Notes: " The HTR2A rs6311 C|T vs. C|C genotype inversely predicted the; HTR group membership with a significant trend (OR = 0.333; B = −1.1; p = 0.059)."
Article: Genetic markers in CYP2C19 and CYP2B6 for prediction of cyclophosphamide's 4‐hydroxylation, efficacy and side effects in Chinese patients with systemic lupus erythematosus
Gene: GSTP1
Variant/haplotype: rs1695
Drug(s): cyclophosphamide
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of cyclophosphamide in people with as compared to allele A.
Article: Effect of N-Acetyltransferase 2 (NAT2) Genotype on the Pharmacokinetics of Hydralazine during Pregnancy
Gene: NAT2
Variant/haplotype: NAT2*4, NAT2*6, NAT2*7, NAT2*16
Drug(s): hydralazine
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 *4/*16 + *4/*6 + *4/*7 (assigned as rapid acetylator phenotype) are associated with increased metabolism of hydralazine in women with Hypertension and Pregnancy as compared to NAT2 *16/*16 + *16/*6 + *16/*7 + *6/*6 (assigned as slow acetylator phenotype) .
Notes: Originally annotated as NAT2 *4/*5D + *4/*6B + *4/*7A (assigned as rapid acetylator phenotype) compared to NAT2 *5D/*5D + *5D/*6B + *5D/*7A + *6B/*6B (assigned as slow acetylator phenotype). RA group had faster weight-adjusted hydralazine apparent oral clearance (70.0 ± 13.6 vs 20.1 ± 6.9 L/h, P < .05), lower dose-normalized area under the concentration-time curve (AUC; 1.5 ± 0.8 vs 5.9 ± 3.7 ng·h/mL, P < .05), lower dose-normalized peak concentrations (0.77 ± 0.51 vs 4.04 ± 3.18 ng/mL, P < .05), and larger weight-adjusted apparent oral volume of distribution (302 ± 112 vs 116 ± 45 L/kg, P < .05) compared to slow acetylators.; Single-nucleotide polymorphisms (SNPs) in the NAT2 coding region and their corresponding haplotypes were determined using 4-SNP assays, that is, rs181280,c.341T > C; rs1799930, c.590G > A; rs1799931,c.857G > A; rs1801279, c.191G > A, with TaqMan Assays. Subjects were classified as slow acetylators if they had 2 reduced-activity NAT2 alleles (*5, *6, *7, or*14), or rapid acetylators if they carried 1 reduced-activity allele and 1 fully functional allele (*4) or 2 fully functional alleles.; The arylamine N-acetyltransferases (NATs) database was transitioned into the PharmVar database in March 2024. The alleles in this annotation are mapped as following: NAT2*5D under the *16 core allele; NAT2*6B under the *6 core allele; NAT2*7A under the *7 core allele.
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with decreased dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotype CC.
Notes: When considering DONOR genotype - those with the CT or TT genotype had decreased concentration/dose ratios as compared to those with the CC genotype at weeks 1-4 of treatment. In multiple linear regression analysis, donor rs776746 genotype was significantly associated with concentration/dose ratio at week 1 (p<0.001), 3 (p=0.031) and 4 (p=0.027) of treatment. Patients with hepatocellular carcinoma. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Genetic variation in the Catechol-O-Methyltransferase (COMT) gene and morphine requirements in cancer patients with pain
Gene: COMT
Variant/haplotype: rs5746849
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele A 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, rs737866, rs740603, rs6269, rs2239393, rs4818, 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.
Article: Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes GT + TT are not associated with concentrations of ritonavir in children with HIV Infections as compared to genotype GG.
Article: Tacrolimus dose requirements in paediatric renal allograft recipients are characterized by a biphasic course determined by age and bone maturation
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of tacrolimus in children with Kidney Transplantation as compared to genotypes AG + GG.
Notes: Dose-corrected tacrolimus exposure (AUC0-12/doseBW). Please note that alleles have been complemented to the plus chromosomal strand.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: COMT
Variant/haplotype: rs4818
Drug(s): butorphanol
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to butorphanol in healthy individuals as compared to allele C.
Notes: Study-wide significance was set to p<0.017.