shlokn/autogkb huggingface dataset:
Article: ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): methadone
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with increased dose of methadone in people with Heroin Dependence as compared to genotypes AG + GG.
Notes: Please note that alleles have been complemented to the positive strand.
Article: A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients
Variant/haplotype: rs368245720
Drug(s): 6-hydroxy s-warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with increased concentrations of 6-hydroxy s-warfarin in people with Atrial Fibrillation, venous thromboembolism or Heart Valve Diseases as compared to allele T.
Notes: measured as increased S-6OH-warfarin and using a genome wide significance threshold of < 3.846 × 10−9. Effect direction from supplementary table S9. There were five SNPs in the same intergenic region on chromosome 10 with same p value (rs368245720, rs541817388, 10:107692518:AC:A, rs112552343, rs372488899).
Article: Polymorphisms in ABCB1 and CYP19A1 genes affect anastrozole plasma concentrations and clinical outcomes in postmenopausal breast cancer patients
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): anastrozole
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased concentrations of anastrozole in women with Breast Neoplasms as compared to genotypes AC + CC.
Notes: Alleles have been complemented to the positive strand.
Article: Influence of (ATP)-Binding Cassette Transporter Subfamily B Member 1 (ABCB1) Gene Polymorphism on the Efficacy of Remifentanil
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): remifentanil
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of remifentanil as compared to genotype AA.
Notes: Patients with the GG genotype had significantly increased consumption of remifentanil during surgery than patients with the AA genotype.
Article: Pilot Study: Personalized Medicine in Endoscopy, Can Pharmacogenomics Predict Response to Conscious Sedation?
Gene: UGT1A1
Variant/haplotype: UGT1A1 poor metabolizer
Drug(s): fentanyl, meperidine, midazolam
Phenotype category: Metabolism/PK
Significant: yes
Association: UGT1A1 poor metabolizer is associated with decreased dose of fentanyl, meperidine or midazolam in people with sedation as compared to UGT1A1 normal metabolizer.
Notes: "Patients were divided into two groups based on sedation requirements during endoscopy (high vs. normal sedation). The high sedation requirement group was defined by a sedation requirement of midazolam >10 mg, fentanyl >100 mcg, meperidine >100 mg, or an aborted procedure due to failed moderate sedation and/or the transition to propofol sedation to complete the procedure. The normal sedation requirement group was defined as the complete absence of the above conditions that define the high sedation requirement group." "Patients with reduced CYP2C19 metabolism (poor + intermediate metabolizers) (OR = 0.38, 95% CI: 0.16–0.91, p = 0.03), poor CYP3A5 metabolism (OR = 0.25, 95% CI: 0.095–0.65, p = 0.0046), and poor UGT1A1 (OR = 2.76, 95% CI: 1.07–7.13, p = 0.08) had higher odds of requiring normal sedation compared to those with CYP2C19 increased metabolism, CYP3A5 intermediate metabolism, and UGT1A1 intermediate metabolism"
Article: Polymorphisms of MTHFR Associated with Higher Relapse/Death Ratio and Delayed Weekly MTX Administration in Pediatric Lymphoid Malignancies
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in children with Lymphoma, Non-Hodgkin or Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
Notes: No significant difference in relapse-free survival between genotype groups.
Article: Plasma Letrozole Concentrations in Postmenopausal Women With Breast Cancer Are Associated With CYP2A6 Genetic Variants, Body Mass Index, and Age
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*26
Drug(s): letrozole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2A6 *1/*26 is associated with metabolism of letrozole in women with Breast Neoplasms.
Notes: CYP2A6*1/*26 is associated with normal metabolism of letrozole (compared to slow metabolism of nicotine).
Article: Polymorphisms in drug-metabolizing enzymes and steady-state exemestane concentration in post-menopausal patients with breast cancer
Gene: CYP1B1
Variant/haplotype: rs162555
Drug(s): exemestane
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT are not associated with concentrations of exemestane in women with Breast Neoplasms as compared to genotype CC.
Notes: No significant difference in exemestane concentrations were seen between the three genotypes. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: GREM2
Variant/haplotype: rs4659982
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with increased response to allopurinol.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment.
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: CYP2C9
Variant/haplotype: rs1799853
Drug(s): sitagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to sitagliptin in people with Diabetes Mellitus, Type 2.
Notes: "CYP2C9 gene polymorphisms also significantly influenced treatment efficacy. Patients with the rs1799853 TT genotype in the study group had a median HbA1c improvement of 0.70 (IQR, 0.69–0.72), while the control group showed 1.07 (IQR, 0.82–1.42; P < .001)."
Article: Polymorphisms associated with everolimus pharmacokinetics, toxicity and survival in metastatic breast cancer
Gene: CYP2C8
Variant/haplotype: rs11572080
Drug(s): everolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT are not associated with concentrations of everolimus in women with Breast Neoplasms as compared to genotype CC.
Notes: Please note: alleles have been complemented to the positive chromosomal strand.
Article: Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate
Gene: GLRB
Variant/haplotype: rs17035723
Drug(s): acamprosate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to acamprosate in people with Alcoholism as compared to allele C.
Notes: Tag SNPs (518 total) were selected within genes associated with alcoholism as well as genes encoding enzymes involved in glycine metabolism, glycine transporters, subunits of glycine receptors, NMDA receptors, genes involved in glutamate reuptake, synthesis or degradation and genes with reported associations with acamprosate treatment outcomes in human or animal studies. The length of time to first alcohol use “survival analysis method” was used to examine associations between clinical variables and genetic markers with efficacy of acomprasate (its ability to length  the duration of abstinence from alcohol).  The analyses were replicated in a subset of 110 participants from PREDICT, a double-blind randomized controlled trial that compared treatment outcomes including length of abstinence among alcohol- dependent subjects of German descent recruited from inpatient facilities and treated with acamprosate, naltrexone or placebo for 3 months.  rs17035723 A allele was nominally associated with shorter abstinence after Bonferroni correction for the number of SNPs included in the analyses in the male only cohort (N=148) of the discovery sample (P = 9.8 × 10 - 5, corrected P = 0.0507).
Article: Optimal predictor for 6-mercaptopurine intolerance in Chinese children with acute lymphoblastic leukemia: NUDT15, TPMT, or ITPA genetic variants?
Gene: NUDT15
Variant/haplotype: rs116855232
Drug(s): mercaptopurine
Phenotype category: Dosage, Toxicity
Significant: no
Association: Allele T is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele C.
Notes: as measured by 6-MP dose intensity, which is a measure dose adjustment due to toxicity calculated by the ratio of the prescribed 6-MP dose over the protocol dose of 50 mg/m2/d. TT had lowest intensity, heterozygotes had intermediate intensity and CC highest intensity.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: DPYD
Variant/haplotype: rs2297595
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 3.3E-3.
Article: Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy
Gene: CYP19A1
Variant/haplotype: rs10046
Drug(s): hdl cholesterol
Phenotype category: Other
Significant: yes
Association: Allele G is associated with decreased concentrations of hdl cholesterol in women with Breast Neoplasms and Menopause as compared to allele A.
Notes: when taking letrozole and lipid lowering agents (LLA), such as statins. Data are from a sub-analysis of the Exemestane and Letrozole Pharmacogenomics (ELPh) study, where post-menopausal women with early stage breast cancer were randomized to receive exemestane or letrozole. Of the 303 eligible women, 160 were randomized to the letrozole group, 52 of whom were also taking LLA. This SNP was associated with decreases in HDL-cholesterol of 6.2 mg/dL (SE 1.6).
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA5
Variant/haplotype: rs680244
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele T is not associated with exposure to nicotine in men as compared to allele C.
Notes: The T allele was initially associated with an increased likelihood of being a smoker but this lost significance following correction for multiple testing.
Article: Effects of cytochrome P450 2B6 and constitutive androstane receptor genetic variation on Efavirenz plasma concentrations among HIV patients in Kenya
Gene: CYP2B6
Variant/haplotype: rs8192719
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele C.
Notes: Described as 21563C>T
Article: Gene‐Wide Tagging Study of the Association Between KCNT1 Polymorphisms and the Susceptibility and Efficacy of Genetic Generalized Epilepsy in Chinese Population
Gene: KCNT1
Variant/haplotype: rs10776845
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele C.
Notes: No significant differences in genotype frequencies were seen between patients who were responsive to antiepileptic drugs (n=279; those who had not experienced any type of seizure for a minimum of 1 year after receiving antiepileptic drugs) and patients who were resistant to antiepileptic drugs (n=204; those who had at least four seizures during the previous year while trying at least three antiepileptic medications at the maximal tolerated doses).
Article: First-line eradication for Helicobacter pylori-positive gastritis by esomeprazole-based triple therapy is influenced by CYP2C19 genotype
Gene: CYP2C19
Variant/haplotype: CYP2C19 normal metabolizer genotype
Drug(s): amoxicillin, clarithromycin, esomeprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 normal metabolizer is associated with decreased response to amoxicillin, clarithromycin and esomeprazole in people with Gastritis as compared to CYP2C19 intermediate metabolizer and poor metabolizer.
Notes: Patients tested positive for h. pylori and were treated with 400 mg/d EPZ, 1500 mg/d AMPC, and 400 mg/d CAM for 7 days. All drugs were given twice per day.
Article: PCK1 and SLC22A2 gene variants associated with response to metformin treatment in type 2 diabetes
Gene: PCK1
Variant/haplotype: rs4810083
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to genotype CC.
Notes: "NRs were predominantly homozygous for the alternative allele (55.0%). In comparison, in responders, only 18.0% were homozygous for the alternative allele. Thus, individuals that are homozygous carriers of the PCK1-rs4810083 alternative allele have 5.6 times more risk of being NRs to metformin than the 2 other genotype’s carriers (recessive model: OR =  5.56, IC 95% [1.86–16.63])."
Article: Polymorphism of μ-Opioid Receptor Gene (OPRM1:c.118A>G) Might Not Protect against or Enhance Morphine-Induced Nausea or Vomiting
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): morphine
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of morphine in women with Pain, Postoperative as compared to allele A.
Article: Adverse Cardiovascular Outcomes and Antihypertensive Treatment: A Genome-Wide Interaction Meta-Analysis in the International Consortium for Antihypertensive Pharmacogenomics Studies
Variant/haplotype: rs139945292
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to Beta Blocking Agents in people with Hypertension as compared to allele C.
Notes: The T-allele of this variant was associated with less BP reduction (systolic BP response P = 6 × 10−4, Beta = 3.09, diastolic BP response P = 5 × 10−3, Beta = 1.53) after treatment with β-blockers.
Article: Influence of common and rare genetic variation on warfarin dose among African–Americans and European–Americans using the exome array
Variant/haplotype: rs12772169
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with dose of warfarin as compared to allele C.
Notes: in patients initiating warfarin treatment with a target international normalized ratio (INR) of 2 to 3. Direction of the relationship of allele to dose is not explicitly stated. Table 4 lists minor allele as A, dbSNP lists as C/T with T as minor allele.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: NTRK2
Variant/haplotype: rs4877900
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotype CC is associated with decreased dose of methadone in people with Heroin Dependence as compared to genotypes CT + TT.
Notes: This association was not statistically significant after permutation analysis based on 40,000 replicates, and not statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction). Note; this SNP was in LD with rs4358872, rs1948308, and rs2378676 (r^2>0.7).
Article: Angiotensin-converting enzyme gene polymorphism predicts the time-course of blood pressure response to angiotensin converting enzyme inhibition in the AASK trial
Gene: ACE
Variant/haplotype: rs4363
Drug(s): ramipril
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are not associated with increased response to ramipril in people with Hypertension as compared to genotype GG.
Notes: This SNP was also reported as ACE G20037A. No association was seen between this SNP and time to target blood pressure.
Article: Association of variants in NEDD4L with blood pressure response and adverse cardiovascular outcomes in hypertensive patients treated with thiazide diuretics
Gene: NEDD4L
Variant/haplotype: rs4149601
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype AA.
Notes: AG and GG patients had significantly greater reduction in Systolic and in Diastolic Blood pressure than those with AA genotype.  As this association was tested as a replication attempt, p was not adjusted for multiple testing as it was for the other SNPs in this study.; A significant association was also seen between the haplotype rs4149601G/rs292449C and greater response to hydrachlorothiazide in Whites.
Article: Pharmacodynamic and kinetic effect of rabeprazole on serum gastrin level in relation to CYP2C19 polymorphism in Chinese Hans
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): rabeprazole
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *1/*2 + *1/*3 is not associated with metabolism of rabeprazole in healthy individuals as compared to CYP2C19 *2/*2.
Notes: No significant difference in area under the concentration-time curve (AUC) for rabeprazole were seen between the two genotype groups. Subjects were given rabeprazole for 8 days; AUC was measured on day 1 and day 8 after rabeprazole administration. Please note that the *2 and *3 alleles were referred to by their previous designations (CYP2C19*m1 and *m2, respectively).
Article: Thiopurine dose intensity and treatment outcome in childhood lymphoblastic leukaemia: the influence of thiopurine methyltransferase pharmacogenetics
Gene: TPMT
Variant/haplotype: TPMT*1, TPMT*3C
Drug(s): mercaptopurine, thioguanine
Phenotype category: Dosage
Significant: yes
Association: TPMT *1/*3C is associated with decreased dose of mercaptopurine or thioguanine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to TPMT *1/*1.
Notes: As compared to those with the wild-type genotype (*1/*1), those patients with the *1/*3C genotype had a lower average dose (72.5% vs 78.0%, where dose given as the % of standard protocol dose).
Article: Genome-wide and candidate gene approaches of clopidogrel efficacy using pharmacodynamic and clinical endpoints - Rationale and design of the International Clopidogrel Pharmacogenomics Consortium (ICPC)
Gene: CYP2C19
Variant/haplotype: CYP2C19*2
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *2 is associated with decreased response to clopidogrel.
Notes: Validation of ICPC central database. CYP2C19*2 was associated with increased on-treatment platelet reactivity.
Article: Analysis of Genetic and Clinical Factors Associated with Buprenorphine Response
Variant/haplotype: rs62368105
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to buprenorphine in people with Opioid-Related Disorders as compared to allele A.
Notes: Authors note that this association is nominally significant.
Article: Association of clozapine-related metabolic disturbances with CYP3A4 expression in patients with schizophrenia
Gene: CYP1A2
Variant/haplotype: CYP1A2 low activity
Drug(s): n-desmethylclozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP1A2 low activity is associated with decreased concentrations of n-desmethylclozapine in people with Schizophrenia as compared to CYP1A2 high activity.
Notes: comapring n-desemethylclozapine in patients’ peripheral leukocytes with low and normal/high CYP1A2 expression where all had normal/high CYP3A4 expression. AUthors describe "further contribution of CYP1A2 to norclozapine production was also demonstrated".  Authors did genotype for some CYP1A2 and CYP3A4/5 alleles but these "alleles did not explain the inter-individual differences in CYP3A4 mRNA levels" and "hepatic CYP1A2 and CYP3A4 activities were therefore estimated from mRNA levels in patients’ leukocytes, categorizing the patients into low, normal and high expresser groups"
Article: Phase II study of S-1 combined with oxaliplatin as therapy for patients with metastatic biliary tract cancer: influence of the CYP2A6 polymorphism on pharmacokinetics and clinical activity
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*4, CYP2A6*7, CYP2A6*9, CYP2A6*10
Drug(s): tegafur
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2A6 *1/*1 is associated with increased metabolism of tegafur in people with biliary tract neoplasms as compared to CYP2A6 *1/*10 + *1/*4 + *1/*7 + *1/*9 + *4/*9 + *7/*10 + *7/*9 + *9/*9.
Notes: *1/*1 carriers had a metabolic ratio of fluorouracil/tegafur around 1.85-fold higher compared to carriers of *4, *7, *9 and *10 alleles.
Article: Impact of Polymorphism of CYP2D6 on Equilibrium Concentration of Duloxetine in Patients Suffering from Major Depressive Disorder
Gene: CYP2D6
Variant/haplotype: rs3892097
Drug(s): duloxetine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased clinical benefit to duloxetine in men with Alcoholism and Depressive Disorder as compared to genotype CT.
Notes: CC had greater decreases in score on HAMD after 8 weeks. Alleles complemented. No TT were observed.
Article: Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CC + CT are not associated with concentrations of lopinavir in children with HIV Infections as compared to genotype TT.
Article: A pharmacogenetic pilot study reveals MTHFR, DRD3, and MDR1 polymorphisms as biomarker candidates for slow atorvastatin metabolizers
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): atorvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with increased concentrations of atorvastatin in healthy individuals as compared to genotype GG.
Article: Role of rs3846662 and HMGCR alternative splicing in statin efficacy and baseline lipid levels in familial hypercholesterolemia
Gene: HMGCR
Variant/haplotype: rs3846662
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased response to hmg coa reductase inhibitors in women with familial hypercholesterolemia as compared to allele G.
Notes: The percentage reduction in LDL-cholesterol upon statin treatment was significantly decreased in women with the AA genotype
Article: GENE AND GENE BY SEX ASSOCIATIONS WITH INITIAL SENSITIVITY TO NICOTINE IN NONSMOKERS
Gene: DRD2
Variant/haplotype: rs6277
Drug(s): nicotine
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to nicotine in women as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand. No significant association between this variant and nicotine reward, perception, mood or reinforcement or physiological responses to nicotine.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with decreased metabolism of carbamazepine in men with Epilepsy as compared to genotype CC.
Notes: as measured by a lower carbamazepine-10-11 epoxide:carbamazepine metabolite ratio. This association was only significant in male patients.