shlokn/autogkb huggingface dataset:
Article: Serotonin transporter 5-HTTLPR polymorphism and escitalopram treatment response in patients with major depressive disorder
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: yes
Association: SLC6A4 HTTLPR short form (S allele) is associated with decreased response to escitalopram in people with Major Depressive Disorder as compared to SLC6A4 HTTLPR long form (L allele).
Notes: "For each S-allele of the 5-HTTLPR variant, a significantly decreased response to escitalopram by 58% was observed in the log-additive model (OR 0.42, 95% CI 0.20–0.85, p = 0.015). The association between the 5-HTTLPR genotype and response to escitalopram treatment was not affected by adjustment for the presence of different metabolizers status of CYP2C19 and CYP2D6 (Model 2), the association between the 5-HTTLPR genotype and response to escitalopram treatment remained significant."
Article: CYP3A4*1B but Not CYP3A5*3 as Determinant of Long-Term Tacrolimus Dose Requirements in Spanish Solid Organ Transplant Patients
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased dose of tacrolimus in people with Transplantation as compared to genotype TT.
Notes: "Significant differences in weight-adjusted dose (p = 0.007) and a trend in Co/dose (p = 0.056) were found between CYP3A4*1B allele carriers and non-carriers. Figure 2 and Figure 3 show plots of weight-adjusted dose and Co/dose for the two groups of CYP3A4 genotypes (rs2740574)." Transplants included 14 hepatic, 9 renal, 2 cardiac and one pulmonary (from table 1). Alleles complemented.
Article: A Common Susceptibility Gene for Type 2 Diabetes Is Associated with Drug Response to a DPP-4 Inhibitor: Pharmacogenomic Cohort in Okinawa Japan
Gene: CDKAL1
Variant/haplotype: rs7754840
Drug(s): Dipeptidyl peptidase 4 (DPP-4) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to Dipeptidyl peptidase 4 (DPP-4) inhibitors in people with Diabetes Mellitus as compared to allele G.
Notes: The SNP was significantly associated with improved response to DPP-4 inhibitors (as assayed by reductions in HbA1c). Most of the patients were on combination anti-diabetic agent (ADA) therapy, but the relationship was only significant for regimens that included DPP-4 (alone or in combination with other ADAs).
Article: Pharmacogenomic diversity of tamoxifen metabolites and estrogen receptor genes in Hispanics and non-Hispanic whites with breast cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer is associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 normal metabolizer.
Notes: Article compares endoxifen concentrations in Hispanic vs. White. No statistical analysis done for association of CYP2D6 genotype and endoxifen concentration in individual ethnicites. Endoxifen concentrations are given for AS1, AS 0.5 and AS 0. Pre- (23% Hispanic-30% NHW) and postmenopausal (77% Hispanic-65% NHW) ER-positive Breast cancer patients receiving tamoxifen (20 mg daily) for at least 8 weeks with 50% in both cohorts also receive aromatase inhibitor therapy. DNA extracted from blood. *1, *2, *3, *4, *6 were evaluated for CYP2D6. [pre-menopausal][post-menopausal] [adjuvant] [DNA source: blood]
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with increased clearance of carbamazepine in people with Epilepsy as compared to genotype GG.
Notes: This association was only significant in Caucasian patients and not in African American patients. It was also associated with higher higher carbamazepine-10-11 epoxide:  carbamazepine ratio in women (p=0.002).
Article: A PHARMACOGENETIC STUDY OF ALDEHYDE OXIDASE I IN PATIENTS TREATED WITH XK469
Gene: AOX1
Variant/haplotype: rs10931910
Drug(s): XK469
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with decreased clearance of XK469 in people with Neoplasms as compared to allele A.
Article: Drug Metabolizing Enzyme and Transporter Gene Variation, Nicotine Metabolism, Prospective Abstinence, and Cigarette Consumption
Gene: CYP2A6
Variant/haplotype: rs1137115
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with metabolism of nicotine as compared to allele T.
Notes: In the discovery stage: Participants derived from 1) the PKTWIN study and 2) the SMOFAM studyBoth were assessed for nicotine metabolite ratio (NMR) which was used as a biomarker of CYP2A6 activity. Nominally significant SNPs in the discovery stage were tested in the validation stage. Validation stage participants were self-identified White participants from 8 clinical trials of smoking cessation therapies conducted in six US sites.
Article: Sub‐ and supratherapeutic efavirenz plasma concentrations with risk for HIV therapy failure are mainly genetically explained in Ugandan children: The prospective GENEFA cohort study
Gene: CYP2B6
Variant/haplotype: rs4803419
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of efavirenz in children with HIV infectious disease as compared to genotypes CC + CT.
Notes: "Homozygosity for CYP2B615582C>T predicted lower log EFV,"
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer and intermediate metabolizer genotypes
Drug(s): N-desmethyltamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of n-desmethyltamoxifen in women with Breast Neoplasms.
Article: ABCB1 Polymorphism Is Associated with Higher Carbamazepine Clearance in Children
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele A is associated with increased clearance of carbamazepine in children with Epilepsy as compared to allele C.
Notes: Alleles complemented. "Our main finding was that the presence of the ABCB1 1236T-2677T-3435T haplotype was associated with an increased clearance of CBZ in children. " "rs2032582 (2677G>T/A)"
Article: Inherited amplification of an active gene in the cytochrome P450 CYP2D locus as a cause of ultrarapid metabolism of debrisoquine
Gene: CYP2D6
Variant/haplotype: CYP2D6*2xN
Drug(s): debrisoquine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *2xN is associated with increased metabolism of debrisoquine.
Notes: Very rapid metabolism of debrisoquine was seen in two families [metabolic ratio (MR) for debrisoquine = 0.01-0.1].  Allele was reported as CYP2D6L with two mutations: one in exon 6 (Arg-296-->Cys) and one in exon 9 (Ser-486-->Thr).
Article: Variants in Pharmacokinetic Transporters and Glycemic Response to Metformin: A Metgen Meta‐Analysis
Gene: SLC22A1
Variant/haplotype: rs72552763
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele del is not associated with response to metformin in people with Diabetes Mellitus, Type 2 as compared to allele GAT.
Notes: This variant is not associated with metformin glycemic response assessed as HbA1c reduction in patients on metformin monotherapy.
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizers and intermediate metabolizers
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 poor metabolizers and intermediate metabolizers is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to CYP2C19 normal metabolizer and ultra-metabolizer.
Notes: Response defined by changes in the rate of dropout from treatment between metabolizer phenotypes. Study genotyped for the CYP2C19 *1, *2, *3, *4, *5, *6, *7, *8 and *17 and then assigned metabolizer phenotypes.
Article: PPAR-γ2 and PTPRD gene polymorphisms influence type 2 diabetes patients' response to pioglitazone in China
Gene: PPARG
Variant/haplotype: rs1801282
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CG is associated with increased response to pioglitazone in people with Diabetes Mellitus, Type 2 as compared to genotype CC.
Notes: Patients with the CG genotype showed significantly greater decreases in fasting plasma glucose levels and triglyceride levels after 3 months of pioglitazone treatment. However, changes in other biochemical measures were not significant.
Article: Effects of genetic variants of organic cation transporters on metformin response in newly diagnosed patients with type 2 diabetes
Gene: ATM
Variant/haplotype: rs11212617
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with decreased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: "Other SNPs (rs4621031, rs34399035, rs1800058, and rs11212617) had no significant impact on metformin response. "
Article: IL28B polymorphisms associated with therapy response in Chilean chronic hepatitis C patients
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CT + TT.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs4587017
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is associated with decreased response to fentanyl in people with Pain, Postoperative as compared to genotypes GG + GT.
Notes: There was a significant difference in PPLpost-PPLpre between the genotype groups.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: PAPPA2
Variant/haplotype: rs77977790
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to salbutamol in children with Asthma as compared to genotype TT.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  This association was significant in the initial GWAS (in GALA II), but it was not significant in an attempted replication by imputation in silico in GALA I.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.
Article: Correlation of MDR1 gene polymorphism with propofol combined with remifentanil anesthesia in pediatric tonsillectomy
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): propofol, remifentanil
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to propofol and remifentanil in children as compared to allele A.
Notes: Referred to as 2677 G>T/A Please note that alleles have been complemented to the positive strand.
Article: Germline Genetic Variants in TEK, ANGPT1, ANGPT2, MMP9, FGF2 and VEGFA Are Associated with Pathologic Complete Response to Bevacizumab in Breast Cancer Patients
Gene: ANGPT2
Variant/haplotype: rs2515462
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to bevacizumab in women with Breast Neoplasms as compared to allele G.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: OPRM1
Variant/haplotype: rs558025
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotypes AG + GG are associated with decreased dose of methadone in people with Heroin Dependence as compared to genotype AA.
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 is in LD with rs660756 (r^2>0.7).
Article: Pharmacogenetics of TNF inhibitor response in rheumatoid arthritis utilizing the two-component disease activity score
Variant/haplotype: rs1350948
Drug(s): adalimumab, certolizumab pegol, etanercept, infliximab, Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to adalimumab, certolizumab pegol, etanercept, infliximab or Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: as measured by change in 2C-DAS28. Table 2 shows change was a negative value for this variant suggesting decreased 2C-DAS28 and increased response, it was not attributed to a particular allele at this rs number location so assumed minor allele based on dbSNP frequencies.
Article: Artemisinin-resistant Plasmodium falciparum in Pursat province, western Cambodia: a parasite clearance rate study
Gene: G6PD
Variant/haplotype: rs1050828
Drug(s): artemisinin and derivatives
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to artemisinin and derivatives in people with Malaria, Falciparum as compared to allele C.
Notes: G6PD deficient (those with genotype TT, TC, or T in males) compared to non-deficient (genotype CC or C in males). No difference in efficacy of parasite clearance was observed. Patients were treated with artemether-lumefantrine or artesunate and mefloquine.
Article: Effect of NOS3 gene polymorphism on response to Tricyclic antidepressants in migraine attacks
Gene: NOS3
Variant/haplotype: rs1799983
Drug(s): nortriptyline
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to nortriptyline in people with Migraine without Aura or Migraine with Aura as compared to genotypes GG + GT.
Notes: SNP referred to as Glu298Asp in the paper and mapped to rs1799983 by PharmGKB. The TT genotype was significantly associated with a reduced frequency of migraine attacks in patients using tricyclic antidepressants
Article: A novel treatment of cystic fibrosis acting on-target: cysteamine plus epigallocatechin gallate for the autophagy-dependent rescue of class II-mutated CFTR
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): cysteamine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CTT/del + del/del are associated with increased response to cysteamine in people with Cystic Fibrosis as compared to genotype CTT/CTT.
Notes: Improvement measured as change in CFTR function by changes in chloride concentration. Patients with class II mutations benefit from cysteamine, whereas patients carrying 2 class I mutations do not. Schedule of treatment was cysteamine alone for 8 weeks, followed by cysteamine plus EGCG for 4 weeks, then EGCG alone for 8 weeks. Subjects continued other therapy throughout.
Article: Azathioprine Biotransformation in Young Patients with Inflammatory Bowel Disease: Contribution of Glutathione-S Transferase M1 and A1 Variants
Gene: GSTM1
Variant/haplotype: GSTM1 non-null, GSTM1 null
Drug(s): azathioprine
Phenotype category: Efficacy
Significant: yes
Association: GSTM1 null is associated with decreased clinical benefit to azathioprine in children with Colitis, Ulcerative or Crohn Disease as compared to GSTM1 non-null.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: POU2F2
Variant/haplotype: rs1869641
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: The association of COMT genotype with buproprion treatment response in the treatment of major depressive disorder
Gene: COMT
Variant/haplotype: rs4680
Drug(s): bupropion
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased response to bupropion in people with Depressive Disorder, Major as compared to genotype AA.
Notes: Relationship is reported as beneficial for Met/Val or Val/Val compared to Met/Met. The rs number is listed but not which base corresponds to the protein change: Met = rs4680A and Val = rs4680G.
Article: Observational Study of Associations between Voriconazole Therapeutic Drug Monitoring, Toxicity, and Outcome in Liver Transplant Patients
Gene: CYP2C19
Variant/haplotype: CYP2C19 ultrarapid metabolizer
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 ultrarapid metabolizer is associated with decreased trough concentration of voriconazole in people with Mycoses as compared to CYP2C19 normal metabolizer.
Notes: Poor metabolizers = PMs (n=7); Intermediate metabolizers = IMs (n=24); Extensive metabolizers = EMs (n=30); Ultrarapid metabolizers = UMs (n=14). Patients were liver transplant recipients with known or suspected invasive fungal infections.
Article: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Gene: COMT
Variant/haplotype: rs4680
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 A.
Notes: Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: PSMD14
Variant/haplotype: rs9713
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to risperidone in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Influence of SLCO1B3 haplotype-tag SNPs on docetaxel disposition in Chinese nasopharyngeal cancer patients
Gene: SLCO1B3
Variant/haplotype: rs7311358
Drug(s): docetaxel
Phenotype category: Other, Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of docetaxel in people with Nasopharyngeal Neoplasms.
Notes: Significance as part of a haplotype with rs4149118, rs11045585 and rs3834935.
Article: TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives
Gene: CSMD1
Variant/haplotype: rs7387065
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with decreased response to hydrochlorothiazide in people with Essential hypertension as compared to allele G.
Notes: The SNP was discovered in two independent cohorts, although no SNPs reached genome wide significance. The authors then considered P<1 x10^-5 as a threshold for significance (based on the results from a Q-Q plot distribution reference line). Using this revised threshold the authors reported that this SNP was associated with a lower decrease in systolic blood pressure after hydrochlorothiazide treatment.
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: CYP3A5
Variant/haplotype: rs776746
Drug(s): rivaroxaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased steady-state concentration of rivaroxaban in people with Atrial Fibrillation as compared to genotypes CC + CT.
Notes: "In our results, the heterozygous and homozygous mutated groups of CYP3A5*3 displayed lower plasma concentrations than the individuals having wild-type genotypes, as shown in Table 1."
Article: G Protein-Coupled Receptor Kinase 5 Gene Polymorphisms Are Associated with Postoperative Atrial Fibrillation Following Coronary Artery Bypass Graft Surgery in Patients Receiving Beta-Blockers
Gene: CYP2D6
Variant/haplotype: rs16947
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Beta Blocking Agents in people with Coronary Artery Disease as compared to allele G.
Notes: Single-nucleotide polymorphisms in 10 candidate genes were tested for association with atrial fibrillation after coronary artery bypass grafting despite perioperative beta blocker therapy.
Article: Nephrotoxicity in a Patient With Inadequate Pain Control: Potential Role of Pharmacogenetic Testing for Cytochrome P450 2D6 and Apolipoprotein L1
Gene: CYP2D6
Variant/haplotype: CYP2D6*5, CYP2D6*17
Drug(s): hydromorphone
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *5/*17 is associated with decreased concentrations of hydromorphone in women.
Notes: Case report of a patient taking hydromorphone for back pain with no detectable hydromorphone concentrations in urine screen.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs4235108
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele G.
Notes: There was no significant difference in 24 hour fentanyl use between the genotype groups.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ATIC
Variant/haplotype: rs2372536
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Notes: The allele was initially significant did not remain significant after multiple-testing corrections.
Article: The impact of diuretic use and ABCG2 genotype on the predictive performance of a published allopurinol dosing tool
Gene: SLC17A1
Variant/haplotype: rs1183201
Drug(s): allopurinol
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of allopurinol in people with Gout as compared to allele A.