shlokn/autogkb huggingface dataset:
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs2535764
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele C.
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: Association of CYP3A4-392A/G, CYP3A5-6986A/G, and ABCB1-3435C/T Polymorphisms with Tacrolimus Dose, Serum Concentration, and Biochemical Parameters in Mexican Patients with Kidney Transplant
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype TT is not associated with increased concentrations of tacrolimus in people with Kidney Transplantation as compared to genotype CT.
Notes: Alleles complemented.
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to allopurinol as compared to allele G.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment. This SNP is in perfect LD with rs45499402.
Article: Disposition Kinetics and Metabolism of Nicotine and Cotinine in African American smokers: Impact of CYP2A6 Genetic Variation and Enzymatic Activity
Gene: CYP2A6
Variant/haplotype: CYP2A6*4, CYP2A6*9, CYP2A6*17, CYP2A6*26
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2A6 *4/*17 + *9/*26 are associated with decreased metabolism of nicotine.
Notes: The two slowest metabolizers in the study (*4/*17 and *9/*26 genotypes) showing much lower cotinine levels than expected for their daily nicotine intake, which is the result of not converting much nicotine to cotinine.
Article: Dolutegravir pharmacokinetics in Ugandan patients with TB and HIV receiving standard- versus high-dose rifampicin
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28, UGT1A1*36
Drug(s): dolutegravir
Phenotype category: Metabolism/PK
Significant: no
Association: UGT1A1 *1/*28 + *1/*36 + *28/*28 is not associated with metabolism of dolutegravir in people with HIV Infections and Tuberculosis as compared to UGT1A1 *1/*1.
Notes: "Genetic polymorphism of UGT1A1 did not significantly affect dolutegravir pharmacokinetics."
Article: Effects of OPRM1 and ABCB1 gene polymorphisms on the analgesic effect and dose of sufentanil after thoracoscopic-assisted radical resection of lung cancer
Gene: OPRM1
Variant/haplotype: rs563649
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of sufentanil in people with Lung Neoplasms and Pain, Postoperative as compared to allele T.
Notes: No significant association between this variant and consumption of sufentanil. While this variant is described in the text as a C>T SNP, it is displayed in the table as a G>A SNP. dbSNP confirms that this is a C>T SNP so it has been assumed that this is an error in the tables. As a result, information from the tables has been assigned to the following genotypes: AA=CC, AG=CT and GG=TT.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC47A1
Variant/haplotype: rs2289669
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with exposure to metformin as compared to allele G.
Article: CYP2D6 Haplotype Determination Using Long Range Allele-Specific Amplification: Resolution of a Complex Genotype and a Discordant Genotype Involving the CYP2D6*59 Allele
Gene: CYP2D6
Variant/haplotype: CYP2D6*4, CYP2D6*59
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*59 (assigned as intermediate metabolizer phenotype) is associated with decreased metabolism of dextromethorphan.
Notes: Subject with the *4/*59 diplotype had a dextromethorphan/dextrorphan urinary metabolic ratio of 0.165 with was consistent with intermediate metabolizer phenotype.
Article: Pharmacogenetic association with early response to intravitreal ranibizumab for age-related macular degeneration in a Korean population
Gene: VEGFA
Variant/haplotype: rs833069
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to ranibizumab in people with Macular Degeneration as compared to allele T.
Notes: Age-related macular degeneration. No significant differences in best-corrected visual acuity (BCVA) changes were seen between baseline and 3 or 6 months of treatment between any of the genotypes.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: SPSB2
Variant/haplotype: rs12302749
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele C 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: Functional Mu Opioid Receptor Polymorphism (OPRM1 A118G) Associated With Heroin Use Outcomes in Caucasian Males: A Pilot Study
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): heroin
Phenotype category: Toxicity
Significant: no
Association: Allele G is not associated with dose of heroin in men Heroin Dependence as compared to allele A.
Notes: No association between this variant and heroin use in the last month.
Article: Genetic Variant in CHRNA5 and Response to Varenicline and Combination Nicotine Replacement in a randomized placebo-controlled trial
Gene: CHRNA5
Variant/haplotype: rs16969968
Drug(s): varenicline
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to varenicline in people with Tobacco Use Disorder.
Notes: compared to placebo. In African American smokers, varenicline was more effective in smokers of GA/AA genotypes vs. placebo. There was no significant genotype-by-treatment interaction in smokers of European ancestry.
Article: Tamoxifen Dose Escalation in Patients With Diminished CYP2D6 Activity Normalizes Endoxifen Concentrations Without Increasing Toxicity
Gene: CYP2D6
Variant/haplotype: CYP2D6 normal metabolizer and ultrarapid metabolizer
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 normal metabolizer and ultra-metabolizer are associated with increased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 poor metabolizers and intermediate metabolizers.
Notes: at baseline before genotype guided dosing. In this CYP2D6 genotype-guided study, women who were initially receiving 20 mg/day of tamoxifen, were given 40 mg/day if they were CYP2D6 poor (N=17) or intermediate metabolizers (N=212), but remained on the 20 mg/day dose if they were CYP2D6 extensive (N=119) or ultra-metabolizer phenotype (N=5). The UM/PM had significantly higher concentrations of endoxifen at baseline as compared to the IM and PM phenotypes.
Article: Effect of deletion polymorphism of angiotensin converting enzyme gene on progression of diabetic nephropathy during inhibition of angiotensin converting enzyme: observational follow up study
Gene: ACE
Variant/haplotype: rs1799752
Drug(s): captopril
Phenotype category: Efficacy
Significant: yes
Association: Genotype del/del is associated with increased resistance to captopril in people with Diabetes Mellitus as compared to genotypes ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC + ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del.
Notes: Patients with the del/del genotype had steeper decline in glomerular filtration rate (GFR) compared to the other genotypes, indicating a decline in renal function.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRK1
Variant/haplotype: rs16918941
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele G.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: C6
Variant/haplotype: rs10052999
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is not associated with dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotypes CC + TT.
Notes: When considering RECIPIENT genotype -  no significant difference in concentration/dose ratio was seen between those with the CT genotype and those with the CC or TT genotypes at weeks 1-4 of treatment. Patients with hepatocellular carcinoma.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: P2RY12
Variant/haplotype: rs6809699
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with increased resistance to clopidogrel in people with Coronary Disease as compared to genotype CC.
Notes: was significant in Recessive and co-dominant models. This was also seen when examined in just CYP2C19*1/*1 in discovery cohort but not whole cohort. Paper talks about using 2 cohorts, one for discovery and one for replication but it is not explicit about which are in which table of results. "Patients carrying the P2RY12 rs6809699 CA genotype or the rs6809699 A allele also showed significantly increased risk of CR (CA vs CC genotype: OR 2.270, 95% CI 1.019–5.059, P = 0.045; CA + AA vs CC genotype: OR 2.636, 95% CI 1.199–5.796; P = 0.016). "
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: AQP2
Variant/haplotype: rs3759126
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele G.
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: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C19
Variant/haplotype: rs61311738
Drug(s): mephenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased clearance of mephenytoin as compared to allele C.
Notes: In vitro analysis showed that intrinsic clearance of S-mephenytoin by CYP2C19 protein containing the T allele was 0.7% of that of the WT protein. Variant referred to as 518C>T in the paper.
Article: Polymorphisms of SLC19A1 80 G>A, MTHFR 677 C>T, and Tandem TS Repeats Influence Pharmacokinetics, Acute Liver Toxicity, and Vomiting in Children With Acute Lymphoblastic Leukemia Treated With High Doses of Methotrexate
Gene: TYMS
Variant/haplotype: rs45445694
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 is associated with increased steady-state concentration of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 + (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3.
Notes: Variant mapped to rs45445694 by PharmGKB.
Article: Lumacaftor/Ivacaftor Treatment of Patients with Cystic Fibrosis Heterozygous for F508del‐CFTR
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor, lumacaftor
Phenotype category: Efficacy
Significant: yes
Association: Genotype CTT/del is associated with response to ivacaftor and lumacaftor in people with Cystic Fibrosis.
Notes: F508del allele. All study participants had the F508del allele on one allele and a second that was predicted to not respond to ivacaftor/lumacaftor treatment. Two out of five outcomes showed a significant improvement following 56 days of ivacaftor/lumacaftor treatment.
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: MMP9
Variant/haplotype: rs2274755
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to bevacizumab in women with Breast Neoplasms as compared to allele G.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: GGCX
Variant/haplotype: rs699664
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin in people with heart valve replacement as compared to allele T.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: Nerve growth factor beta polypeptide (NGFB) genetic variability: association with the methadone dose required for effective maintenance treatment
Gene: NGF
Variant/haplotype: rs2239622
Drug(s): methadone
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with decreased dose of methadone in people with Opioid-Related Disorders as compared to genotypes AG + GG.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: DGCR5
Variant/haplotype: rs1210638
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele T.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to amlodipine in men with Hypertension as compared to genotypes CC + CT.
Notes: No significant change in the likelihood of a man reaching a target mean arterial pressure concentration of <= 92 mmHg or <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: Exploring the contribution of genetic variants to high sunitinib exposure in patients with cancer
Gene: ABCG2
Variant/haplotype: rs2231137
Drug(s): sunitinib
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is associated with increased concentrations of sunitinib in people with Carcinoma, Renal Cell or Gastrointestinal Stromal Tumors as compared to allele C.
Notes: " Of note, rs2231137, 1 of the top SNVs reported in previous studies located on the ABCG2 gene, showed a P-value of 6.52  x10-6. While above our predefined thresholds, this does not completely exclude involvement of ABCG2 in sunitinib PK, though the effect size will be small and not likely to be clinically relevant." Assumed that minor allele is associated with increased concentration/toxicity.
Article: Tamoxifen Metabolite Concentrations, CYP2D6 Genotype and Breast Cancer Outcomes
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers
Drug(s): 4-hydroxytamoxifen, endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer is associated with decreased concentrations of 4-hydroxytamoxifen or endoxifen in women with Breast Neoplasms as compared to CYP2D6 normal metabolizer.
Notes: Concentrations of endoxifen, 4-hydroxytamoxifen, and N-desmethyltamoxifen  were strongly associated with CYP2D6 phenotype.  No evidence for a linear relationship between the concentration levels of tamoxifen and/or any of the measured metabolites and breast cancer outcomes. Increased risk of breast cancer recurrence was found for patients with endoxifen concentrations in the bottom quintile of the distribution. Participants were diagnosed with breast cancer and completed primary treatment. Included were patients with ER-positive tumor who had been taking tamoxifen for at least 4 month. no info on menopausal status. Genotyped using AmpliChip CYP450 Test. (i) nonfunctional (PM) alleles include CYP2D6*3, *4, *5, *6, *7, *8, *11, *14A, *15, *19, *20, and *40, and the *4XN gene duplication; (ii) reduced function (intermediate metabolizer) alleles include CYP2D6*9, *10, *17, *29, *36, and *41, and gene duplications *10XN, *17XN, and *41XN; (iii) fully functional (extensive metabolizer or EM) alleles include CYP2D6*1, *2, and *35 and (iv) increased function (ultrarapid metabolizer) phenotype alleles include gene duplications such as CYP2D6*1XN, *2XN, and *35XN. [pre-menopausal][post-menopausal] [adjuvant] [DNA source: blood] [HWE: yes]
Article: Analgesic therapy failure in a COMT HPS/HPS diplotype carrier heterozygous for the CYP2D6 *4 allele with fibromyalgia—a case report
Gene: COMT
Variant/haplotype: COMT low activity
Drug(s): acetaminophen, duloxetine, ibuprofen, oxycodone, pregabalin
Phenotype category: Efficacy
Significant: no
Association: COMT low activity is associated with decreased clinical benefit to acetaminophen, duloxetine, ibuprofen, oxycodone and pregabalin in women with Fibromyalgia and Low Back Pain.
Notes: "40-year-old female patient was diagnosed with chronic lumbalgia and fibromyalgia" " insufficient pain relief" "COMT HPS/HPS diplotype carrier implicating lower COMT activity and higher pain sensitivity" Genotypes from table 2: rs6269 AA, rs4633 CC, rs4818 CC, rs4680 GG and CYP2D6 *1/*4
Article: Association of genetic variations with pharmacokinetics and lipid-lowering response to atorvastatin in healthy Korean subjects
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with decreased response to atorvastatin in healthy individuals as compared to genotype GG.
Notes: This variant was associated with changes in total cholesterol and LDL-C at 48 hours after atorvastatin administration. The decrease in total cholesterol and LDL-C was smaller in those with G/A (n=7) than in the 43 subjects with G/G.
Article: Replicated Association between an IL28B Gene Variant and a Sustained Response to Pegylated Interferon and Ribavirin
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele C is not associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b or ribavirin in people with Hepatitis C, Chronic as compared to allele T.
Notes: Treatment was with peginterferon- type was not specified.  Authors noted that small sample size of Black subjects limited power to detect an association.
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs3819479
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele A 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: VKORC1 variants as significant predictors of warfarin dose in Emiratis
Gene: VKORC1
Variant/haplotype: rs8050894
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CG + GG are associated with decreased dose of warfarin as compared to genotype CC.
Notes: Please note that alleles have been complemented to the positive strand.
Article: The influence of CYP3A, PPARA, and POR genetic variants on the pharmacokinetics of tacrolimus and cyclosporine in renal transplant recipients
Gene: POR
Variant/haplotype: rs1057868
Drug(s): cyclosporine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with increased metabolism of cyclosporine in people with Kidney Transplantation as compared to allele C.
Notes: A single steady-state concentration of cyclosporine was collected for each patient 2-7 wks post-transplant and compared to dose of cyclosporine administered to patients at Oslo University Hospital. Reported concentrations are "steady-state dose-adjusted concentration" of cyclosporine. Steady-state is defined as at least 3 days after last dose adjustment for Tac and 4 days for cyclosporine.
Article: Escitalopram pharmacogenetics: CYP2C19 relationships with dosing and clinical outcomes in Autism Spectrum Disorder
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): escitalopram
Phenotype category: Dosage
Significant: no
Association: CYP2C19 *1/*2 + *2/*2 are not associated with dose of escitalopram in people with Autistic Disorder as compared to CYP2C19 *1/*1.
Notes: No difference was found between intermediate/poor metabolizer vs extensive metabolizer or ultra rapid metabolizer. *3 was genotyped but no carrier identified. *2/*2 N=1 and was grouped with *1/*2. *1/*17 and *17/*17 were grouped together as UM. Final doses (mean ± SD, mg/day) across metabolizer groups were ultrarapid metabolizers (12.5 ± 7.8), extensive metabolizers (15.4 ± 6.4), and reduced metabolizers (16.7 ± 5.8). Ultrarapid metabolizers showed a slower rate of change in dose over time.