shlokn/autogkb huggingface dataset:
Article: Toward precision prescribing for methadone: Determinants of methadone deposition
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*5, CYP2B6*6, CYP2B6*7, CYP2B6*18
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*6 + *1/*18 + *6/*6 + *6/*18 are associated with decreased metabolism of methadone in people with Opioid-Related Disorders as compared to CYP2B6 *1/*1 + *1/*5 + *1/*7.
Notes: Patients with the *1/*6, *1/*18, *6.*6 or *6/*16 genotypes (designated os loss of function genotypes) had significantly decreased metabolism of metabolism compared to patients with the *1/*1, *1/*5 or *1/*7 genotypes (designated as normal function genotypes). See Table 4 for details of genotyping and assignation of CYP2B6 star alleles. Please note that *16 was merged into *18 based on PharmVar.
Article: Possible effect of norepinephrine transporter polymorphisms on methylphenidate-induced changes in neuropsychological function in attention-deficit hyperactivity disorder
Gene: SLC6A2
Variant/haplotype: rs28386840
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: not stated
Association: Genotypes AT + TT are associated with increased response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype AA.
Notes: After 8 weeks of treatment, subjects with the A/A genotype at the A-3081T polymorphism showed less improvement in the mean commission error scores (p = 0.003) than those with the A/T or T/T genotypes. Subjects with the T/T genotype showed the greatest decrease in commission errors, followed by the A/T genotype and A/A genotype (p = 0.007). Test of variables of attention (TOVA) described as continuous performance test (CPT).
Article: Effect of Genetic Variant (rs11887534) in ABCG8 Gene in Coronary Artery Disease and Response to Atorvastatin Therapy
Gene: ABCG8
Variant/haplotype: rs11887534
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: no
Association: Genotype CG is not associated with increased response to atorvastatin in people with Coronary Artery Disease as compared to genotype GG.
Notes: Alleles were reported as "D = wildtype" and "H = variant".  This gene is on the + strand, and dbSNP reports G to be the extremely major allele in every population, so I interpreted D to be G and H to be C.  There were no HH (CC) homozygotes.  The response measured was lowering of LDL-C.
Article: GRK5 Gln41Leu polymorphism is not associated with sensitivity to β1-adrenergic blockade in humans
Gene: GRK5
Variant/haplotype: rs2230345
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to atenolol in healthy individuals as compared to genotypes AT + TT.
Notes: Subjects performed exercise on a supine bicycle ergometer. No differences between genotypes were seen for change in heart rate at rest, heart rate at maximal exercise, or heart rate area under the curve (AUC) after atenolol administration.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: PEBP4
Variant/haplotype: rs17685420
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
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.; Variant achieved significance in the meta-analysis after Bonferroni correction had been applied, but was only 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: ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence
Gene: ABCB1
Variant/haplotype: rs1922242
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of methadone in people with Heroin Dependence as compared to allele T.
Notes: Please note that alleles have been complemented to the positive strand. Alleles were not associated with the need for a higher (>150mg) or lower (<150 mg) dose of methadone.
Article: Genetic variability in the glucocorticoid pathway and treatment outcomes in hospitalized patients with COVID-19: a pilot study
Gene: NR3C1
Variant/haplotype: rs33389
Drug(s): dexamethasone
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased time to response to dexamethasone in people with COVID-19 as compared to genotypes CC + CT.
Notes: "Homozygotes for polymorphic NR3C1 rs33389 allele also needed longer (12 days) hospitalization when compared to carriers of one or two reference alleles (both 9 days) (p adj = 0.025)."
Article: Pharmacogenetic Influence of LOC387715/HTRA1 on the Efficacy of Bevacizumab Treatment for Age-Related Macular Degeneration in a Korean Population
Gene: ARMS2
Variant/haplotype: rs10490924
Drug(s): bevacizumab
Phenotype category: Dosage
Significant: no
Association: Genotypes GT + TT are not associated with dose of bevacizumab in people with Macular Degeneration as compared to genotype GG.
Notes: No significant differences in the average number of additional bevacizumab injections (after the initial three intravitreal injections), were seen between any of the genotypes.
Article: Risperidone plasma level, and its correlation with CYP2D6 gene polymorphism, clinical response and side effects in chronic schizophrenia patients
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10, CYP2D6*41, CYP2D6*65
Drug(s): risperidone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *10/*10 + *10/*65 + *10/*41 (assigned as intermediate metabolizer phenotype) is associated with increased concentrations of risperidone in people with Schizophrenia as compared to CYP2D6 *1/*1 + *1/*10 + *1/*2 + *2/*2 + *2/*41 (assigned as normal metabolizer phenotype) .
Notes: "Plasma levels of RIP and dose corrected RIP concentration in IM group were significantly higher than those in NM group (both p-value were < 0.001). Similarly, IMs had a significantly higher RIP/9-OH-RIP ratio and C/D ratio than those value in NMs (p = 0.009 and 0.003, respectively). However, we didn’t observe this kind of difference in blood levels of 9-OH-RIP and dose-corrected 9-OH-RIP, and active moiety (all p > 0.05). All those data were listed in Table ​Table4." "IMs, activity score = 0.5 or 0.75), normal metabolizers (NMs, activity score = 1.25, 1.5 or 2.0"
Article: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Variant/haplotype: rs11564750
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele C.
Notes: Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: Impact of SLCO1B3 Polymorphisms on Clinical Outcomes in Lung Allograft Recipients Receiving Mycophenolic Acid
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): azathioprine, mycophenolic acid
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to azathioprine or mycophenolic acid in people with lung transplantation as compared to allele C.
Notes: No significant association between this variant and survival post-transplantation or development of acute cellular rejection, lymphocytic bronchiolitis or chronic lung allograft dysfunction (CLAD).
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs581111
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to buprenorphine in people with Opioid-Related Disorders as compared to allele A.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment.; Please note that alleles have been complemented to the positive strand.
Article: Prediction of Tacrolimus Exposure by CYP3A5 Genotype and Exposure of Co-Administered Everolimus in Japanese Renal Transplant Recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with decreased metabolism of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: Patients with the *3/*3 genotype had increased dose-adjusted area under the blood concentration-time curves (AUC/D) and dose-adjusted trough concentrations (C0/D) of tacrolimus as compared to those with the *1/*1 or *1/*3 genotype. Significant at 1 month (p<0.001 for both) and 1 year (<0.001 for AUC/D and p=0.004 for C0/D) post-transplant. Note that at 1 year post transplant only 31 patients remained for analysis.
Article: No Association of a Set of Candidate Genes on Haloperidol Side Effects
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): haloperidol
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is associated with increased concentrations of haloperidol in people with Psychotic Disorders as compared to genotype CC.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs10085144
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of vancomycin as compared to allele A.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: CYP2C9*8 is prevalent among African–Americans: implications for pharmacogenetic dosing
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*8
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *8/*8 is associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: An African-American male previously typed as *1/*1 but whose therapeutic warfarin dose was low (14.4 mg/wk) was sequenced and found to be *8/*8.  Out of 600 African American alleles genotyped, the frequency of *8 was 0.047 .
Article: Novel Gene Polymorphisms for Stable Warfarin Dose in a Korean Population: Genome-Wide Association Study
Gene: NKX2-6
Variant/haplotype: rs310279
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AG + GG is associated with increased dose of warfarin in people with heart valve replacement as compared to genotype AA.
Notes: in univariate analysis of patients on stable dose. "FIn this GWAS analysis, we identified three novel variants (FRAS1 rs4386623, FAM201A rs1890109, and NKX2-6 rs310279) that were significantly associated with stable warfarin dose requirements in patients who underwent heart valve replacements. "
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: rs514743
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele T is not associated with exposure to nicotine in men as compared to allele A.
Notes: No significant association between this allele and status as a smoker or non-smoker.
Article: Allelic Variant in the Glucagon-Like Peptide 1 Receptor Gene Associated with Greater Effect of Liraglutide and Exenatide on Gastric Emptying: A Pilot Pharmacogenetics Study
Gene: TCF7L2
Variant/haplotype: rs7903146
Drug(s): exenatide, liraglutide
Phenotype category: PD
Significant: no
Association: Genotypes CT + TT is not associated with increased response to exenatide or liraglutide in people with Obesity as compared to genotype CC.
Notes: "For the TCF7L2 (rs7903146) genotype (major vs. minor allele), assessment, changes in gastric emptying at 5 weeks (p=0.93) and weight loss at 5 weeks (p=0.72) were not different."
Article: RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients
Gene: RRM2
Variant/haplotype: rs5030743
Drug(s): cladribine, cytarabine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CG + GG is associated with decreased response to cladribine and cytarabine in children with Leukemia, Myeloid, Acute as compared to genotype CC.
Notes: As measured by a poorer overall survival. Note this is a G/C SNP, therefore the risk allele could potentially get mixed up.
Article: Impact of CYP3A4*1G Allele on Clinical Pharmacokinetics and Pharmacodynamics of Clopidogrel
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotype C/T is not associated with response to clopidogrel in people with Coronary Artery Disease as compared to genotype C/C.
Notes: No significant difference in platelet aggregation between genotype groups. The publication reports the finding for CYP3A4*1G. PharmVar re-assigned CYP3A4*1G to CYP3A4*36. Previously, this annotation used CYP3A4*36 which has been retired by PharmVar. All references to *36 have been replaced by rs2242480 alleles.
Article: Predictors of clozapine concentration and psychiatric symptoms in patients with schizophrenia
Gene: CYP2D6
Variant/haplotype: rs28371726
Drug(s): clozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased concentrations of clozapine in people with Schizophrenia or Psychotic Disorder as compared to allele A.
Notes: "In the model adjusted for clinical predictors of clozapine concentration, including smoking status and cumulative dose of clozapine, five SNPs (rs28371726 and rs202102799 in CYP2D6; rs4148323 and rs34946978 in UGT1A1; and rs2011404 in UGT1A4) showed significant associations with clozapine concentration. The rs number for each SNP associated with clozapine concentration is shown in Table 3." Table does not state which allele or direction of effect for these SNPs, so assuming minor allele and decreased concentration (beta value in table is negative).
Article: Therapeutic drug monitoring of voriconazole: a case report of multiple drug interactions in a patient with an increased CYP2C19 activity
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *1/*17 is associated with decreased concentrations of voriconazole.
Notes: Case report: Patient receiving voriconazole had subtherapeutic levels. After administration of esomeprazole (CYP2C19 inhibitor) level within therapeutic range.
Article: Meta-analysis of the effects of CYP3A5*3 gene polymorphisms on tacrolimus blood concentration and effectiveness in Chinese patients with membranous nephropathy
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT is associated with increased clinical benefit to tacrolimus in people with Glomerulonephritis, Membranous as compared to genotype CC.
Notes: "The results showed that at 3 months [OR = 0.98, 95% CI (0.55, 1.76), p = 0.949], 6 months [OR = 1.14, 95% CI (0.84, 1.56), p = 0.401], and 12 months [OR = 1.20, 95% CI (0.66, 2.21), p = 0.551], the remission rates of expressers were higher than those of non-expressers, but there was no statistically significant difference between the two groups (p > 0.05) (Figure 4)." "AA + AG genotype (referred to as expressers) and the GG genotype (referred to as non-expressers)"
Article: CYP2D6 Phenotyping Using Urine, Plasma, and Saliva Metabolic Ratios to Assess the Impact of CYP2D6∗10 on Interindividual Variation in a Chinese Population
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*10
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *1/*10 is associated with decreased metabolism of dextromethorphan in healthy individuals as compared to CYP2D6 *1/*1.
Notes: Single dose study with 15mg dextromethorphan DM. Urine, Plasma, and Saliva Metabolic Ratios were accessed. Subjects were  genotyped by DNA sequencing analysis for CYP2D6*1, *2, *3, *4, *6, *7, *10, *14, *18, *21, *28, *33, *34, *35, *36, *39, *41, *43, *49, *51, *52, *54, *60, *63, *65, *69, *71, and *75 and CNV were determined. *1/*1 n= 22; *1/*10 n=93. The urinary, plasma, or salivary MRs increased successively in subjects with CYP*1/*1, *1/*10, *10/*10, and *5/*10 with statistical significance (all P-values < 0.001).
Article: Clinical Evaluation of Cisplatin Sensitivity Germline Polymorphisms in Neoadjuvant Chemotherapy for Urothelial Cancer
Gene: GALNT18
Variant/haplotype: rs7937567
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to cisplatin in people with Urinary Bladder Neoplasms as compared to genotypes AA + AG.
Notes: This SNP was significantly associated with complete pathologic response in the discovery cohort, but not the replication cohort.
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Gene: IFNL3
Variant/haplotype: rs8103142
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C and HIV Infections as compared to genotypes CC + CT.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy
Gene: SLC22A4
Variant/haplotype: rs1050152
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotypes CC + CT.
Notes: Patients with the TT genotype had a decreased likelihood of achieving major molecular response (MMR) within 12 months, as compared to those with the CC or CT genotype. MMR was classified based on BCR-ABL to control gene transcript ratios, expressed on the International Scale; MMR was a ratio <= 0.1%.
Article: Common Variants in 40 Genes Assessed for Diabetes Incidence and Response to Metformin and Lifestyle Intervention in the Diabetes Prevention Program
Gene: SLC47A1
Variant/haplotype: rs8065082
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to metformin in people with Glucose Intolerance as compared to genotype CC.
Notes: as measured by metformin ability to prevent diabetes in people at risk for diabetes. "At this locus, major allele homozygotes did not benefit from metformin with regard to diabetes prevention, whereas minor allele carriers did".
Article: Dose-Finding and Pharmacokinetic Study to Optimize the Dosing of Irinotecan According to the UGT1A1 Genotype of Patients With Cancer
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: yes
Association: UGT1A1 *1/*28 + *28/*28 is associated with increased concentrations of SN-38 in people with Neoplasms as compared to UGT1A1 *1/*1.
Notes: The dose-adjusted area under the concentration-time curve (AUC) of SN-38 is increased in patients with the *1/*28 or *28/*28 genotype as compared to those with the *1/*1 genotype.
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs362814
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: Safety of codeine during breastfeeding: Fatal morphine poisoning in the breastfed neonate of a mother prescribed codeine
Gene: CYP2D6
Variant/haplotype: CYP2D6*2, CYP2D6*2xN
Drug(s): codeine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *2/*2xN is associated with increased metabolism of codeine in women.
Notes: Case report of an infant exposed to fatal levels of morphine through breastmilk while the mother was taking codeine/acetaminophen. Genotyping of the mother found her to have a *2/*2xN genotype. Details of the genotyping assay are not given.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: SLC29A1
Variant/haplotype: rs9394992
Drug(s): gemcitabine
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes CT + TT.
Notes: Tumor response to therapy and progression free survival did not significantly differ between genotype groups.
Article: Associations between P2RY12 gene polymorphisms and risks of clopidogrel resistance and adverse cardiovascular events after PCI in patients with acute coronary syndrome
Gene: P2RY12
Variant/haplotype: rs6809699
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with increased resistance to clopidogrel as compared to genotype CC.
Notes: in Chinese patients with acute coronary syndrome undergoing PCI. This variant is also called P2RY12 G52T.
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 Bipolar Disorder or Schizophrenia as compared to genotype GG.
Notes: Analysis of the total cohort found no significant difference in number of cigarettes smoked per day between genotype groups.
Article: Integration of genetic, clinical, and INR data to refine warfarin dosing
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 is associated with decreased dose of warfarin as compared to CYP2C9 *1.
Notes: Each CYP2C9*2 allele resulted in a 15% (11-19%) decrease in therapeutic dose on Day 4 or 5 of therapy.
Article: Clinical significance of UGT1A1 gene polymorphisms on irinotecan-based regimens as the treatment in metastatic colorectal cancer
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*6
Drug(s): irinotecan
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *6 is not associated with response to irinotecan in people with Colorectal Neoplasms as compared to UGT1A1 *1.
Notes: Response rates were complete and partial response (CR + PR), or complete and partial response and stable disease (CR + PR + SD). No significant differences between any of the genotypes (*1/*1, *1/*6, *6/*6; rs4148323 GG, AG, AA) were seen for either type of response rate.
Article: Genetic variants in the KIF6 region and coronary event reduction from statin therapy
Gene: KIF6
Variant/haplotype: rs9462535
Drug(s): atorvastatin, pravastatin
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with increased response to atorvastatin or pravastatin.