shlokn/autogkb huggingface dataset:
Article: Genetic variants related to successful migraine prophylaxis with verapamil
Gene: ITGAL
Variant/haplotype: rs2230433
Drug(s): verapamil
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased clinical benefit to verapamil in people with Migraine NOS as compared to allele G.
Notes: "There are 3 highly significant SNPs (p‐value < 0.008) in both the arithmetic and percentage change models: rs2230433 within the Integrin Subunit Alpha L gene (ITGAL) [OMIM#153370], rs17844444 in Protocadherin Beta 6 gene (PCDHB6) [OMIM#606332] and rs3733694 in Protocadherin Beta 7 gene (PCDHB7) [OMIM#606333]. The minor allele of rs2230433 was associated with a mean reduction in headache days of about 20%."
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: PON1
Variant/haplotype: rs854560
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is not associated with response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms.
Article: ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence
Gene: ABCB1
Variant/haplotype: rs6949448
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of methadone in people with Heroin Dependence as compared to allele C.
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: An Unusual Presentation of Succinic Semialdehyde Dehydrogenase Deficiency: A Fatal Case of Severe Progressive Seizures in a Four-Month-Old Infant
Gene: ALDH5A1
Variant/haplotype: rs72552282
Drug(s): antiepileptics, levetiracetam, phenytoin, valproic acid
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is associated with increased resistance to antiepileptics, levetiracetam, phenytoin and valproic acid in children Epilepsy, Infant and Metabolism, Inborn Errors.
Notes: "Here we describe an unusual presentation of a four-month-old female patient diagnosed with SSADH deficiency who presented with severe progressive seizure leading to the death of the patient." "Whole exome sequencing was done from the blood sample. It showed a homozygous mutation G->A substitution at chr6:24505155. Akaboshi et al. predicted this mutation to cause an abnormal protein translation of the ALDH5A1 protein at amino acid position 223 "
Article: The Influence of CYP2C19 Polymorphism on Eradication of Helicobacter pylori: A Prospective Randomized Study of Lansoprazole and Rabeprazole
Gene: CYP2C19
Variant/haplotype: CYP2C19*1
Drug(s): rabeprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*1 is not associated with response to rabeprazole in people with Helicobacter Infections.
Notes: as compared to the *1/*2 or *1/*3 genotype, or the *2/*2, *2/*3 or *3/*3 genotype. No significant differences in percent eradication rate of Helicobacter pylori (H. pylori) were seen between any of the genotype groups. Patients were also given amoxicillin and clarithromycin, and were treated for 1 week. Please note these genotypes were referred to by their previous designations of m1 (*2) and m2 (*3).
Article: Tacrolimus dose requirement based on the CYP3A5 genotype in renal transplant patients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: Patients with the CT or TT genotype need a higher dose of tacrolimus to achieve target blood concentrations as compared to those with the CC genotype. The authors note that patients with the CC genotype were significantly younger as compared to those with the CT or TT genotype (p=0.0011). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Genetic Determinants of Response to Warfarin during Initial Anticoagulation
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with decreased dose of warfarin as compared to genotype CC.
Notes: With *1/*2 (CT) requiring intermediate dose. This was most marked at day 28 to end of follow-up with average doses of 3.66mg/day for *2*2 (HaplotypeA/HaplotypeA"), 4.45mg/day for HaplotypeA/nonA and 5.68mg/day for nonA/nonA. Authors also used rs2884737, rs9934438, rs8050894, and rs2359612 to define HaplotypeA.
Article: Absence of ethnic differences in the pharmacokinetics of moxifloxacin, simvastatin, and meloxicam among three East Asian populations and Caucasians
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): meloxicam
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 *1/*3 + *2/*2 are associated with decreased metabolism of meloxicam in healthy individuals as compared to CYP2C9 *1/*1.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype TT is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype CC.
Notes: Genotypes of CC, TC and TT did not influence donepezil clearance in a covariate model. Alleles have been complemented to the plus chromosomal strand.
Article: Predictors of clozapine concentration and psychiatric symptoms in patients with schizophrenia
Gene: CYP1A2
Variant/haplotype: CYP1A2 ultrarapid metabolizer
Drug(s): clozapine, n-desmethylclozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP1A2 ultrarapid metabolizer is associated with decreased concentrations of clozapine and n-desmethylclozapine in people with Schizophrenia or Psychotic Disorder as compared to CYP1A2 normal metabolizer.
Notes: "CYP1A2 phenotypes were significantly associated with the metabolic ratio (clozapine/NDMC ratio) (p = 0.006, Mann–Whitney U test) at visit 4, with higher metabolic ratios in NMs (n = 14) than that in UMs (n = 26) (S1 Fig)." Paper uses old nomenclature for CYP1A2 "Of the 45 enrolled patients, 17 were normal metabolizers (NMs) of CYP1A2 (*1A/ * 1A, * 1C * 1F/ * 1C * 1F, * 1C/ * 1F, or * 1A/ * 1C * 1F), while 28 were ultrarapid metabolizers (UMs) (*1F/ * 1F, * 1F/ * 1C * 1F, or * 1A/ * 1F)." "CYP1A2 phenotypes were determined by a combination of two SNPs, namely rs2069514 (c.-3860G > A) and rs762551 (c.-9-154C > A)."
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: no
Association: Genotype AG is not associated with dose of remifentanil as compared to genotypes AA + GG.
Notes: No significant different in remifentanil consumption between patients with the AG or AA genotypes, or between patients with the AG or GG genotypes.
Article: Genetic Variants of SLC22A1 rs628031 and rs622342 and Glycemic Control in T2DM Patients from Northern Mexico
Gene: SLC22A1
Variant/haplotype: rs628031
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to genotype GG.
Notes: "Carriers of at least one minor allele of A-rs628031 and C-rs622342 had lower HbA1c values than individuals homozygous for the major allele in both genes."
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ATIC
Variant/haplotype: rs12995526
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Article: A functional variant in the serotonin receptor 7 gene (HTR7), rs7905446, is associated with good response to SSRIs in bipolar and unipolar depression
Gene: HTR7
Variant/haplotype: rs7905446
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to Selective serotonin reuptake inhibitors in people with Depression as compared to genotypes GG + GT.
Notes: The TT genotype was associated with non-remission, white the GG and GT genotypes were associated with treatment remission at 6 weeks.
Article: Pharmacokinetics of lamotrigine and its metabolite N‐2‐glucuronide: Influence of polymorphism of UDP‐glucuronosyltransferases and drug transporters
Gene: UGT2B7
Variant/haplotype: rs7668258
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased clearance of lamotrigine in people with Epilepsy as compared to genotypes CC + CT.
Notes: This study was conducted in 100 patients -- 54 receiving monotherapy for lamotrigine, and 46 receiving combination therapy with carbamazepine, oxcarbazepine, valproic acid, phenytoin, phenobarbital, levetiracetam, topiramate, lacosamide, zonisamide, pregabalin, clonazepam, or clobazam. All patients were on stable therapy for at least 2 months. The significant difference in clearance was found between patients with the TT genotype and with the CC genotype, with clearance in patients with the CT genotype not being significantly different than in patients with the CC genotype.
Article: Predicting Inhaled Corticosteroid Response in Asthma with Two Associated SNPs
Gene: GLCCI1
Variant/haplotype: rs37973
Drug(s): glucocorticoids
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to glucocorticoids in people with Asthma as compared to allele A.
Notes: as part of a two SNP predictive test of FEV1 change, which identified patients with good or poor steroid response (highest or lowest quartile, respectively). P values are for predictive performance of the test.
Article: A genetic determinant of the striatal dopamine response to alcohol in men
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to ethanol in men as compared to genotype AA.
Notes: Subjects with the AG genotype showed significantly increased striatal dopamine release following administration of alcohol compared to AA subjects.
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with decreased dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotype CC.
Notes: When considering RECIPIENT genotype - those with the CT or TT genotype had decreased concentration/dose ratios as compared to those with the CC genotype at weeks 1 and 2 of treatment. No significant difference was seen at weeks 3 or 4. In multiple linear regression analysis, rs776746 recipient genotype was associated with concentration/dose ratio at week 1 (p=0.001) of treatment. Patients with hepatocellular carcinoma. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population
Gene: CALU
Variant/haplotype: rs2290228
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of warfarin as compared to allele G.
Notes: Neither the addition of race, number of concurrent medications nor the number of concurrent medications interacting with warfarin enhanced algorithm performance. Similarly, consideration of CYP4F2, CALU or GGCX variant genotypes did not improve algorithms.
Article: The Relationship Between Single Nucleotide Polymorphisms in 5-HT2A Signal Transduction-Related Genes and the Response Efficacy to Selective Serotonin Reuptake Inhibitor Treatments in Chinese Patients with Major Depressive Disorder
Gene: HTR2A
Variant/haplotype: rs6305
Drug(s): citalopram, paroxetine, sertraline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to citalopram, paroxetine or sertraline in people with Depressive Disorder, Major as compared to allele G.
Notes: Response measure with HAMD.
Article: MHC class I-related chain B gene polymorphism is associated with virological response to pegylated interferon plus ribavirin therapy in patients with chronic hepatitis C infection
Gene: MICB
Variant/haplotype: rs3828913
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes AA + AC.
Notes: Patients with MICB major (CC) alleles had higher SVR rate (62.3%) than that of the patients with MICB minor (CA and AA) alleles (27.2%). A multivariate logistic model showed that the MICB major genotype (CC) was an independent factor contributing to SVR (OR, 4.47; 95% CI, 1.46-13.70; P=0.009), similar to the IL28B major genotype (rs8099917).
Article: Genetic Polymorphisms Associated with Vincristine Pharmacokinetics and Vincristine-Induced Peripheral Neuropathy in Pediatric Oncology Patients
Gene: SNU13
Variant/haplotype: rs6519270
Drug(s): vincristine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of vincristine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma, Hodgkin Disease, Rhabdomyosarcoma, Medulloblastoma or Glioma as compared to allele A.
Notes: in a subset of study of vincristine-induced peripheral neuropathy with PK measurements. Association is reported for rs6519270 A > C however dbSNP and gnoMAD have this as an A>G variant.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: ABCB1
Variant/haplotype: rs3213619
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele G.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs727505292
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the G allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Ile253Thr.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ZNF134
Variant/haplotype: rs10413455
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele A 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: Impact of GGCX, STX1B and FPGS Polymorphisms on Warfarin Dose Requirements in European‐Americans and Egyptians
Gene: FPGS
Variant/haplotype: rs7856096
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotype AA is not associated with dose of warfarin as compared to genotypes AG + GG.
Notes: in European-Americans, and Egyptians.
Article: Influence of G-protein β-Polypeptide 3 C825T Polymorphism on Antihypertensive Response to Telmisartan and Amlodipine in Chinese Patients
Gene: GNB3
Variant/haplotype: rs5443
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to amlodipine in people with Essential hypertension as compared to genotypes CC + CT.
Notes: As measured by reduction in diastolic blood pressure
Article: Influence of genetic polymorphisms in homocysteine and lipid metabolism systems on antidepressant drug response
Gene: APOE
Variant/haplotype: rs405509
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to genotypes GG + GT.
Notes: response measured by HDRS-17 score. Patients received SSRI or SNRI but exact drug not specified.
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: PON1
Variant/haplotype: rs662
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms as compared to genotypes CT + TT.
Notes: Response refers to overall survival (OS). In the Kaplan–Meier analysis of OS genotypes of rs662 were associated with OS. In Cox regression analysis number of lesions as well as s662 genotype were independent predictors of OS. When comparing OS between the CC genotype and TT and CT genotypes there was no significant difference in OS (days) but when comparing between TT and CC only, the difference is significant (p=0.032). Please note: alleles have been complemented to the + strand.
Article: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway
Gene: CTNNA3
Variant/haplotype: rs10997242
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to antidepressants in people with Depressive Disorder, Major as compared to allele T.
Notes: Identity of minor allele not specified, so minor allele of dbSNP used here. Response considered to be successful with a 50% reduction at discharge of the Hamilton Rating Scale for Depression (HRSD17). Patients measured at admission and discharge, 4-6 weeks later. Specific antidepressants not listed.
Article: OCT1 genetic variants influence the pharmacokinetics of morphine in children
Gene: SLC22A1
Variant/haplotype: rs34130495
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased clearance of morphine in children with adenotonsillectomy as compared to genotypes AG + GG.
Notes: Children with two loss of function SLC22A1 alleles (*2 rs72552763 GAT>del, *3 rs12208357C>T, *4 rs34130495 G>A, or *5 rs34059508 G>A) were grouped together and had significantly lower clearance compared to children with the *1/*1 or *1/variant genotype.
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: SLC19A1
Variant/haplotype: rs2838958
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG are not associated with concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.
Notes: There is no association between selected SNPs and methotrexate plasma level at 48 h between the first dose of methotrexate infusion. med. MTX concentration: AG+GG 0.41 (0.09–34.05)) vs. AA (0.59 (0.16–41.63)).
Article: CYP4F2 1347 G>A & GGCX 12970 C>G polymorphisms: frequency in north Indians & their effect on dosing of acenocoumarol oral anticoagulant
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: no
Association: Genotypes CT + TT is not associated with dose of acenocoumarol as compared to genotype CC.
Notes: No significant differences in mean weight normalized acenocoumarol doses were found for these CYP4F2 genotypes.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: TLR4
Variant/haplotype: rs1927907
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele C.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients.
Article: Opioid response in paediatric cancer patients and the Val158Met polymorphism of the human catechol-O-methyltransferase (COMT) gene: an Italian study on 87 cancer children and a systematic review
Gene: COMT
Variant/haplotype: rs4680
Drug(s): opioids
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to opioids in children as compared to genotype GG.
Notes: Patients with the AA or AG genotypes reached the lowest pain intensity faster than those with the GG genotype.
Article: Effect of UGT1A1, UGT1A3, DIO1 and DIO2 polymorphisms on L-thyroxine doses required for TSH suppression in patients with differentiated thyroid cancer
Gene: DIO1
Variant/haplotype: rs2235544
Drug(s): levothyroxine
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of levothyroxine in people with Thyroid Neoplasms as compared to allele C.
Notes: This SNP was not associated with dose in univariate  regression.
Article: Methadone Dosage and Plasma Levels, SNPs of OPRM1 Gene and Age of First Drug Use Were Associated With Outcomes of Methadone Maintenance Treatment
Gene: OPRM1
Variant/haplotype: rs2236258
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methadone in people with Heroin Dependence as compared to allele T.
Notes: This SNP was not significantly associated with compliance with methadone maintenance therapy or 'negative rate of morphine urine test'.