Journal: Pharmacogenetics and genomics

Article Title: The functional G143E variant of carboxylesterase 1 is associated with increased clopidogrel active metabolite levels and greater clopidogrel response

doi: 10.1097/FPC.0b013e32835aa8a2

Figure Lengend Snippet: Schematic of the major enzymatic steps in clopidogrel metabolism. CES1, carboxylesterase 1; CYP, cytochrome P450.

Article Snippet: CES1 G143E (rs71647871) SNP genotyping was performed using a TaqMan SNP genotyping assay (Applied Biosystems, Foster City, California, USA).

Techniques:

Journal: Pharmacogenetics and genomics

Article Title: The functional G143E variant of carboxylesterase 1 is associated with increased clopidogrel active metabolite levels and greater clopidogrel response

doi: 10.1097/FPC.0b013e32835aa8a2

Figure Lengend Snippet: Association of the carboxylesterase 1 (CES1) G143E variant (rs71647871) with ADP-stimulated platelet aggregation before (a, b) and after (c, d) clopidogrel administration in participants of the Pharmacogenomics of Anti-Platelet Intervention (PAPI) study (a, c) and coronary intervention patients at Sinai Hospital of Baltimore (b, d).

Article Snippet: CES1 G143E (rs71647871) SNP genotyping was performed using a TaqMan SNP genotyping assay (Applied Biosystems, Foster City, California, USA).

Techniques: Variant Assay

Journal: Pharmacogenetics and genomics

Article Title: The functional G143E variant of carboxylesterase 1 is associated with increased clopidogrel active metabolite levels and greater clopidogrel response

doi: 10.1097/FPC.0b013e32835aa8a2

Figure Lengend Snippet: Effect of CES1 143E, CYP2C19 *2, and CYP2C19 *17 variants on postclopidogrel ADP-stimulated platelet aggregation in participants of the Amish Pharmacogenomics of Anti-Platelet Intervention study

Article Snippet: CES1 G143E (rs71647871) SNP genotyping was performed using a TaqMan SNP genotyping assay (Applied Biosystems, Foster City, California, USA).

Techniques:

Journal: Annals of Clinical and Translational Neurology

Article Title: Identification of Srp9 as a febrile seizure susceptibility gene

doi: 10.1002/acn3.48

Figure Lengend Snippet: SRP9 expression and sequencing in patients with mTLE and/or FS. (A) SRP9 mRNA levels (normalized qPCR data: Rn) in hippocampal homogenates of autopsy controls (Control; n = 15; Rn = 112.3 ± 12.3) and mTLE patients without (non-HS; n = 19; Rn = 100.0 ± 8.2) and with hippocampal sclerosis (HS; n = 21; Rn = 209.0 ± 24.4). ( F 2,52 = 12.023, P = 0.0001; non-HS vs. HS: P = 0.008; Control vs. HS: P = 0.001; Control vs. non-HS: P = 1.000). SRP68 mRNA levels did not differ between groups (Control Rn = 107.8 ± 17.6; non-HS Rn = 100.0 ± 8.1; HS Rn = 115.1 ± 19.3; F 2,36 = 0.203, P = 0.817. (B) SRP9 protein (insert shows Western blot with loading control β -actin) in hippocampal homogenates of Controls ( n = 6; 53.9 ± 12.2), non-HS ( n = 12; Rn = 100.0 ± 11.6), and HS ( n = 11; Rn = 223.2 ± 47.6) patients. ( F 2,26 = 6.685, P = 0.005; non-HS vs. HS: P = 0.023; Controls vs. HS: P = 0.009; Controls vs. non-HS: P = 1.000). Error bar indicates SEM. *Significantly different after multiple testing correction P < 0.01. (C) Sequencing of SRP9 exons, intron/exon boundaries and promoter region (5 kb) in healthy controls ( n = 169), mTLE patients ( n = 368) and mTLE patients with FS ( n = 91) revealed a significant ( P < 0.01 bold) difference in allele frequencies of one common promoter SNP (rs12403575 G/A) in mTLE patients. P -value corrected for multiple SNP testing P < 0.01. All SNPs in the sequenced region with an allele frequency >0.05 were selected for the assocation study. In the HS group 46% had antecedent FS, in the non-HS group only 6%. (D) Further single SNP analysis using a larger control cohort ( n = 730) identified a significant association between rs12403575 and mTLE ( n = 368, P = 0.01, odds ratio (OR) = 1.238). This association was replicated in patients with FS without mTLE ( n = 236, P = 0.038, OR = 1.212). (E) Patients with AA genotype had a significantly ( F 2,33 = 4.142, P = 0.023) higher hippocampal SRP9 expression (Rn = 169.7 ± 22.9) than patients with AG genotype (Rn = 105.9 ± 13.1, P = 0.044), and GG genotype (Rn = 103.1 ± 19.6, P = 0.058). Data are expressed as means ± SEM. *Significantly different P < 0.05.

Article Snippet: SNP (rs12403575) genotyping (TaqMan SNP Genotyping Assays; Applied Biosystems, Foster City, CA) was performed on an ABI PRISM 7900 Sequence Detection System (Applied Biosystems, Foster City, CA) and SDS 2.2.3 software for allelic discrimination.

Techniques: Expressing, Sequencing, Control, Western Blot

Journal: Hematological Oncology

Article Title: B‐cell activating factor (BAFF), BAFF promoter and BAFF receptor allelic variants in hepatitis C virus related Cryoglobulinemic Vasculitis and Non‐Hodgkin's Lymphoma

doi: 10.1002/hon.3008

Figure Lengend Snippet: Genotype and allele distribution of rs9514828, rs61756766 and rs12428930 SNPs of BAFF/BAFF‐R system in HCV, HCV‐CV and HCV‐NHL subgroups. Panel (A) Genotype and allele distribution of rs9514828 in HCV, HCV‐CV and HCV‐NHL sub‐groups. Panel (B) Genotype and allele distribution of rs61756766 in HCV, HCV‐CV and HCV‐NHL subgroups. Panel (C) Genotype distribution of rs12428930 in HCV, HCV‐CV and HCV‐NHL subgroups. * p ≤ 0.01. HCV, Hepatitis C Virus positive patients without signs/symptoms of lymphoproliferative disorders and/or autoimmune diseases; HCV‐CV, Hepatitis C Virus positive patients with Cryoglobulinemic Vasculitis; HCV‐NHL, Hepatitis C Virus positive patients with Non‐Hodgkin's Lymphoma

Article Snippet: The rs9514828, rs12428930 and rs61756766 SNP genotyping was conducted using TaqMan SNP‐Genotyping Assay (Life Technologies Corporation, Carlsbad CA‐USA) based on allele‐specific dual‐labeled probes on a Rotor Gene 6000 (Corbett Research, Sidney, Australia), as previously described.

Techniques: Virus

Journal: Hematological Oncology

Article Title: B‐cell activating factor (BAFF), BAFF promoter and BAFF receptor allelic variants in hepatitis C virus related Cryoglobulinemic Vasculitis and Non‐Hodgkin's Lymphoma

doi: 10.1002/hon.3008

Figure Lengend Snippet: Genotype and allele frequency of rs9514828, rs61756766 and rs12428930 SNPs of BAFF/BAFF‐R system in HCV, HCV‐CV and HCV‐NHL subgroups

Article Snippet: The rs9514828, rs12428930 and rs61756766 SNP genotyping was conducted using TaqMan SNP‐Genotyping Assay (Life Technologies Corporation, Carlsbad CA‐USA) based on allele‐specific dual‐labeled probes on a Rotor Gene 6000 (Corbett Research, Sidney, Australia), as previously described.

Techniques:

Journal: bioRxiv

Article Title: Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

doi: 10.1101/2023.10.05.561076

Figure Lengend Snippet: (A) Schematic of the five prioritized SNPs arranged in genomic space. SNP rs57494551 is in the first intron of DDX6 . The other four SNPs span 978 bp in a shared promoter/enhancer region between DDX6 and CXCR5 . Risk alleles are indicated by red font; non-risk alleles by black. SNPs rs57494551 and rs4938572 (blue boxes) are representative SNPs. HindIII restriction sites (red dotted line), CTCF site (green box), and positions of 3C-qPCR primers #1-3 are also indicated. (B-F) Publicly reported cell type-specific functional annotations (horizontal rectangles), select eQTLs (top triangles), and chromatin-chromatin interactions (bottom triangles) are shown for (B) rs57494551, (C) rs4936443, (D) rs4938572, (E) rs7117261, and (F) rs4938573 across 10 different immune cell types or disease-specific tissues (GM12878 EBV B cells and primary human B cells, CD4+ T cells, CD8+ T cells, monocytes, macrophages, neutrophils, salivary gland tissue, kidney tissue, and whole blood).

Article Snippet: Taqman reactions were performed on a QuantStudio 6 qPCR machine (Thermo Fisher, #A43168) following manufacturer instructions using ∼25ng of DNA, TaqMan Genotyping Master Mix (ThermoFisher, #4371355), and TaqMan SNP Genotyping probes for rs57494551 (ThermoFisher, #4351379, Assay ID#C_90471390_10) and rs4938572 (ThermoFisher, #4351379, Assay ID#C_28012712_10) ( Supplemental Table 1 ).

Techniques: Functional Assay

Journal: bioRxiv

Article Title: Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

doi: 10.1101/2023.10.05.561076

Figure Lengend Snippet: (A-D) Radiolabeled electromobility shift assays (EMSA) were performed to assess the binding affinity of ribonucleoproteins isolated from EBV B or A253 cells to oligonucleotides containing the non-risk (NR) or risk (R) allele of (A-B) rs57494551 or (C-D) rs4938572. Probes incubated in the absence of nuclear lysate were used as negative control (Lanes 1, 2). Cold competitors were used to assess non-specific binding (Lanes 5, 6). Images shown in (A) and (C) are representative of n>6 biological replicates. (B, D) Bands indicated in (A, C) by the orange or green circles were quantified by densitometry and analyzed using paired t-test (n>6); p-values indicated. (E) Summary analysis of the allele-specific nuclear protein affinities of the five prioritized SNPs in EBV B, Daudi, Jurkat, THP1, and A253 cells shown in A-D and Supplemental Figures 4-9 . Increases in binding relative to NR are shown in red; decreases relative to NR in blue; no change relative to NR in grey; no detected band in black; data not available in white.

Article Snippet: Taqman reactions were performed on a QuantStudio 6 qPCR machine (Thermo Fisher, #A43168) following manufacturer instructions using ∼25ng of DNA, TaqMan Genotyping Master Mix (ThermoFisher, #4371355), and TaqMan SNP Genotyping probes for rs57494551 (ThermoFisher, #4351379, Assay ID#C_90471390_10) and rs4938572 (ThermoFisher, #4351379, Assay ID#C_28012712_10) ( Supplemental Table 1 ).

Techniques: Binding Assay, Isolation, Incubation, Negative Control

Journal: bioRxiv

Article Title: Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

doi: 10.1101/2023.10.05.561076

Figure Lengend Snippet: (A-E) gBlocks carrying the non-risk or risk alleles of (A) rs57494551, (B) rs4936443, (C) rs4938572, (D) rs7117261, or (E) rs4938573 were cloned into a promoter-less (pGL4.14; noP) or minimal promoter (pGL4.26; minP) luciferase vector. Plasmids were transfected into EBV B, Daudi, Jurkat, THP1, A253, or 293T cells. Luciferase activity was measured after 24 hours and normalized to the Renilla transfection control and then the vector-only control; reported as Relative Luciferase Activity. Statistical comparisons were performed using a paired t-test (n>3); p-values are indicated. (F) Summary analysis of the allele-specific luciferase activity of the five prioritized SNPs in EBV B, Daudi, Jurkat, THP1, A253 and 293Tcells. Increases in luciferase activity relative to non-risk are shown in purple; decreases relative to non-risk in orange; no change relative to non-risk in grey. (G) gBlocks carrying all non-risk or all risk alleles of rs4936443, rs4938572, and rs7117261 were cloned into the promoter-less or minimal promoter above, transfected into EBV B, Jurkat, THP1, A253, or 293T cells, and luciferase activity tested as described above. Statistical comparisons were performed using a paired t-test (n>3); p-values are indicated.

Article Snippet: Taqman reactions were performed on a QuantStudio 6 qPCR machine (Thermo Fisher, #A43168) following manufacturer instructions using ∼25ng of DNA, TaqMan Genotyping Master Mix (ThermoFisher, #4371355), and TaqMan SNP Genotyping probes for rs57494551 (ThermoFisher, #4351379, Assay ID#C_90471390_10) and rs4938572 (ThermoFisher, #4351379, Assay ID#C_28012712_10) ( Supplemental Table 1 ).

Techniques: Clone Assay, Luciferase, Plasmid Preparation, Transfection, Activity Assay, Control

Journal: bioRxiv

Article Title: Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

doi: 10.1101/2023.10.05.561076

Figure Lengend Snippet: (A, B) Chromatin conformation capture with quantitative PCR (3C-qPCR) across the DDX6-CXCR5 region where (A) rs57494551 or (B) rs4938572 is the anchor SNP (grey dot). Relative interaction frequency (RIF) is plotted relative to the primer number in 5’-3’ genomic orientation (blue dots; see for additional detail). Primers 9-12 are shown in a text box for simplicity in (B). (C) SjD GWAS association (top panel) and publicly available epigenomic enrichment across the DDX6-CXCR5 region in GM12878 EBV B cells. Vertical grey lines indicate the locations of rs57494551 or rs4938572, respectively. Promoter-capture Hi-C looping (purple lines) contrasts the summary 3C-qPCR results (red lines); line thickness indicates relative interaction frequency (RIF) of the 3C data. (D) SjD GWAS association (top panel) across the DDX6-CXCR5 region in A253 cells. In house ATAC-seq, CUT & RUN: H3K27me3 (Epicypher), and RNA-seq data from A253 cells are shown because of limited publicly available epigenetic data on salivary gland. Vertical grey lines indicate the locations of rs57494551 or rs4938572, respectively. Summary 3C-qPCR results are shown (red lines); line thickness indicates relative interaction frequency (RIF).

Article Snippet: Taqman reactions were performed on a QuantStudio 6 qPCR machine (Thermo Fisher, #A43168) following manufacturer instructions using ∼25ng of DNA, TaqMan Genotyping Master Mix (ThermoFisher, #4371355), and TaqMan SNP Genotyping probes for rs57494551 (ThermoFisher, #4351379, Assay ID#C_90471390_10) and rs4938572 (ThermoFisher, #4351379, Assay ID#C_28012712_10) ( Supplemental Table 1 ).

Techniques: Real-time Polymerase Chain Reaction, Hi-C, RNA Sequencing