Journal: Age

Article Title: Modulation of human longevity by SIRT3 single nucleotide polymorphisms in the prospective study “Treviso Longeva (TRELONG)”

doi: 10.1007/s11357-013-9559-2

Figure Lengend Snippet: SIRT3 Western blotting in peripheral blood mononucleate cells. To assess a possible functional correlation of rs11555236 variants with SIRT3 expression, we selected a group of subjects from the TRELONG study, balanced for gender, and evaluated SIRT3 protein

Article Snippet: To assess rs3825075, rs4980329, and rs11555236 genotypes, a gDNA aliquot (about 20 ng) was used in an allelic discrimination assay using a real-time PCR apparatus and TaqMan technology according to the manufacturer's instructions (Applied Biosystems, Foster City, CA).

Techniques: Western Blot, Functional Assay, Expressing

Journal: Journal of Biomedical Research

Article Title: Impact of IL28B gene polymorphisms rs8099917 and rs12980275 on response to pegylated interferon-α/ribavirin therapy in chronic hepatitis C genotype 4 patients

doi: 10.7555/JBR.30.20150002

Figure Lengend Snippet: Agarose gel electrophoresis analysis of rs8099917 and rs12980275 polymorphism in IL28 gene. A: TT genotype produced only one 400 bp band, GG genotype produced 2 small fragments at 234 and 166 bp, respectively, and TG genotype produced 3 bands: 400, 234, and 166 bp, respectively. M Lane represents the 50 bp molecular marker. B: The AA genotype produced two bands 178, 115 bp, the AG genotype produced 3 bands: 178, 148, and 115 bp, the GG genotype produced 2 small fragments at 148, 115 (30 bp band not appear) respectively. M lane represents the 50bp molecular marker.

Article Snippet: For RFLP assay for rs12980275 genotype, amplicons were digested with 2 U BseL I restriction endonuclease (Fermentas) at 55°C for 12 hours.

Techniques: Agarose Gel Electrophoresis, Produced, Marker

Journal: American Journal of Human Genetics

Article Title: IRF4 Variants Have Age-Specific Effects on Nevus Count and Predispose to Melanoma

doi: 10.1016/j.ajhg.2010.05.017

Figure Lengend Snippet: Self-Reported Mole Scores in Queensland Melanoma Cases versus Age and Genotype at rs12203592 in IRF4

Article Snippet: The rs12203592 genotypes were assessed with the use of the Taqman SNP genotyping assay C_31918199_10 (Applied Biosystems).

Techniques:

Journal: American Journal of Human Genetics

Article Title: IRF4 Variants Have Age-Specific Effects on Nevus Count and Predispose to Melanoma

doi: 10.1016/j.ajhg.2010.05.017

Figure Lengend Snippet: Adolescent Macular and Papular Mole Counts versus rs12203592 Genotype, Stratified on the Four Levels of Freckling Score

Article Snippet: The rs12203592 genotypes were assessed with the use of the Taqman SNP genotyping assay C_31918199_10 (Applied Biosystems).

Techniques:

Journal: American Journal of Human Genetics

Article Title: IRF4 Variants Have Age-Specific Effects on Nevus Count and Predispose to Melanoma

doi: 10.1016/j.ajhg.2010.05.017

Figure Lengend Snippet: Combined Analysis of Melanoma Case-Control Data from Australia, the UK, and Sweden for rs12203592 by Tumor Site, Showing the Strongest Association with Melanoma on the Trunk: OR = 1.32, p = 2.5 × 10 −5

Article Snippet: The rs12203592 genotypes were assessed with the use of the Taqman SNP genotyping assay C_31918199_10 (Applied Biosystems).

Techniques:

Journal: Journal of Neuroinflammation

Article Title: Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course

doi: 10.1186/s12974-018-1307-1

Figure Lengend Snippet: Flowchart showing the study design and analysis. Patients were classified according to their disease course into benign and aggressive MS, as described in the Methods. By means of exome sequencing, a total of 915 single-nucleotide polymorphisms (SNPs) were identified from 10 MS patients with benign and 10 with aggressive disease courses as being differentially distributed between both groups (discovery cohort). After applying several selection criteria on the list of 915 SNPs including odds ratio difference, phenotype prevalence, number of statistically significant SNPs per gene, type and variant effects on the predicted protein, and relevance of target genes to MS, a total of 16 SNPs were chosen for further validation in two independent cohorts of patients also classified into benign and aggressive phenotypes. The first validation cohort comprised 194 MS patients, 107 with benign and 87 with aggressive disease courses, and genotyping was conducting using an OpenArray technology. The second validation cohort consisted of 257 MS patients, 224 with benign and 33 with aggressive disease courses, and genotyping was performed on a MassArray iPLEX platform. Finally, a meta-analysis was performed in the two validation cohorts

Article Snippet: TaqMan OpenArray genotyping Genotyping of selected variants in the first validation cohort was performed using an OpenArray technology (Thermo Fisher Scientific, Massachusetts, USA) and following the manufacturer’s instructions.

Techniques: Mass Spectrometry, Sequencing, Selection, Variant Assay

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: IGV visualization of human liver CYP2C19 mRNA. RNA-Seq results for human livers that were heterozygous (half-filled box) or homozygous wild type (open box). (A) rs12769205 were visualized across CYP2C19 exons 2-Exon3; and (B) rs4244285 were visualized

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques: RNA Sequencing Assay

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: rs12769205 Is in LD with rs4244285 on CYP2C19*2 , but Occurs Independently on the CYP2C19*35 Allele in Some Blacks.

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques:

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: CYP2C19 haplotype frequencies, extended haplotype homozygosity, and ancestral tree in 216 YRI chromosomes. (A) Sweep was used to determine CYP2C19 haplotypes (SNP positions rs12769205, rs4244285, rs4417205, and rs3758580) and their frequencies. The online

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques:

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: Effect of rs4244285 and rs12769205 on CYP2C19 splicing. (A) Eight liver samples were analyzed by PCR for (A) the CYP2C19 exon 5–40 bp deletion, caused by rs4244285, using primers in exons 4 and 6, and (B) the CYP2C19 exon 2B insertion, caused

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques: Polymerase Chain Reaction

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: Structure of alternative CYP2C19 mRNAs in livers with rs4244285 and rs12769205 genotypes. CYP2C19 was PCR amplified using exon 2 and 6 primers in liver samples with indicated genotypes and the products were analyzed on agarose gels. Arrows indicate the

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques: Polymerase Chain Reaction, Amplification

Journal: Drug Metabolism and Disposition

Article Title: The CYP2C19 Intron 2 Branch Point SNP is the Ancestral Polymorphism Contributing to the Poor Metabolizer Phenotype in Livers with CYP2C19*35 and CYP2C19*2

doi: 10.1124/dmd.115.064428

Figure Lengend Snippet: CYP2C19 peptides downstream from exon 2 failed to detect residual CYP2C19 wild-type protein in CYP2C19*2 and CYP2C19*35 liver microsomes. (A) The location of the peptide probes used relative to CYP2C19 exons and to rs12769205 and rs4244285. (B) Expression

Article Snippet: Total RNA was extracted from human livers with rs4244285 and rs12769205 genotypes using TRIzol reagent (Invitrogen, Carlsbad, CA).

Techniques: Expressing

Journal: BioMed Research International

Article Title: Identification of IL-28B Genotype Modification in Hepatocytes after Living Donor Liver Transplantation by Laser Capture Microdissection and Pyrosequencing Analysis

doi: 10.1155/2018/1826140

Figure Lengend Snippet: 3.2. Modification of IL-28B SNP rs8099917 and rs12979860 Genotypes after LDLT

Article Snippet: IL-28B SNP rs8099917 and rs12979860 genotypes were studied in liver tissues, donor's blood samples, and recipient's blood samples on POD0, POD7, and POD30, using a 7500 Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with Custom TaqMan SNP Genotyping Assays (Applied Biosystems) for allele discrimination.

Techniques: Modification

Journal: BioMed Research International

Article Title: Identification of IL-28B Genotype Modification in Hepatocytes after Living Donor Liver Transplantation by Laser Capture Microdissection and Pyrosequencing Analysis

doi: 10.1155/2018/1826140

Figure Lengend Snippet: 3.2. Modification of IL-28B SNP rs8099917 and rs12979860 Genotypes after LDLT

Article Snippet: IL-28B SNP rs8099917 and rs12979860 genotypes were studied in liver tissues, donor's blood samples, and recipient's blood samples on POD0, POD7, and POD30, using a 7500 Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with Custom TaqMan SNP Genotyping Assays (Applied Biosystems) for allele discrimination.

Techniques: Modification

Journal: Molecular Ecology Resources

Article Title: Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array

doi: 10.1111/1755-0998.12270

Figure Lengend Snippet: Genotyping and characterization of linkage disequilibrium

Article Snippet: Genotyping and characterization of linkage disequilibrium Genotyping was performed on an Illumina iScan instrument at the SNP & Seq Technology Platform at Uppsala University ( http://www.molmed.medsci.uu.se/SNP+SEQ+Technology+Platform/ ).

Techniques:

Journal: Diabetologia

Article Title: Adiponectin receptor genes: mutation screening in syndromes of insulin resistance and association studies for type 2 diabetes and metabolic traits in UK populations

doi: 10.1007/s00125-006-0534-7

Figure Lengend Snippet: Genomic structure and pair-wise marker LD in ADIPOR1 ( a ) and ADIPOR2 ( b ). The location of SNPs identified in this study and/or genotyped is represented along the gene ( bold type : SNPs selected for genotyping, and failed or monomorphic SNPs ). Exons are represented in boxes ( black for coding and open for untranslated ). Introns and flanking sequences appear as lines . The pair-wise marker LD measured by r 2 statistics is shown below the genomic structures and indicated by the shade of grey blocks ( white to black ) and the r 2 value. a , b , isoforms a and b in ADIPOR2

Article Snippet: Genotyping of samples was performed in 384-well plates at the Wellcome Trust Sanger Institute, Cambridge, using an adaptation of the homogenous MassExtend protocol for the MassArray system (Sequenom, San Diego, CA, USA) [ ].

Techniques: Marker

Journal: Scientific Reports

Article Title: Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

doi: 10.1038/srep40577

Figure Lengend Snippet: SNP calling pattern, genome density and polymorphism of SNPs in ‘Reference Set’ using Axiom_ Arachis SNP array. This figure shows ( a , b ) monomorphic SNPs identified in the genotyping data, ( c ) polymorphic SNPs without heterozygosity i.e., homozygous SNPs, ( d ) polymorphic SNPs with heterozygosity, ( e ) genome-wide distribution of SNPs, and ( f ) pseudomolecule-wise distribution of SNPs on array and polymorphic SNPs in the ‘Reference Set’.

Article Snippet: SNP allele calling and data analysis Allele calling was done using Axiom™ Analysis Suite version 1.0 using its three workflows i.e., Best Practices, Sample QC, Genotyping and Summary Only ( http://media.affymetrix.com/support/downloads/manuals/axiom_analysis_suite_user_guide.pdf ).

Techniques: Genome Wide

Journal: eLife

Article Title: Shear stimulation of FOXC1 and FOXC2 differentially regulates cytoskeletal activity during lymphatic valve maturation

doi: 10.7554/eLife.53814

Figure Lengend Snippet: FOXC2 is able to functionally substitute for FOXC1 during lymphatic valve development. ( a ) Schematic representation of the targeting vector and targeted allele. The entire protein coding region of Foxc1 is replaced with that of Foxc2 . ACN, self-excision cassette including Cre driven by the testis-specific promoter. ( b ) Southern blot analysis to detect double-resistant ES cell colonies using 5’ and 3’ probes. ( c ) PCR genotyping of F1 heterozygotes to detect the Foxc1 c2 allele. ( d, e ) Representative images of lymphatic valves in mesenteric collecting vessels immunostained with antibodies targeted to FOXC1 and VEGFR-3 from P12 P6 Foxc1 +/+ ( d ) and Foxc1 c2/c2 ( e ) mice. Scale bars are 25 µm. (f – h) Representative images of lymphatic valves in mesenteric collecting vessels immunostained with antibodies targeted to FOXC1, FOXC2, and VE-Cadherin from P6 Foxc1 +/+ ( f ) , Foxc1 c2/+ ( g ), and Foxc1 c2/c2 mice ( h ). Scale bars are 50 μm. (i – k) Representative images of the mesenteric vasculature immunostained with antibodies targeted to PROX1 and CD31 in P6 Foxc1 +/+ ( i ) , Foxc1 c2/+ ( j ), and Foxc1 c2/c2 mice ( k ). Scale bars are 200 μm. (l – n) Representative images of P6 mesenteric vasculature from P6 Foxc1 +/+ ( l ) , Foxc1 c2/+ ( m ), and Foxc1 c2/c2 mice ( n ) immunostained with antibodies targeted to FOXC1, FOXC2, and VE-Cadherin show gradual loss of FOXC1 expression in the blood and lymphatic vasculature and smooth muscle cells and conversely the increase of FOXC2 expression in blood vasculature and smooth muscle. Scale bars are 200 μm. ( o ) Quantification of total lymphatic valve number in lymphatic collecting vessels of P6 Foxc1 +/+ , Foxc1 c2/+ , and Foxc1 c2/c2 individuals. N = 6 for Foxc1 +/+ , N = 8 for Foxc1 c2/+ , and N = 8 for Foxc1 c2/c2 individuals. ( p ) Percentage of mature and immature lymphatic valves normalized to total valves counted in P6 Foxc1 +/+ , Foxc1 c2/+ , and Foxc1 c2/c2 individuals. Data are presented as mean (± SD) and analyzed using Student’s t-test. NS denotes no significance.

Article Snippet: Genotyping of mice for use in analysis was performed by Transnetyx Inc (Cordova, TN) using real-time PCR.

Techniques: Plasmid Preparation, Southern Blot, Polymerase Chain Reaction, Mouse Assay, Expressing

Journal: PLoS ONE

Article Title: Constitutive Expression of Yes-Associated Protein (Yap) in Adult Skeletal Muscle Fibres Induces Muscle Atrophy and Myopathy

doi: 10.1371/journal.pone.0059622

Figure Lengend Snippet: Characterisation of MCK-tTA-hYAP1 S127A mouse model. A) Schematic outline of the inducible ‘Tet-Off’ transgenic system. B) Genotyping of MCK-tTA and TRE-hYAP1 S127A alleles in single and double transgenic mice. C) Yap protein levels in skeletal muscles of transgenic mice of indicated genotypes following 25 days with (+) or without (−) doxycycline (dox). Tibialis anterior (TA), gastrocnemius (Gas) and extensor digitorum longus (EDL). D) Muscle specific expression of hYAP mRNA in MCK-tTA-hYAP1 S127A mice 25 days after doxycycline withdrawal. E) Time course of Yap protein expression in tibialis anterior of MCK-tTA-hYAP1 S127A mice following doxycycline removal.

Article Snippet: PCR primers for genotyping, end-point PCR primers for hYAP and Gapdh mRNA and qRT-PCR primers and probes (Roche Universal Probe Library). (DOCX) Click here for additional data file.

Techniques: Transgenic Assay, Mouse Assay, Expressing