№ files_lp_4_process_3_082399
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Methodological description of genotyping, quality control, population structure analysis and association testing applied to an Immunochip dataset investigating genetic variants in the major histocompatibility complex related to psoriasis and psoriatic arthritis.
Research field: Genetic epidemiology
Topic: Genetic association analysis of psoriasis and psoriatic arthritis
Document type: Research methods and supplementary materials description
Dataset: Immunochip dataset
Genotyping centres: Wellcome Trust Sanger Institute; Centre for Public Health Genomics at the University of Virginia; Arthritis Research UK Centre for Genetics and Genomics at the University of Manchester; University of Queensland Diamantina Institute; Trinity Translational Medicine at the University of Dublin
Genotyping software: GenomeStudio Data Analysis Software Platform (Genotyping Module v1.8.4)
Quality control tools: PLINK v1.07; EIGENSOFT v4.2; flashpca
Statistical methods: Identity-by-descent analysis; principal component analysis; logistic regression; Hardy–Weinberg equilibrium filtering
Genetic markers: SNPs from Immunochip array
Genomic region of interest: Major Histocompatibility Complex (MHC)
Genes analyzed: HLA-C; HLA-B; HLA-A
Phenotypes studied: Psoriasis; Psoriatic arthritis
Population reference datasets: HapMap3 CEU; CHB; JPT; YRI
Variables analyzed: Allele frequency; genotype call rate; heterozygosity; age of disease onset
Associated amino acid position: Position 45 of HLA-B
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Methotrexate for Subcutaneous Injection: Guidelines and Responsibilities in Rheumatoid and Psoriatic Arthritis Treatment
Note: Year
Theme: Rheumatology, Methotrexate Therapy, Drug Interaction
Document Type: Medical Guidelines
Target Audience: Healthcare Professionals, Specialists
Request for Authorization of Treatment with STELARA® for Active Psoriatic Arthritis
Year: [Insert Year]
Region / City: [Insert City, State]
Subject: Authorization request for treatment with STELARA®
Document Type: Request for prior authorization
Organization: [Insert Payer Name]
Target Audience: Medical Director or individual responsible for prior authorization
Treatment Period: [Insert relevant time period if specified]
Approval Date: [Insert Date if available]
Amendment Date: [Insert Date if available]
Rubella genotyping RT-PCR 2-fragment, Invitrogen (CDC)RT-PCR protocol for rubella genotyping (2 Fragment System)
Year: 2012
Region / city: CDC
Topic: Molecular Epidemiology, Genotyping
Document type: Protocol
Organization: CDC
Author: CDC
Target audience: Laboratories, Research Institutions
Period of validity: N/A
Approval date: 03/06/2012
Date of amendments: N/A
Purpose: Amplification of 2 fragments from the rubella virus (RuV) envelope protein 1 (E1) coding region
PCR product sizes: Fragment 1 (480 nts), Fragment 2 (633 nts)
Required equipment: Thermocycler, Micropipettors, Class II biological safety cabinet
RNA preparation: Extraction from clinical samples or cell cultures
Primers: RV8633, RV8945, RV9112, RV9577
Control RNA: Dried rubella RNA control
Handling instructions: Store primers and control RNA at specified temperatures, prepare working solutions before use
Safety recommendations: Use dedicated equipment and workspaces for RNA procedures
Contextual description: Protocol for Rubella virus genotyping using RT-PCR to amplify specific RNA fragments, primarily for molecular epidemiological research.
Policy on Identification Methods and Genotyping Laboratory Rodents
Re-Approval Date: 12/05/2024
Year: 2024
Region / City: Northeastern University
Subject: Animal Research Methods
Document Type: Policy
Organization / Institution: Northeastern University Institutional Animal Care and Use Committee (IACUC)
Author: Institutional Animal Care and Use Committee (IACUC)
Target Audience: Researchers, Animal Care Staff
Period of Validity: Indefinite until the next review
Approval Date: 12/05/2024
Modification Date: N/A
Supplementary Table 1 Primer sequences used for genotyping the ACE Gene
Year: 2023
Region / City: Not specified
Topic: Genotyping, ACE Gene, Primers
Document Type: Research Supplementary Table
Institution: Not specified
Author: Not specified
Target Audience: Researchers, Geneticists
Period of validity: Not specified
Approval Date: Not specified
Date of changes: Not specified
Performance of ASLC1/LHX8 DNA methylation and extended HPV genotyping in first-void urine for high-grade cervical intraepithelial neoplasia detection in an HPV-positive referral population - a cross-sectional study
Year: 2023
Region / City: Denmark
Theme: Cervical Cancer Screening, HPV Testing, DNA Methylation
Document Type: Research Article
Organization / Institution: University Research Clinic for Cancer Screening, Aarhus University
Authors: Mette Tranberg, Severien Van Keer, Albertus T Hesselink, Pia Nørgaard, Rikke Brøndum, Chunsen WU, Line Winther Gustafson, Anne Hammer, Pinar Bor, Karen Omann Binderup, Christina Blach, Alex Vorsters, Renske Steenbergen
Target Audience: Researchers, Healthcare Professionals, Medical Community
Period of Application: Not specified
Approval Date: Not specified
Date of Changes: Not specified
Study Registration: Clinicaltrials.gov: NCT05065853
Keywords: DNA methylation, cervical cancer screening, HPV DNA testing, urinary HPV testing, early detection of cancer/methods
Abstract: The study evaluates the performance of ASCL1/LHX8 DNA methylation markers and HPV genotyping in first-void urine samples for detecting high-grade cervical intraepithelial neoplasia (CIN2+) and cervical cancer in HPV-positive women, comparing it with clinician-collected cervical samples.
Supplementary Table S1. List of oligonucleotide primers for genotyping and vector construction
Note: Year
Topic: Genotyping and vector construction
Document Type: Supplementary table
Target Audience: Researchers in molecular biology
Topics: Immunochip Psoriatic genotyping