№ files_lp_4_process_3_132624
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Supplementary data regarding rare damaging heterozygotes and homozygotes, detailing specific gene alterations, types, CADD scores, and associated OMIM phenotypes.
Year:
2017
Region / City:
N/A
Topic:
Genomic research, whole exome sequencing
Document Type:
Research Table
Author:
N/A
Target Audience:
Researchers, geneticists
Period of validity:
N/A
Date of approval:
N/A
Date of modifications:
N/A
OMIM Phenotypes:
Nephrotic syndrome, Gaucher disease, Cardiomyopathy, and others
Related pathways:
SOX9 biological pathway, transcription factors
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Year:
2026
Region / City:
N/A
Topic:
Genetic Testing, Exome Sequencing
Document Type:
Letter
Organization / Institution:
N/A
Author:
N/A
Target Audience:
Healthcare providers, medical practitioners
Validity Period:
N/A
Approval Date:
N/A
Modification Date:
N/A
Section:
Supplemental Materials
Abbreviations:
IOP; MEE/RHC; QC; GSA; PCA; LD; MAF; PC; WES; BAM; VCF; EUR; AFR; AMR; EAS; SAS; GQ; SNPs; MAD; GTEx; Non-PAR; Indels; HWE; AB; GWAS; FAME; GC; QTL; eQTL; CLPP; FDR; OHTN; RINT
Methodology:
Whole exome sequencing and statistical genetic analysis
Sequencing Platform:
NovaSeq S4 flow cell (2x151bp)
Library Preparation Kit:
KAPA Hyper Prep with Library Amplification Primer Mix (KK8504)
Capture Kit:
IDT XGen hybridization and wash kit
Custom Bait:
TWIST Biosciences exome bait
Liquid Handling Systems:
Agilent Bravo; Hamilton Starlet
Quantification Method:
qPCR; Invitrogen Quant-It broad range dsDNA assay
Genotyping Platform:
Global Screening Array (GSA)
Software:
PLINK 1.9; PLINK 2.0; R; Python; Hail v0.2
Reference Panel:
1000 Genomes Project Phase 3
Ancestry Groups:
European (EUR); African (AFR); Admixed American (AMR); East Asian (EAS); South Asian (SAS)
Statistical Analysis:
Analysis of variance (aov in R); Tukey honest significant difference test
Quality Control Criteria:
Sample-level and variant-level QC including genotype missingness, heterozygosity, relatedness (PI_HAT), sex concordance, ancestry inference, BAM and VCF metrics
Note:
Year
Topic:
Exome sequencing data
Document Type:
Statistical report
Target Audience:
Researchers, geneticists
Language:
English
Document Type:
Clinical documentation template
Medical Field:
Medical genetics
Subject:
Justification of medical necessity for exome sequencing
Purpose:
Clinical justification for ordering exome testing
Healthcare Context:
Diagnostic evaluation of patients with suspected genetic conditions
Test Type:
Exome sequencing
Clinical Components:
Patient medical history, family history, differential diagnosis, clinical management considerations
Clinical Actions Referenced:
Medication changes, dietary modifications, procedural or surveillance adjustments
Genetic Counseling Elements:
Inheritance education, recurrence risk assessment, prenatal diagnosis discussion
Patient Considerations:
Individuals with complex or unexplained clinical features suggesting genetic disease
Family Considerations:
Impact on relatives and reproductive planning
Post-Test Activity:
Follow-up genetic counseling after results disclosure
Year:
2026
Region / City:
Kolkata, Serampore, Shantiniketan, West Bengal, India
Field:
Pharmacology, Biochemistry, Molecular Biology
Document Type:
Research Article
Institution:
Techno India University, Serampore College, Seacom Skills University
Authors:
Debojyoti Roychowdhury, Partha Talukdar, Soumendra Nath Talapatra
Target Audience:
Researchers in pharmacology, biochemistry, molecular biology, and related fields
Keywords:
Andrographis paniculata, flavonoids, antibacterial properties, molecular docking, bacterial DNA gyrase, phytochemicals, receptor-ligand binding, in silico
Period of Study:
2026
Date of Approval:
2026
Date of Last Revision:
2026
Context:
This research focuses on the molecular docking analysis of flavonoid compounds from Andrographis paniculata to evaluate their antibacterial properties against bacterial DNA gyrase B, suggesting potential alternatives to synthetic antibiotics.
Year:
2023
Methodology:
In silico simulation of species identification
Technology:
Illumina HiSeq 2000
Sequencing strategy:
100 bp paired-end (PE) shotgun reads
Reference library:
COI barcode library (when available)
Assembly software:
SOAPdenovo
Taxonomic scope:
Insect mitochondrial genomes
Sample type:
Mock-up pooled insect communities
Species tested:
209 complete mitochondrial genomes
Analysis depth:
100X and 1,000X sequencing coverage
Objective:
Comparison of reference-based and reference-independent taxonomic identification methods
Key variables:
Relatedness of species, abundance, sequencing depth, barcode length
Validation:
Alignment criteria >99% identity, coverage >90% for reference detection
Year:
2026
Region / Location:
Oryza sativa indica (long-grained rice)
Subject:
Plant molecular biology, protein analysis
Document type:
Research article
Institution:
Not specified
Author:
Not specified
Target audience:
Plant biologists, molecular biologists, bioinformaticians
Methods:
In silico computational analysis, molecular dynamics simulations, homology modeling, secondary and tertiary structure prediction, post-translational modification prediction, primer design
Protein studied:
bHLH transcription factor at locus WGL47969
Key findings:
Physicochemical properties, structural validation, predicted sub-cellular localization, protein-protein interactions, potential functional roles in growth and stress responses
Applications:
Foundation for experimental studies, insights into stress tolerance and crop improvement
Year:
2023
Region / City:
Global
Topic:
Molecular biology, Rice genetics
Document Type:
Research Paper
Organization / Institution:
Not specified
Author:
Not specified
Target Audience:
Researchers, Geneticists, Agronomists
Period of Validity:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2016
Region / City:
London, Swindon, Berkshire, Merseyside, Yorkshire, Sunderland
Topic:
Clostridium difficile infection, hospital infection control
Document Type:
Research article
Organization:
Guy’s & St Thomas’ NHS Foundation Trust, Great Western Hospitals NHS Foundation Trust, Heatherwood and Wexham Park Hospitals NHS Foundation Trust, St Helens & Knowsley Hospitals NHS Trust, Calderdale & Huddersfield NHS Foundation Trust, City Hospitals Sunderland NHS Foundation Trust
Author:
Not specified
Target Audience:
Healthcare professionals, researchers
Period of Validity:
Not specified
Approval Date:
Not specified
Modification Date:
Not specified
Context:
A research article detailing the comparison of C. difficile infection control measures across six hospitals in England using whole-genome sequencing to track transmission patterns.
Year:
2018
Region / City:
Not specified
Topic:
Performance Qualification for Sequencing System
Document Type:
Protocol
Organization / Institution:
Illumina, Inc.
Author:
Illumina, Inc.
Target Audience:
Illumina certified personnel
Period of Validity:
Not specified
Approval Date:
Not specified
Amendment Date:
Not specified
Year:
Annually
Region / City:
United States (CDC)
Topic:
Healthcare-Associated Infections, Antimicrobial Resistance
Document Type:
Report
Organ / Institution:
Centers for Disease Control and Prevention (CDC)
Author:
Not specified
Target Audience:
Funded laboratories, public health officials
Period of Validity:
Annual
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2024
Region / city:
Montclair, NJ
Topic:
DNA sequencing protocol
Document type:
Standard Operating Protocol (SOP)
Institution:
Montclair State University, Biology Department
Author:
Adam Parker
Target audience:
Laboratory technicians, researchers
Effective period:
Ongoing
Approval date:
8/22/2024
Revision date:
N/A
Year:
2015
Region / City:
N/A
Theme:
Molecular Ecology, Fungal Studies
Document Type:
Research Protocol
Organization:
Kennedy Lab
Authors:
Nhu Nguyen, Peter Kennedy
Target Audience:
Researchers in molecular ecology and fungal studies
Effective Period:
N/A
Approval Date:
N/A
Date of Changes:
April 22, 2015
Year:
2026
Region / City:
N/A
Topic:
Genetic Testing, Exome Sequencing
Document Type:
Letter
Organization / Institution:
N/A
Author:
N/A
Target Audience:
Healthcare providers, medical practitioners
Validity Period:
N/A
Approval Date:
N/A
Modification Date:
N/A
Year:
2021
Region / city:
UK
Theme:
Carbon Capture, Usage and Storage (CCUS), Environmental Policy
Document Type:
Project Plan, Government Report
Organization / institution:
Department for Business, Energy and Industrial Strategy (BEIS)
Author:
BEIS (Department for Business, Energy and Industrial Strategy)
Target audience:
Power CCUS Project applicants, governmental and regulatory bodies
Action period:
2021–2030
Approval date:
Not specified
Revision date:
Not specified
Year:
2019-2020
Region / City:
Shanghai, China
Field:
Medical research, oncology
Document type:
Research article
Institution:
Zhongshan Hospital Fudan University
Authors:
Not specified
Target audience:
Researchers, medical professionals
Study period:
May 2019 - February 2020
Approval date:
B2019-060R
Follow-up end date:
March 31, 2020
Year:
2002
Region / city:
Canada
Theme:
Molecular biology
Document type:
Scientific research data
Organization / institution:
Jones et al.
Author:
Jones et al.
Target audience:
Researchers in molecular biology
Period of validity:
Not specified
Approval date:
Not specified
Date of changes:
Not specified
Year:
2018
Region / City:
San Diego, California
Topic:
Genetic testing, Whole Genome Sequencing, Clinical Genetics
Document Type:
Medical Necessity Letter
Target Audience:
Medical professionals, insurance providers
Period of Validity:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified