№ files_lp_3_process_7_062257
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Administrative research planning document outlining policies, standards, repositories, timelines, and access conditions for the generation, submission, preservation, and controlled sharing of genomic, phenotypic, and clinical data within an NIH-funded human subjects study.
Document Type:
Data Management and Sharing Plan
Policy Framework:
NIH Policy for Data Management and Sharing; Genomic Data Sharing Policy
Funding Agency:
National Institutes of Health (NIH)
Related Repositories:
NIMH Data Archive (NDA); dbGaP
Study Registration:
dbGaP
Subject Population:
500 human research subjects
Data Types:
Whole genome sequencing data; phenotypic data; clinical data
Genomic Data Formats:
FASTQ; SAM/BAM; BED; VCF
Data Standards:
NOT-MH-20-067 common data elements; Genomics Subject (genomics_subject02); Genomics Sample (genomics_sample03); Structured Clinical Interview for DSM-V (scidv_dep01); MATRICS Consensus Cognitive Battery (matrics01)
Assessment Instruments:
DSM Crosscutting; WHODAS 2.0; PHQ-9; GAD-7
Software and Tools:
Illumina sequencing pipelines; Genome Analysis Toolkit (GATK)
Data Submission Timeline:
Initial deposit 12 months after award start; subsequent deposits every six months
Data Access Conditions:
Broad data sharing consent; controlled access via NDA
Data Availability Period:
At end of grant award or upon publication submission; long-term preservation managed by NDA
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Year:
2023
Region / city:
Not specified
Topic:
Chronic kidney disease, Genetic and phenotypic analysis
Document type:
Research paper
Institution / organization:
Not specified
Author:
Not specified
Target audience:
Researchers, healthcare professionals, geneticists
Period of validity:
Not specified
Approval date:
Not specified
Date of changes:
Not specified
Document type:
Supplementary material
Subject:
Microbiology and bacterial taxonomy
Focus organism:
Pseudescherichia liriopis sp. nov. L3T
Associated plant host:
Liriope platyphylla
Test plant species:
Daucus carota subsp. sativus
Authors:
Inhyup Kim; Haejin Woo; Geeta Chhetri; Sunho Park; Taegun Seo
Affiliation:
Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
Corresponding author:
Taegun Seo
Contact email:
[email protected]
Methods included:
FastANI analysis; antiSMASH analysis; API 20NE tests; dDDH and ANI genomic comparisons
Data included:
EPS production assay; PEG and NaCl resistance; growth range; hydrolysis tests; genome statistics; phylogenetic comparisons
Genome accession number (L3T):
JANKYC000000000
Genome size (L3T):
4,304,575 bp
DNA G+C content:
56.5 mol%
Number of compared species:
29
Year:
2024-25
Region / City:
Varanasi, Uttar Pradesh, India
Subject:
Genotype × Environment Interactions, Phenotypic Plasticity
Document Type:
Research Article
Organization / Institution:
ICAR-IIVR
Author:
Choudhary et al.
Target Audience:
Researchers, Plant Breeders
Period of Validity:
Not specified
Approval Date:
Not specified
Modification Date:
Not specified
Keywords:
Brinjal, climate-resilient breeding, genotype × environment interaction, hybrids, inbreds, phenotypic plasticity, seasonal stability
Context:
The document is an academic research article examining genotype by environment interactions in brinjal, focusing on the phenotypic stability and plasticity of qualitative traits across two different seasonal environments.
Year:
2019–2021
Region / Location:
United States
Topic:
Psychiatric Genetics, PTSD
Document Type:
Research Summary / Scientific Review
Institution:
Rosalind Franklin University of Medicine and Science
Author:
Monika A. Waszczuk
Target Audience:
Researchers and clinicians in psychiatry and genetics
Study Cohorts:
Psychiatric Genomics Consortium (PGC), Million Veterans Program (MVP)
Methods:
Genome-Wide Association Studies, Dimensional Phenotypic Analysis
Phenotypes Studied:
PTSD symptoms, trauma exposure, related psychiatric conditions
Sample Size:
30,000–250,000 participants across studies
Findings:
Identification of multiple genetic loci associated with PTSD and trauma-related traits
Endophenotypes:
Dimensional measures of symptom severity, lifetime trauma exposure
Relevance:
Genetic architecture of PTSD and transdiagnostic loci in psychiatric disorders
Data Collection Tools:
Clinician-Administered PTSD Scale (CAPS), PTSD Checklist (PCL)
Publication Date:
2021
Description:
Scientific article presenting GWAS findings on PTSD and trauma, emphasizing dimensional phenotypic approaches to reveal genetic loci associated with symptom severity and trauma exposure.
Year:
Not specified
Country:
United States
Field:
Genomics; Biomedical Research; Data Management
Document Type:
Research Data Management and Sharing Plan
Organization:
National Institutes of Health (NIH)
Related Repositories:
NIMH Data Archive (NDA); dbGaP
Research Data Types:
Genomic sequencing data; Phenotypic data; Clinical data
Number of Research Subjects:
500
Data Standards:
DSM Crosscutting; WHODAS 2.0; PHQ-9; GAD-7; MATRICS Consensus Cognitive Battery
File Formats:
FASTQ; SAM/BAM; BED; VCF
Software / Tools:
Illumina pipelines; Genome Analysis Toolkit (GATK)
Data Submission Timeline:
Starting 12 months after award and every six months thereafter
Data Access Conditions:
Broad data sharing with participant consent; controlled access through NDA
Persistent Identifier:
Digital Object Identifier (DOI) assigned to NDA studies
Associated Policies:
NIH Policy for Data Management and Sharing; Genomic Data Sharing Policy
Year:
2025
Region / City:
North West NHS GMS region
Topic:
ctDNA testing for NSCLC and breast cancer
Document Type:
Notification
Organization:
NHS England
Author:
Genomics Unit
Target Audience:
NHS Trusts
Period of Action:
2025/26 financial year
Approval Date:
7 November 2025
Date of Changes:
N/A
Context:
Notification regarding the continuation and expansion of ctDNA testing for lung and breast cancer in the North West NHS region for the 2025/26 financial year.
Year:
2016
Region / city:
Geneva, CH
Theme:
Biotechnology, Genomic Information Processing, Data Compression
Document Type:
Call for Proposals
Organization:
ISO/IEC JTC 1/SC 29/WG 11, ISO/TC 276/WG 5
Author:
ISO/IEC JTC 1/SC 29/WG 11, ISO/TC 276/WG 5
Target Audience:
Scientific and technical communities in biotechnology, bioinformatics, and data compression
Effective Period:
N/A
Approval Date:
June 2016
Revision Date:
N/A
Year:
2023
Region / City:
Not specified
Theme:
Genetic and Genomic Research
Document Type:
Consent Form
Organization / Institution:
Not specified
Author:
Not specified
Target Audience:
Participants of a research study
Duration of Action:
Until the study is concluded and data is used up
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2008
Region / Institution:
University of Otago, New Zealand
Field:
Genetics / Molecular Biology
Document type:
Research Abstract
Authors:
A.J. Stevens, S. Stuffrein-Roberts, A.L. Miller, A. Gibb, K. Doudney, A. Bagshaw, A. Aitchison, M.R. Eccles, V.V. Filichev, M.A. Kennedy
Target audience:
Researchers in genetics and molecular biology
Affiliations:
Department of Pathology, University of Otago, Christchurch; Department of Pathology, University of Otago, Dunedin School of Medicine; Institute of Fundamental Sciences, Massey University, Palmerston North
References included:
Yes
Research focus:
Investigation of allelic dropout related to G-quadruplex DNA structures and genomic imprinting in PCR assays
Year:
2024
Region / city:
Manchester, Liverpool
Subject:
Genomic Laboratory Services
Document Type:
Quality Manual
Organization / Institution:
Manchester University NHS Foundation Trust
Author:
NW GLH
Target Audience:
Laboratory staff, accreditation bodies, service users
Effective Period:
Ongoing
Approval Date:
2024-06-01
Amendment Date:
2024-06-01
This document provides detailed information on the structure, policies, and procedures of the North West Genomic Laboratory Hub (NW GLH) and the Willink Laboratory to meet ISO 15189:
2022 requirements.
Note:
Year
The document is a Quality Manual outlining the quality management system, policies, and procedures of the Genomic Diagnostics Laboratory, ensuring compliance with ISO 15189:
2012 standards.
Year:
2023
Region / city:
Canada
Subject:
Genomic Applications, Research Proposal
Document Type:
Guidelines
Organization:
Genome Canada
Author:
Genome Canada
Target Audience:
Researchers, Institutions, Project Leaders
Validity Period:
From submission until project completion
Approval Date:
Not specified
Amendment Date:
Not specified
Note:
Year
Document type:
Podcast Transcript
Organization / institution:
Genomics England
Author:
Francisco Azuaje, Karim Beguir, Harry Farmer, Rich Scott
Target audience:
Healthcare professionals, researchers, AI developers
Year:
2022
Region / city:
N/A
Topic:
Genomic Constraint, Z Score, Genomic Windows
Document Type:
Dataset
Institution:
Broad Institute
Author:
N/A
Target Audience:
Researchers, Genomics Professionals
Period of Action:
N/A
Approval Date:
N/A
Date of Changes:
Oct 27, 2022
Note:
Year
Year:
N/A
Region / City:
N/A
Subject:
Genomic Data Sharing
Document Type:
Evaluation Worksheet
Institution / Organization:
IRB Office
Author:
N/A
Target Audience:
IRB Director or Designee, Investigators
Period of Validity:
N/A
Approval Date:
N/A
Amendment Date:
N/A
Year:
2000–2022
Study Type:
Clinical research
Patient Population:
ABL-class leukemia patients
Sample Type:
Bone marrow and blood DNA
Assay Methods:
RNA sequencing, targeted locus amplification (TLA), genomic capture high throughput sequencing (gc-HTS), Fusion Detection by Gene Enrichment (FUDGE), long-range PCR, Sanger sequencing
Quantitative Assay:
MRD Q-PCR based on genomic breakpoints and IG/TR targets
Institution:
Princess Máxima Centrum, Netherlands; USEQ sequencing facility, Utrecht, Netherlands; Macrogen Europe
Ethics:
Written informed consent obtained according to the Declaration of Helsinki
Data Tables:
Supplemental Digital Tables 1–3
Figures:
Supplemental Digital Figures 1–2
Reference Protocols:
EuroMRD guidelines
Year:
2026
Region / City:
Huntington Botanical Garden, Lyon Arboretum, Fairchild Tropical Botanical Garden, United States Botanical Research Greenhouse, U.C. Davis Botanical Conservatory, New York Botanical Garden
Theme:
Genomic Resources, Plant Phylogeny
Document Type:
Research Data
Organization / Institution:
Various botanical gardens and research institutions
Author:
Not specified
Target Audience:
Researchers in plant genomics and phylogeny
Period of validity:
Not specified
Date of approval:
Not specified
Date of amendments:
Not specified
Year:
2020
Region:
Guangdong Province, China
Topic:
Genomic epidemiology of SARS-CoV-2
Document type:
Supplementary information to a scientific research article
Associated article:
Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China
Authors:
Jing Lu; Louis du Plessis; Zhe Liu; Verity Hill; Min Kang; Huifang Lin; Jiufeng Sun; Sarah François; Moritz U G Kraemer; Nuno R Faria; John T McCrone; Jingju Peng; Qianlin Xiong; Runyu Yuan; Lilian Zeng; Pingping Zhou; Chuming Liang; Lina Yi; Jun Liu; Jianpeng Xiao; Jianxiong Hu; Tao Liu; Wenjun Ma; Wei Li; Juan Su; Huanying Zheng; Bo Peng; Shisong Fang; Wenzhe Su; Kuibiao Li; Ruilin Sun; Ru Bai; Xi Tang; Minfeng Liang; Josh Quick; Tie Song; Andrew Rambaut; Nick Loman; Jayna Raghwani; Oliver G Pybus; Changwen Ke
Affiliated institutions:
Guangdong Provincial Center for Disease Control and Prevention; University of Oxford; University of Edinburgh; Shenzhen Center for Disease Control and Prevention; Guangzhou Center for Disease Control and Prevention; Guangdong Provincial Second People’s Hospital; Foshan First People’s Hospital; University of Birmingham
Data coverage period:
Up to 19 March 2020
Number of reported genomes:
53 newly reported SARS-CoV-2 genomes
Total cases referenced:
1388 laboratory-confirmed COVID-19 cases
Figures:
S1–S4
Tables:
S1–S2
Data sources:
RT-PCR testing; whole-genome sequencing; GISAID database
Geographic scope of comparative data:
Guangdong; Hubei; USA (California, Wisconsin); Japan; Singapore; Jiangsu; Fujian; India; Vietnam
Year:
2026
Region / city:
Not specified
Topic:
Genomic manipulation, yeast transformation, molecular biology
Document type:
Protocol
Organization / Institution:
Not specified
Author:
Not specified
Target audience:
Researchers, Molecular biologists
Period of validity:
Not specified
Approval date:
Not specified
Date of amendments:
Not specified
Note:
Contextual description