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Monday, November 5, 2012
i2b2 informatics for integrating Biology & the bedside
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DNA Transcription
http://biology.about.com/od/cellularprocesses/ss/Dna-Transcription.htm
DNA Transcription
By Regina Bailey, About.com Guide
DNA Transcription
National Human Genome Research Institute
.DNA transcription is a process that involves the transcribing of genetic information from DNA to RNA. The transcribed DNA message is used to produce proteins. DNA is housed within the nucleus of our cells. It controls cellular activity by coding for the production of enzymes and proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA. This ensures that the information contained within the DNA does not become tainted.
DNA Transcription
DNA consists of four nucleotide bases [adenine (A), guanine (G), cytosine (C) and thymine (T)] that are paired together (A-T and C-G) to give DNA its double helical shape.
There are three main steps to the process of DNA transcription.
•RNA Polymerase Binds to DNA
DNA is transcribed by an enzyme called RNA polymerase. Specific nucleotide sequences tell RNA polymerase where to begin and where to end. RNA polymerase attaches to the DNA at a specific area called the promoter region.
•Elongation
Certain proteins called transcription factors unwind the DNA strand and allow RNA polymerase to transcribe only a single strand of DNA into a single stranded RNA polymer called messenger RNA (mRNA). The strand that serves as the template is called the antisense strand. The strand that is not transcribed is called the sense strand.
Like DNA, RNA is composed of nucleotide bases. RNA however, contains the nucleotides adenine, guanine, cytosine and uricil (U). When RNA polymerase transcribes the DNA, guanine pairs with cytosine and adenine pairs with uricil.
•Termination
RNA polymerase moves along the DNA until it reaches a terminator sequence. At that point, RNA polymerase releases the mRNA polymer and detaches from the DNA.
Since proteins are constructed in the cytoplasm of the cell by a process called translation, mRNA must cross the nuclear membrane to reach the cytoplasm. Once in the cytoplasm, mRNA along with ribosomes and another RNA molecule called transfer RNA, work together to produce proteins. Proteins can be manufactured in large quantities because a single DNA sequence can be transcribed by many RNA polymerase molecules at once.
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The IRB
source ; http://humansubjects.stanford.edu/
The IRB’s Mission
The goal of the IRB is to protect human research participants by ensuring that
The goal of the IRB is to protect human research participants by ensuring that
- participants' rights and welfare are adequately protected,
- research is guided by the ethical principles of respect for persons, beneficence, and justice as set forth in the Belmont Report,
- research is conducted with the highest level of expertise and integrity, and
- research complies with all applicable laws, policies and regulations.
What is an Institutional Review Board (IRB)?
An Institutional Review Board (IRB) is a federally mandated panel that is charged with overseeing the protection of human participants in research. Stanford has eight IRBs, seven that review medical research and one that reviews non-medical research.
An Institutional Review Board (IRB) is a federally mandated panel that is charged with overseeing the protection of human participants in research. Stanford has eight IRBs, seven that review medical research and one that reviews non-medical research.
At Stanford, the IRBs are formally known as Administrative Panels for the Protection of Human Subjects. The IRBs are part of the Research Compliance Office and derive their authority from the Office of the Vice Provost and Dean of Research. They are a major component of the Human Research Protection Program (HRPP). The HRPP is made up of many Stanford component organizations who share a common goal of excellence in protecting human participants in Stanford research.
The HRPP complies with federal, state, and local regulations, and Stanford policies. It is accredited by the American Association of Human Research Protection Programs (AAHRPP).
The IRBs oversee research for the following institutions:
- Stanford University (SU),
- Stanford Hospital and Clinics (SHC),
- Lucile Packard Children’s Hospital (LPCH),
- the Veterans Administration Palo Alto Health Care Services (VAPAHCS) and
- the Palo Alto Institute for Research and Education (PAIRE).
Most IRB members are affiliated with these institutions. Each IRB is comprised of Stanford University faculty members, students and community members. IRBs are also mandated to include non-scientific members and members not affiliated with the institutions listed above.
Getting Started
To help you get started, please see the following resources:
To help you get started, please see the following resources:
Access to Clinical Data
source : https://clinicalinformatics.stanford.edu/services/clinicaldata.html
SCCI is the official SUMC clearing house for all clinical data requests related to research. Our clinical information is provided through STRIDE (Stanford Translational Research Integrated Database Environment). The cornerstone of STRIDE is a clinical data warehouse, integrating health information from both the Lucile Packard Children's Hospital (LPCH) and Stanford Hospital and Clinics (SHC) electronic health record systems, including both historical data and current EPIC and CERNER clinical data.
The following diagram illustrates a typical researcher workflow:
Select a step to highlight
Hypotheses and Feasibility
EMR systems are primarily designed for patient management and billing. Using this data for research purposes can be challenging. We strongly encourage researchers to meet with us in the early stages of a project to gauge the feasibility of clinical queries and to help identify any nuances in the clinical data that could affect their interpretation of the data. This meeting is offered at no cost as part of the free informatics consultation service.
Cohort Identification
Researchers can determine if a cohort of suitable pediatric and/or adult patients exists in the STRIDE clinical warehouse by meeting with us in-person as part of a free informatics consultation, or by independently using the STRIDE Cohort Discovery Tool. The Cohort Discovery Tool is available to all Stanford research personnel with current HIPAA training.
SCCI Approval
Once a potential research patient cohort has been identified, the researcher submits the formal request to SCCI containing the initial cohort query, research question(s) formulated, and all clinical data elements they wish to review. If approved by the School of Medicine's Privacy Officer, the clinical data will be made available to the researcher as an identified or de-identified dataset through the STRIDE Patient Cohort Data Review Tool.
Data Review
The STRIDE Patient Cohort Data Review Tool (DRT) permits users to search across physician notes, labs, radiology and more. Users can include or exclude patients on an individual basis to form a curated cohort ready for export and analysis. As permitted by HIPAA, the DRT allows researchers to review clinical data for a potential research project; however no data can be copied, transcribed or used in any way until IRB approval is received. Upon completion of the data review, the researcher must then apply to the IRB for study approval.
IRB Approval
New research projects will require an approved IRB protocol to move forward. We can assist by supplying anonymous data reports, which typically take the form of the number of patients seen at Stanford matching your proposed research cohort profile.
If you are trying to apply an existing protocol to your extract, it will first be reviewed to ensure all requested data elements are covered. In some cases, the researcher must go back to the IRB to amend their protocol to include additional elements.
Data Extraction
With an approved IRB protocol and curated data review cohort, the researcher submits a formal request for data extraction from the STRIDE clinical data warehouse. After review of the application and an in-person meeting, a clinical informatics specialist on staff will develop the custom query and/or extraction tailored to the specific needs of the research study.
Data Analysis
Stanford and the Center for Clinical Informatics offer a number of research data management options in support of clinical research, including: REDCap, STRIDE Secure Workbenches,custom databases, and MedWiki-Secure. We strongly encourage researchers to consult with a statistician before beginning the analysis of their clinical data.
Cost and Credit
Inquiries and consultations on new research projects are always offered free of charge to Stanford community researchers. In general, we will provide up to four hours of labor working on a project before we need to discus setting up a payment plan. When additional payment is required, you will be responsible for covering the employees salary on an hourly basis for the time spent working on your project.
In projects where expert Informatics expertise is required the Center may engage in a collaborative partnership leading to co-authorship on related publications. In such a collaboration, and particularly where the work is of shared interest, we may be able to extend the duration of our no-cost services.
We ask that all research related to your consultation include appropriate citations to the resources used. Please see our citation information for details.
Thursday, November 1, 2012
Clinical Term
Clinical Trial Management System (CTMS)
Clinical Data Management System (CDMS)
Case Report Form (CRF);
Remote Data Entry (RDE);
Remote Data Capture (RDC)
Electronic Data Capture(EDC)
Clinical Data Management System (CDMS)
Case Report Form (CRF);
Remote Data Entry (RDE);
Remote Data Capture (RDC)
Electronic Data Capture(EDC)
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