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Archive for the ‘Bioinformatics’ Category

When Too Many Lab Tests are Bad for Your Health

Wednesday, April 12th, 2017

Running a Test by Myfuture.com is licensed under CC BY-ND 2.0.

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Imagine you visit your doctor and get some shocking news. You have a rare disease with no cure or treatment and only have a few months left to live. After you come to terms with the news, you start making arrangements, perhaps work on some of those things on your bucket list. Then you get a call from your doctor; there’s been a mistake, you’ve been misdiagnosed, and now have a long life to look forward to.

While this may sound like the plot to a feel-good movie or a hypothetical philosophical debate, the issue of over diagnosis is a very real one. Over diagnosis is a side effect of screening tests, which are given to people who seem healthy to find unnoticed problems. While these screening tests can help catch chronic health conditions early, in some cases the results can be harmful.

Screening tests are not 100% accurate, so while they are helpful for finding hidden disease, they can also give inaccurate results. The situation described above might be the consequence of getting a false positive for a screening test, when the test results incorrectly indicate a disease. Also possible is a false negative, which means you’re told you don’t have the disease when you do, perhaps causing you to ignore symptoms that appear later on.

According to Dr. Barnett S. Kramer, a cancer prevention expert at NIH, “I wouldn’t say that all people should just simply get screening tests. Patients should be aware of both the potential benefits and the harms when they’re choosing what screening test to have and how often.”

When deciding whether to get a screening test, a number of factors should be considered, like your age, family health history, or lifestyle exposures like smoking. You should also consult with your healthcare provider to determine what screening tests are right for you and how regularly you should have them.

To find out more, you’ll soon be able to watch the archived recording of our recent webinar SCR CONNECTions – Over Diagnosis: Why Too Many Lab Tests are Bad for Your Health starting April 17 on our website.

Source: Adapted from NIH News in Health Article “To Screen or Not to Screen? The Benefits and Harms of Screening Tests,” March 2017 <https://newsinhealth.nih.gov/issue/Mar2017/feature2>

National Library of Medicine Announces MedPix®, Free Online Medical Image Database

Thursday, February 18th, 2016

Adapted from:  National Library of Medicine’s News and Events dated 2/05/16

The National Library of Medicine is pleased to announce the launch of MedPix®, a free online medical image database originally developed by the Departments of Radiology and Biomedical Informatics at the Uniformed Services University, Bethesda, Maryland, USA. The URL is https://medpix.nlm.nih.gov/.

The foundation for MedPix was a radiology study tool that was originally developed by Dr. J.G. Smirniotopoulos in 1984. In the early 1990s, as radiology was moving from film to digital imaging, there was simultaneously a merger of the diagnostic imaging residency programs of the two premier military hospitals: Walter Reed Army Medical Center and the National Naval Medical Center. In the summer of 1999, a Web-based digital teaching file based on the radiology study tool was built at USUHS to allow the two military training programs to share teaching file cases, a training requirement. Soon, other military hospitals and several civilian institutions joined MedPix. Over the past 16 years, MedPix has amassed an impressive collection of over 53,000 images from over 13,000 cases.

The MedPix collection categorizes and classifies the image and patient data for each of several subsets of image database applications (e.g. radiology, pathology, ophthalmology, etc.). The content material is both high-quality and high-yield and includes both common and rare conditions. Most cases have a proven diagnosis (pathology, clinical follow-up). The teaching file cases are peer-reviewed by an Editorial Panel.

As a public education service, the NLM and MedPix provide the storage service, indexing, and Web server hosting. Individuals as well as institutions may participate. Contributed content may be copyrighted by the original author/contributor. No additional software required—your Internet browser is all you need!

The primary target audience includes resident and practicing physicians, medical students, nurses and graduate nursing students and other post-graduate trainees. The material is organized by disease category, disease location (organ system), and by patient profiles.

At this time, the new MedPix website is up. Existing users can login, but there is no access to CME credits yet, no new registration, no submitting a case and no search.

NOTE: MedPix provides a quick summary of medical information with images. It is not intended to be encyclopedic.

WARNING: This is not a substitute for medical advice, and the reader is responsible for confirming the accuracy of this information before beginning or changing any therapy or treatment.

For more information see:  MedPix Home Page https://medpix.nlm.nih.gov/  – NLM’s Medical Image Database

Since its founding in 1836, the National Library of Medicine https://www.nlm.nih.gov has played a pivotal role in translating biomedical research into practice and is a leader in information innovation. NLM is the world’s largest medical library, and millions of scientists, health professionals and the public around the world use NLM services every day.

 

NIH Genome Sequencing Program targets the Genomic Bases of common, Rare disease

Wednesday, January 27th, 2016

The National Institutes of Health will fund a set of genome sequencing and analysis centers whose research will focus on understanding the genomic bases of common and rare human diseases. The National Human Genome Research Institute (NHGRI), part of NIH, January 14, 2016 launched the Centers for Common Disease Genomics (CCDG), which will use genome sequencing to explore the genomic contributions to common diseases such as heart disease, diabetes, stroke and autism. NHGRI also announced the next phase of a complementary program, the Centers for Mendelian Genomics (CMG), which will continue investigating the genomic underpinnings of rare, typically inherited diseases, such as cystic fibrosis and muscular dystrophy. “Advances in DNA sequencing are creating tremendous new opportunities for exploring how the genome plays a role in human disease,” said NHGRI Director Eric Green, M.D., Ph.D. “Our continued focus on both rare and common diseases promises to reveal important aspects about the genomic architecture of a wide range of human disorders.”CCDG researchers plan to examine a select group of disorders in order to develop approaches for using genome sequencing to study common disease more broadly. By sequencing an expected 150,000 to 200,000 genomes of individuals with these diseases, the CCDG program aims to improve understanding of how genomic differences among people influence disease risk and to develop models for future studies of common disease.

NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The NHGRI Extramural Research Program supports grants for research and training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.

FDA Launches precisionFDA a Cloud-Based, Portal for Scientific Collaboration and Next-Generation Sequencing

Tuesday, December 22nd, 2015

Adapted from: FDA Voice Blog

The U.S. Food and Drug Administration on Tuesday December 15, 2015 has launched the beta version of precisionFDA, its a new collaborative platform designed to foster innovation and to develop the science behind a method of “reading” DNA also known as Next-Generation Sequencing (or NGS).  Next Generation Sequencing allows scientists to compile data on a person’s exact order or sequence of DNA. The precisionFDA includes more than 20 public and private sector participants including National Institutes of Health (NIH), Centers for Disease Control and Prevention, National Institute of Standards and Technology (NIST) and more. Dr. Francis Collins, NIH’s Director stated on https://precision.fda.gov/ that “PrecisionFDA, is a bold and innovative step towards advancing the regulatory science for precision medicine”.

PrecisionFDA allows users to access tools such as “Genome in the Bottle“https://www.genomeweb.com/sequencing-technology/nist-genome-bottle-release-first-reference-material-assessing-genome, a reference sample of DNA for validating genome sequences developed by NIST. These results can be compared with results of previously validated references, and shared with other users, who can track changes and obtain immediate feedback from precisionFDA users. In FDA Voice http://blogs.fda.gov/fdavoice/, Tasha A. Kass-Hout, MD, chief informatics officer at the FDA wrote, “His hope is to grow the community of platform participants and improve the usability of precisionFDA in the coming months and years by placing the code for the precisionFDA portal on the world’s largest open source software repository, GitHub”.

 

NCBI Webinar: “Accessing 1000 Genomes Project Data”

Tuesday, December 8th, 2015

Adapted from the NLM Tech Bull. 2015 Nov-Dec;(407):b9.

To automatically receive the latest news and announcements regarding major changes and updates to NCBI resources and tools please see the subscribe page.

NCBI Webinar: “Accessing 1000 Genomes Project Data” on December 17, 2015

December 17, 2015, NCBI staff will demonstrate how to access 1000 Genomes data through SRA, dbVar, SNP and BioProject, as well as through tracks on annotated human sequences in the graphical sequence viewer and Variation Viewer. Attendees will also learn how to display, search, and download individual and genotype level data through the dedicated 1000 Genomes Browser that allows searching by chromosomal position, gene names and other genome markers.

Date and Time: December 17, 2015 11:00a.m. – 12:00p.m. MT; 12:00p.m.-1:00p.m. CST
Registration URL: https://attendee.gotowebinar.com/register/5168155820927556866

After the live presentation, the Webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; you can also find information about future Webinars on this page.

BD2K Updates from NIH and NSF

Tuesday, December 1st, 2015

Big Data to Knowledge (BD2K) updates from NIH and NSF

The National Science Foundation recently posted an article on advances in big data and the management of chronic diseases.

The National Institutes of Health has released new Data Science Funding Opportunities: The new NIH Common Fund program Molecular Transducers of Physical Activity has released funding opportunities including one for a bioinformatics center. Applications are due March 18, 2016.

Article of Interest: How to hijack a Journal.

NIH Data Science Webinar Presentation: Data-level Metrics

Monday, October 26th, 2015

LECTURE TITLE: Data-Level Metrics
DATE: Wednesday, October 28, 2015, 8:00-10:00am Mountain, 9:00-11:00am Central
SPEAKER: Martin Fenner

Martin Fenner has been the DataCite Technical Director since August 2015. From 2012 to 2015 he was the technical lead for the PLOS Article-Level Metrics project. Dr. Fenner has a medical degree from the Free University of Berlin and is a Board-certified medical oncologist.

ACTIVITY DESCRIPTION:

The Office of the Associate Director for Data Science (ADDS) is launching a new “Frontiers in Science” webinar series.  NCI Center for Biomedical Informatics and Information Technology (CBIIT) is pleased to co-host one of the first sessions as part of our bi-weekly Speaker Series.

The DataONE repository network, California Digital Library, and Public Library of Science (PLOS) from October 2014 – October 2015, worked on an NSF-funded project to explore metrics – including citations, downloads and social media –  for about 150,000 datasets. This presentation will summarize the major hurdles to complete this work, the most important findings, and some ideas for moving forward, including implementation as a production service.

REASONABLE ACCOMMODATION:
Individuals with disabilities who need Sign Language Interpreters and/or reasonable accommodation to participate in this event should contact Sonynka Ngosso, at 301-402-9816. Requests should be made at least 5 business days in advance of the event.

Please join us for this exciting talk!

Webinar Details:

Online link: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e4de82de30d86900b1a7b4b4e490040b9
Password: $Peakerseries15

Dial-In for Audio Only: 1-855-244-8681
Event number: 733 789 875

On-site:  Shady Grove, room 2W910 – 912

NLM Informatics Lecture Series: Use of Clinical Big Data to Inform Precision Medicine

Thursday, October 22nd, 2015

Shared from NIH:

The next session of the National Library of Medicine Informatics Lecture Series will be held on November 4, 12:00-1:00pm Mountain, 1:00-2:00pm Central.  This talk will be broadcast live and archived at http://videocast.nih.gov/. The feature presentation is Use of Clinical Big Data to Inform Precision Medicine with speaker Joshua Denny, MD, Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center.

For more details and to add the event to your calendar, visit http://videocast.nih.gov/summary.asp?live=17452&bhcp=1.

Abstract: Precision medicine offers the promise of improved diagnosis and more effective, patient-specific therapies. Typically, clinical research studies have been pursued by enrolling a cohort of willing participants in a town or region, and obtaining information and tissue samples from them. At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort. This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes. The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS). PheWAS requires a densely-phenotyped population such as found in the EHR. Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations. They have also used PheWAS to identify characteristics within disease subtypes.

This event will be broadcast at http://videocast.nih.gov when the event is live.

Use of Clinical Big Data to Inform Precision Medicine Webinar

Sunday, October 18th, 2015

National Library of Medicine Informatics Lecture Series
Title: Use of Clinical Big Data to Inform Precision Medicine
Speaker: Joshua Denny, MD
Date: Wednesday, November 4, 2015
Time: 1:00 pm – 2:00 pm Central Time
Location: Lister Hill Center Auditorium

Abstract: Precision medicine offers the promise of improved diagnosis and more effective, patient-specific therapies.  Typically, clinical research studies have been pursued by enrolling a cohort of willing participants in a town or region, and obtaining information and tissue samples from them.  At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort.  This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes.  The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support.  The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS).  PheWAS requires a densely-phenotyped population such as found in the EHR. Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations.  They have also used PheWAS to identify characteristics within disease subtypes.

Brief Bio: Joshua Denny, MD is an Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. A primary interest of his lab has been development of the PheWAS method applied to EHRs to rapidly uncover genetic pleiotropy and highlight potential drivers of genetic associations with endophenotypes.  He helps lead efforts for local and network pharmacogenetics implementation activities.  He is part of the NIH-supported Electronic Medical Records and Genomics (eMERGE) network, Pharmacogenomics Research Network (PGRN), and Implementing Genomics in Practice (IGNITE) networks. He is past recipient of the American Medical Informatics Association New Investigator Award, Homer Warner Award, and Vanderbilt Chancellor’s Award for Research. Dr. Denny remains active in clinical care and in teaching students. He is also a member of the National Library of Medicine Biomedical Library and Informatics Review Committee.

This talk will be broadcast live and archived at http://videocast.nih.gov/

Sign Language Interpreters will be provided. Individuals with disabilities who need reasonable accommodation to participate in this lecture should contact Ebony Hughes 301-451-8038 Ebony.Hughes@nih.gov or the Federal Relay (1-800-877-8339).

Event contact:
Jane Ye, Ph.D
Division of Extramural Programs
National Library of Medicine, NIH
301-594-4882
yej@mail.nih.gov

2016 NLM Georgia Biomedical Informatics Course

Friday, October 9th, 2015

Applications are now being accepted for the 2016 National Library of Medicine Georgia Biomedical Informatics Course. One section will be held April 3-9 and another September 11-17 in Young Harris, Georgia. Applications will be accepted until December 7. All applicants will be notified by the end of January or early February of their application status. Travel, hotel, and meals of all successful applicants will be paid for by Georgia Regents University (soon to be Augusta University).

To Prepare Your Application:

  • Describe your short term goals (3-5 years) related to your reasons for wanting to take this course (approx. 300 words.)
  • Summarize your research experience with this course subject (approx. 300 words)
  • State your expectations. Describe what you hope to gain by taking this course (approx. 300 words.)
  • Submit your CV with your application.
For more information and to apply, visit http://www.gru.edu/library/greenblatt/informaticscourse/. For questions, contact Adrienne Hayes at adhayes@gru.edu.