Corporate Banner
Satellite Banner
Genomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

GTEx Project to Expand Functional Studies of Genomic Variation

Published: Wednesday, August 06, 2014
Last Updated: Wednesday, August 06, 2014
Bookmark and Share
Larger set of human tissues to be analyzed to contribute to a database and tissue bank that researchers can use to study how genomic variants influence gene activity.

The National Institutes of Health has awarded eight grants as part of the Genotype-Tissue Expression (GTEx) project to explore how human genes are expressed and regulated in different tissues, and the role that genomic variation plays in modulating that expression. The GTEx awards will contribute to a resource database and tissue bank that researchers can use to study how inherited genomic variants – inherited spelling changes in the DNA code – may influence gene activity and lead to disease. The grants will add data from analyses of tissue samples whose collection began in 2010, as well as expand the resource database and tissue bank.

The research groups will receive approximately $9 million in the first year, and nearly $15 million over three years pending the availability of funds. The project is funded by the NIH Common Fund, the National Institute of Mental Health (NIMH) and the National Heart, Lung, and Blood Institute (NHLBI).

“The new studies complement the current GTEx project in assessing genomic variation and gene expression,” explained Simona Volpi, Pharm.D., Ph.D., GTEx program director in the Division of Genomic Medicine at the National Human Genome Research Institute (NHGRI), which helps administer the program. “They delve deeper into what is happening in tissues on a molecular basis to explain how genomic variation affects how genes work. Ultimately, GTEx will provide an atlas of human gene expression.”

The groups plan to further characterize gene activity in tissues by analyzing several molecular phenotypes, or properties of cells – such as which genes are turned on and off, the various ways genes are regulated and the proteins that cells produce based on such regulation. To do this, scientists will examine part of the more than 30 tissue types available, which were collected through autopsies or organ and tissue transplant programs. The project will eventually include samples from about 900 deceased donors. Researchers will analyze DNA and RNA from the samples to identify and catalog genomic variants and gene expression.

For the last decade, scientists have used genome-wide association studies (GWAS) to study the role that genomic variation plays in complex diseases and traits. In GWAS, researchers compare thousands of genomic variants in individuals with a disease with those without the disease, establishing associations with particular variants and the disease being studied. But understanding what specific genomic variants do and how they influence the development of disease has been much more difficult to pinpoint.

By detailing certain features of cells and tissues, such as methylation patterns, protein levels and other characteristics, Dr. Volpi said that the new studies will “help paint a clearer picture of how genomic variation leads to particular diseases.” In methylation, one way that cells control gene expression is by adding chemicals, such as methyl groups.

“A scientist who is studying asthma or kidney cancer might be particularly interested in studying how genomic variants influence gene expression in the lungs or the kidneys, and the GTEx resource will provide this opportunity,” said Jeffery Struewing, M.D., GTEx program director in the NHGRI Division of Genomic Medicine.

The following research groups have been awarded grants (pending available funds)

University of Washington, Seattle, $1.85 million
Principal Investigator: Joshua Michael Akey, Ph.D.

Somatic mutations – genetic mutations that are not inherited, but instead occur randomly or are caused by environmental factors – can play important roles in many diseases and conditions, especially in cancer. But how these mutations contribute to genetic variability and disease susceptibility is not well understood. 

To find out, Dr. Akey and his coworkers plan to sequence the protein-coding genome regions of more than 15 tissue types and look for variations in DNA sequences and structures. Proteins are the working elements within a cell. They are vital for cellular growth, differentiation and repair. They catalyze chemical reactions and provide defense against disease, among myriad other housekeeping functions. The researchers will develop a comprehensive catalog of somatic mutations, which they hope will aid in identifying and interpreting mutations that cause human disease.

Johns Hopkins University, Baltimore, $3.24 million (including co-funding from NIMH)
Principal Investigator: Andrew Feinberg, M.D., M.P.H.

The investigators plan to analyze DNA methylation patterns across the entire genome, though their main focus is on brain regions that are important in schizophrenia, depression and addiction. Methylation is a process by which cells add chemicals – methyl groups – to genes to control their expression. The work will help researchers understand the relationship between DNA methylation, gene expression and gene sequences in human health and disease.

Massachusetts Institute of Technology, Cambridge, $1.25 million
Principal Investigator: Manolis Kellis, Ph.D. 

Most genetic variants linked to disease don’t code for proteins, but instead have subtle gene regulatory roles, such as altering gene activity levels, or affecting the chemical modifications — epigenomic marks — made to DNA that influence which genes are active in which cells. To better understand the effects of these regulatory variants, researchers plan to characterize the epigenomic effects of genetic variation in nine peripheral tissues with roles in diabetes, heart disease, and cancer. The research will help explain how genetic variation leads to changes in gene expression across tissues, and ultimately how these differences affect a person’s predisposition to disease.

Stanford University, Palo Alto, California, $1.22 million
Principal Investigator: Jin Billy Li, Ph.D.

To gauge the influence of genetic variation on gene regulation and expression in different cells and tissues, researchers can attempt to correlate gene expression with the degree to which a gene is turned on or off. One way to do this is to measure allele-specific expression (ASE). Genes come in pairs, or alleles, and sometimes one allele is expressed to a different degree than the other gene allele. 

Dr. Li, co-investigator Stephen Montgomery, Ph.D., and their colleagues plan to examine ASE in different tissue types to try to better understand the interaction between genetic variants that regulate gene expression and potential disease-causing variants.

University of Washington, Seattle, $2.24 million
Principal Investigator: John Stamatoyannopoulos, Ph.D.

Dr. Stamatoyannopoulos and his group plan to study genetic variants in non-protein coding regions of the genome, where most variants reside. They hope to explore how genetic variation in different types of tissues affects regulatory regions in the genome that control gene activity patterns. To do this, they will use a technique called DNase I-sequencing to examine certain areas in the genome and gauge gene regulation within tissue samples from various ethnic groups.

Stanford University, Palo Alto, California, $2.475 million (including co-funding from NHLBI)
Principal Investigators: Michael P. Snyder, Ph.D., and Hua Tang, Ph.D.

The large-scale project aims to characterize the many different ways in which proteins normally vary, across more than nine tissue types. Scientists will catalog protein variants by mass spectroscopy (a technique to identify chemicals by mass and charge), which will help them understand the genetic basis for protein variation. This will be a valuable resource for researchers to understand the genetic basis of complex traits, and ultimately, in predicting individual disease susceptibility. These research results may also help clinicians design individual prevention and treatment strategies.

University of Chicago, $1 million
Principal Investigator: Barbara Stranger, Ph.D.

Investigators plan to characterize the proteome — the entire set of proteins produced by a genome — in several tissue types to determine the genetic basis of variation in protein expression. They will measure the levels of certain types of proteins that are responsible for sending signals in cells, and another group of proteins that act as switches, affecting which genes are turned on. The researchers will then look for variation associated with differences in protein levels to see if variants associated with protein expression have been previously linked to complex diseases. This may enable them to pinpoint specific proteins or protein networks that may underlie such disease.

University of Chicago, $1.375 million
Principal Investigator: Brandon L. Pierce, Ph.D.

Telomeres are DNA caps at the end of chromosomes that are thought to protect cells from aging. The length of telomeres plays an important role in cell division, growth and genome stability, and evidence suggests that telomere shortening over a lifetime may be involved in disease, including heart disease, dementia and cancer. Interestingly, new research suggests that two common gene variants that lead to longer telomeres may actually increase the risk for deadly brain cancers called gliomas. To better determine the role of telomere length in disease development, Dr. Pierce and his colleagues will ask if telomere length in blood reflects its length in tissues usually associated with cancer, and whether telomere length in specific tissues indicates DNA damage and chromosomes that are unstable. They also will try to gauge the role of variants in genes known to affect telomere length and cancer risk in specific tissues.


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,200+ scientific posters on ePosters
  • More than 4,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Significant Expansion Of Data Available In The Genomic Data Commons
Cancer genomic profile information from 18,000 adult cancer patients will be added to the database.
Wednesday, June 29, 2016
Predicting Effective Drug Combinations For TB
Researchers analyzed gene regulatory networks to explain the effectiveness of an experimental drug combination against drug-resistant tuberculosis bacteria.
Wednesday, June 15, 2016
Genomic Data Commons Launched
Part of the National Cancer Moonshot, the GDC will centralize and standardize accessible data.
Tuesday, June 07, 2016
Drug Might Help Treat Sepsis
A DNA enzyme called Top1 plays a key role in turning on genes that cause inflammation in mouse and human cells in response to pathogens. A drug blocking this enzyme rescued mice from lethal inflammatory responses, suggesting a potential treatment for sepsis.
Wednesday, May 18, 2016
NIH Funds New Studies on Ethical, Legal and Social Impact of Genomic Information
Four new grants from the National Institutes of Health will support research on the ethical, legal and social questions raised by advances in genomics research and the increasing availability of genomic information.
Wednesday, May 18, 2016
Researchers Identify Genetic Links to Educational Attainment
Researchers at NIH have suggested that the large genetics analyses may be able to help discover biological pathways as well.
Thursday, May 12, 2016
Submissions Open for the Cancer Moonshot Program
NCI opens online platform to submit ideas about research for Cancer Moonshot.
Tuesday, April 19, 2016
NIH Sequences Genome of a Fungus
Researchers at the Institute have sequenced genome of human, mouse and rat Pneumocystis that cause life-threatening Pneumonia in immunosuppressed hosts.
Tuesday, April 12, 2016
Decoding Ties Between Vascular Disease, Alzheimer’s
NIH consortium uses big data, team science to uncover complex interplay of factors.
Tuesday, March 15, 2016
Researchers Find Link Between Death of Tumor-Support Cells and Cancer Metastasis
Researchers at NIH have found that the lifespan of supportive cells in a tumor may control the spread of cancer.
Tuesday, February 23, 2016
Tick Genome Reveals Secrets of a Successful Bloodsucker
NIH-funded study could lead to new tick control methods.
Tuesday, February 09, 2016
Genomic Signature Shared by Five Types of Cancer
National Institutes of Health researchers have identified a striking signature in tumor DNA that occurs in five different types of cancer.
Monday, February 08, 2016
Cancer Drug Target Visualized at Atomic Resolution
New study using cryo-electron microscopy shows how potential drugs could inhibit cancer.
Thursday, February 04, 2016
Genome-Wide Study Yields Markers of Lithium Response
An international consortium of scientists has identified a stretch of chromosome that is associated with responsiveness to the mood-stabilizing medication lithium among patients with bipolar disorder.
Monday, February 01, 2016
Schizophrenia’s Strongest Known Genetic Risk Deconstructed
Suspect gene may trigger runaway synaptic pruning during adolescence – NIH-funded study.
Thursday, January 28, 2016
Scientific News
New CAR T Cell Therapy Using Double Target Aimed at Solid Tumors
Researchers at Penn University have described how antibody, carbohydrate combination could apply to range of cancer types.
Erasing Unpleasant Memories with a Genetic Switch
Researchers from KU Leuven and the Leibniz Institute for Neurobiology have managed to erase unpleasant memories in mice using a 'genetic switch'.
New Method Detects Telomere Length for Research into Cancer, Aging
UT Southwestern Medical Center cell biologists have identified a new method for determining the length of telomeres, the endcaps of chromosomes, which can influence cancer progression and aging.
Assessing the Effectiveness of Genome-Editing Technologies
Researchers have developed a cost-effective and rapid method for assessing edits generated by CRISPR-Cas9 and other genome-editing technologies.
New Cancer Drug Target Found in Dual-Function Protein
Findings from a study from TSRI have shown that targeting a protein called GlyRS might help to halt cancer growth.
Alzheimer's Genetics Point To New Research Direction
A University of Adelaide analysis of genetic mutations which cause early-onset Alzheimer’s disease suggests a new focus for research into the causes of the disease.
Contagious Cancers Are Spreading in Shellfish
Direct transmission of cancer among some marine animals may be more common than once thought, suggests a new study published in Nature by researchers at Columbia University Medical Center (CUMC).
Contagious Cancers Are Spreading in Shellfish
Direct transmission of cancer among some marine animals may be more common than once thought, suggests a new study published in Nature by researchers at Columbia University Medical Center (CUMC).
Fix for 3-Billion-Year-Old Genetic Error
Researchers at The University of Texas at Austin have developed a fix that allows RNA to accurately proofread for the first time.
Higher Frequency of Huntington's Disease Mutations Discovered
University of Aberdeen study shows that the gene change that causes Huntington's disease is much more common than previously thought.
Skyscraper Banner

SELECTBIO Market Reports
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,200+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!