Notice Number: NOT-RM-13-007

Key Dates
Release Date: January 4, 2013

Issued by
National Institutes of Health (NIH)
Office of Strategic Coordination (Common Fund)

Purpose

The purpose of this Notice is to inform the scientific community of the upcoming pre-application information teleconference for RFA-RM-12-009 and to clarify and update information in RFA-RM-12-009 "Enhancing GTEx with Molecular Analyses of Stored Biospecimens (U01)."

Pre-application Information Session

NIH will hold a pre-application information teleconference for RFA-RM-12-009 on January 17, 2013 from 11am - 12 noon Eastern Standard Time. Prospective applicants who plan to participate in the information session are encouraged to send an e-mail to Dr. Simona Volpi at [email protected] in order to receive logistical information about the teleconference, including dial-in numbers. Dial-in numbers will also be posted on the Common Fund website at http://commonfund.nih.gov/GTEx. In the Subject line of the email request, please write: “eGTEx Information Session”. The email message should contain:

• Name
  
• Institution
  
• Email address
  
• Number of telephone lines that your group plans to use for the teleconference
  
• Questions to be addressed

Prospective applicants may ask additional questions during the information session. However, we encourage the submission of questions before the meeting to help allocate time for each.

Following the information session, a summary of questions and answers will be posted at http://commonfund.nih.gov/GTEx within 2 weeks. Prospective applicants with inquiries concerning this FOA who are unable to participate in the information session are encouraged to view the summary of questions and answers after they are posted.

Additional Responsiveness Information for FOA

The following assays have already been performed on GTEx samples, and applications proposing them will not be considered responsive:

1) Whole-genome single nucleotide polymorphism (SNP) and copy number variation (CNV) genotyping are performed using high-density genotyping arrays (Illumina Omni5 and HumanExome BeadKit) on the peripheral blood DNA. No other tissues have undergone DNA analysis.
2) RNA-sequencing of all tissues of sufficient quality is performed using TruSeq library preparation on the Illumina Hiseq 2000 platform. This method involves a poly-A selection to analyze mRNA. The RNA-sequencing uses a 72 base paired-end protocol to approximately 50 million mapped reads. A limited number of biospecimens have also undergone gene expression array analysis using Affymetrix Gene 1.0ST or 1.5ST platform.

In addition to demonstrating that the proposed assays are compatible with biospecimens as collected by GTEx (e.g., frozen, fixed with PAXgene Tissue, etc.), applicants are encouraged to address the degree to which the proposed assays are influenced by peri- and post-mortem factors and the steps that will be taken to better understand and mitigate them if present.

All other aspects of the FOA remain unchanged.

Inquiries

Please direct all inquiries to:

Simona Volpi, Ph.D.
Program Director, GTEx
National Human Genome Research Institute (NHGRI)
Telephone: 301-443-6453
Email: [email protected]