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Methods Development for Obtaining Comprehensive Genomic Information from Human Specimens that are Easy to Collect and Store (R43/R44)

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Agency: Department of Health and Human Services
Program/Year: SBIR / 2013
Solicitation Number: PAR-13-203
Release Date: April 19, 2013
Open Date: June 28, 2013
Close Date: March 25, 2016 (closing in 570 days)
001: Funding Opportunity Description
Description:
Background

Genomic technologies have advanced dramatically over the past decade to the point where the prospect of incorporating individuals’ whole genome sequence information into their medical care is under serious discussion and careful study.  Over the next several years, genome sequencing of large numbers of individuals and application of that information in the context of specific clinical studies and ongoing medical care are expected to increase substantially the clinical utility of whole-genome data.  At the same time, the costs of acquiring and interpreting comprehensive genomic data are falling below the costs of conducting some individual genetic tests.  These new, sophisticated, and increasingly cost-effective techniques for DNA-based sequencing and analysis may make it possible to improve access to genetic screening and testing, and to expand the scope of analysis to comprehensive genomic data, thereby substantially enhancing the clinical and public health value of these tests.  This FOA uses the SBIR funding mechanism to address the critical need for sensitive and cost-effective technologies for obtaining high quality and comprehensive genomic data from easy-to-collect and handle human specimens.

 Currently, fresh or frozen whole blood is the most commonly used source from which to obtain high quality and comprehensive genomic data.  However, the use of whole blood often requires stringent collection, handling, and storage conditions.  Alternatively, while limited in specimen quantity, other minimally-invasive specimen types, such as dried blood spots, saliva, urine, or buccal swabs can be collected, handled, and stored under less costly and complicated conditions.  For example, dried blood spots are not only used for newborn screening programs, but also for monitoring drug levels, renal function, diabetes, and lipid levels.  Additionally, dried blood spots are of particular value in remote or under-resourced environments where low-temperature transportation and storage are challenging.  This FOA is intended to stimulate the development of facile, sensitive, and cost-effective technologies or methods for obtaining high quality and comprehensive genomic data from minimally-invasive human specimens that, while limited in quantities, are easy to collect and store. 

Research Scope and Objectives

 This FOA seeks to fund the development of sensitive, facile, and cost-effective technologies or methods for obtaining high quality and comprehensive nucleic acids-based genomic information from minimally-invasive small quantities of human specimen.  While applications that address some or all of the steps from the collection of specimens, through storage and nucleic acids extraction, to obtaining genomic data will be considered appropriate to this FOA, those that address all of the steps and workflows will be considered as having highest priority.  The ease of the proposed sample collection methods should be at least comparable to that of the current dried blood spot collection method.  The genomic data obtained must be at least equivalent to that which can be obtained from fresh whole blood in quality and comprehensiveness.  The developed technologies or methods should be applicable to clinical point–of-care testing in terms of speed and ease, and ultimately have the potential to be scalable to high throughput settings, while maintaining cost effectiveness.    

Program priority will be given to applications that propose development of technologies or methods that are 1) suitable for multiple levels of genomic analysis (e.g., genome sequencing, epigenomic analysis, and expression analysis); or 2) broadly applicable to research labs, clinical settings, private labs, public health labs, etc.  Although the scope of projects proposed could be applicable to any stage of the lifespan, NICHD is particularly interested in projects that address screening of newborns.  Applications that focus on a particular clinical application should address compatibility with currently-used systems for that application.  For example, compatibility with established dried blood spot workflow is highly desirable for applications that address screening of newborns.  Examples of appropriate research include, but are not limited to, the following:

1) Developing novel or improved specimen collection methods that yield higher specimen quantity, and/or maintain better integrity and longer shelf life of nucleic acids from which genomic data are obtained.

2) Developing novel or improved methods for reproducible preparation and/or amplification of nucleic acids from limited amounts of dried blood, saliva, urine, buccal swabs, or other minimally invasive human specimens in order to obtain high quality and comprehensive genomic information.  Applicants should not propose the use of samples such as formalin fixed tissues.        

3)  Developing novel or improved sequencing methods to obtain high quality and comprehensive genomic data from dried blood spots, saliva, urine, buccal swabs, or other minimally invasive human specimens collected using existing laboratory methods or commercial products.  Comprehensive genomic data in the context of this FOA refers to genome-wide data (e.g., whole genome or whole exome, whole transcriptome, whole epigenome, or combinations of these data types).

This FOA seeks methods for obtaining genome-wide data.  It does not seek applications that propose to sequence individual genes or sets of genes, that only use microarray data, or that only assay a small number of elements (e.g., PCR products).

It is anticipated that the proposed studies may use specimens obtained from children or adults with or without any diagnosed disorders.  Non-human samples might also be used to accelerate some aspects of the early development. 

Informed consent and data sharing.  This FOA anticipates funding the collection of human specimens from a small number of individuals from whom the specimens can be collected for repetition of experiments.   Applicants are encouraged to propose collection of specimens from individuals who have already been consented for other studies and can be appropriately sampled for the proposed study.  It is worth noting that, while NHGRI has historically required public data release from programs that generate large data sets that are considered to be a community resource, the genomic data generated from a limited number of individuals under this FOA will not be considered to be a community resource.  Thus, public release of those data will not be required. 

Engagement with clinicians and experts in ethical, legal and social implications (ELSI) of genomic data, and regulatory professionals.  It is anticipated that interactions with the clinical community and ELSI professionals will help address challenges to applying the developed products in clinical settings. 

Coordination and collaboration with related NIH programs.  Awardees under this SBIR program will be expected to coordinate and collaborate as needed with the NICHD funded Newborn Screening Translational Research Network (NBSTRN, www.NBSTRN.org), and other related NICHD, NHGRI, and NIH programs in order to leverage existing resources.