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Novel Nucleic Acid Sequencing Technology Development (R43/R44 Clinical Trial Not Allowed)


  1. This Funding Opportunity Announcement (FOA) solicits R43/R44 grant applications to develop novel technologies that compared to commercial systems will enable no less than one order of magnitude improvement in DNA sequencing, and practical methods for direct RNA sequencing. Advances in genomics and more broadly in biomedical research have been greatly facilitated by significant and sustained DNA sequencing throughput increases and cost decreases. The goal now is to improve the quality and efficiency of DNA sequencing and enable direct RNA sequencing (e.g., longer read lengths, faster turn-around time, greater accuracy, and higher-throughput etc.) at reasonable costs with the anticipation that significant advances in any of these and related areas would make significant contributions to the mission of NHGRI and the field of genomics, including to many of NHGRI’s other technology development goals.


    The ability to rapidly sequence large numbers of complete genomes and transcriptomes coupled with the free dissemination of sequence data have dramatically changed the nature of biological and biomedical research. DNA and direct RNA sequence in combination with other genomic data have the potential to lead to remarkable improvements in many facets of human life and society, including the understanding, diagnosis, treatment and prevention of disease; advances in agriculture, environmental science and remediation; and our understanding of evolution and ecological systems.

    The ability to sequence many genomes and transcriptomes has been made possible by the enormous reduction of the cost of sequencing in the past three decades, from tens of dollars per base in the 1980s to a small fraction of a cent per base today. Technology advances, and in particular the development of a new generation of sequencing systems, have enabled the launch of many projects that are producing stunning insights into biology and disease. Nevertheless, the cost to completely sequence very large numbers of nearly completely phased mammalian-size genomes remains very high, and we remain far from achieving the low costs and high quality needed to fully enable the use of comprehensive and extensive genomic and transcriptomic sequence information in individual health care.

    One of the major contributions by NHGRI has been in the genomic technology domain. Those efforts have been so transformative that it is hard to remember genomics without, for example, a reference human genome, inexpensive short-read sequencing, efficient bacterial artificial chromosome methods, microarrays, defined common human haplotypes, single molecule sequencing, and many other significant technical advances. Bright prospects for future success motivate investing in genomic technology development, specifically for novel nucleic acid sequencing methodologies.


    NHGRI seeks to fund commercial research efforts in novel chemistries, physical approaches and instrumentation for DNA and direct RNA sequencing. New methodologies and substantial advances beyond existing approaches are sought that would, if successful, significantly propel forward the field of genomics.  Applicants may propose work on DNA or direct RNA sequencing, or both, in a single application.

    The FOA deliberately does not specify goals for cost, quality, throughput or read lengths since achievable endpoints are likely to improve over the life of the opportunity, and applicants are encouraged to optimize and balance these key attributes for the technology approach proposed. It is expected that applicants will develop scientific and practical definitions of optimal cost, quality and read lengths relative to enabling significant genomics opportunities. Priority will be given to applications that propose improvements of an order of magnitude (at the minimum), based on state of the art at the time the application is submitted. Such improvements may be achieved by focusing on one critical factor, or a combination of important ones.

    For DNA sequencing, novel methods that generate large numbers of long reads of high quality with a low cost are sought. New physical or chemical detection methods for sequencing are especially encouraged along with substantive (no less than an order of magnitude) improvement to current high-throughput DNA sequencing technologies. Those methods that yield novel sequence-based insights or that solve existing limitations in the field (e.g., de novo assembly of phased human genomes, direct determination of multiple and specific base modifications, complete and quantitative sequencing of all the DNA in a sample, essentially complete genomes of single cells, utilize very small quantities of starting material down to a single cell, long reads of at least 150Kb to a megabase or more, etc.) are of especially high interest.

    For RNA sequencing, the need is for quantitative and high-throughput direct sequencing of entire transcripts from the transcriptome. Applicants are expected to develop novel methods for quantitatively assessing the sequence of full length RNA molecules without a cDNA intermediate.  Enabling new approaches to RNA analysis is a key goal of direct RNA sequencing (e.g., exhaustive sequencing of every RNA molecule in a sample or precise quantification across the entire very high dynamic range of RNA transcripts, direct determination of specific and multiple base modifications, determining RNA secondary structural elements while sequencing, cost-effective and statistically-robust single cell transcriptomics, etc.).

    High-risk and high-reward proposed research may plan to develop complete systems or novel key components for nucleic acid sequencing. Very novel physical or chemical approaches to sequencing are solicited along with novel enzymatic methodologies. The technology developed can either develop an entirely new way of sequencing or significantly improve existing sequencing methodology.

    See Section VIII. Other Information for award authorities and regulations.

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