Description
This acquisition was conducted under the authority of 41 U.S.C. 1901 Simplified Acquisition Procedures, the statutory authority of 41 U.S.C. 3304 Use of noncompetitive procedures and in accordance with FAR subpart 13.501. This is a follow-on requirement being performed by the University of California - Santa Cruz (UCSC) and includes collaboration. This is a continuation of services to support an ongoing requirement. Background The National Institutes of Health (NIH) Center for Alzheimer’s and Related Dementias (CARD) is a collaborative initiative of the National Institute on Aging (NIA) and National Institute of Neurological Disorders and Stroke (NINDS) that supports basic, translational, and clinical research on Alzheimer’s disease and related dementias. CARD’s central mission is to initiate, stimulate, accelerate, and support research that will lead to the development of improved treatments and preventions for these diseases. Technology has demonstrated the power of genomics to unravel the genetic etiology of complex neurological diseases. These efforts include short-read sequencing approaches which are highly accurate for small DNA sequences, and long-read sequencing which allows for the study of complete genomes without fragmentation. The short-read sequencing technologies are not optimized to identify large structural changes in the human genome that may substantially contribute to risk for neurodegenerative diseases. In particular, long-read sequencing can detect the methylation status of sequenced DNA and identify single nucleotide variations in genomic regions that are challenging to sequence with short-read sequencing. Therefore, gaining a full understanding of the genetic architecture of the dementia genome with long-read sequencing will drive forward gene discovery, leading to greater insight into disease and pathway mechanisms and new potential therapeutic targets. CARD generated long-read sequencing data from roughly 4000 patients with Alzheimer’s disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and healthy subjects. The resulting datasets were used to identify DNA methylation changes and single nucleotide variants, both of which have been linked to normal aging and neurodegenerative diseases. The resulting data is being used to evaluate how the epigenetic and genomic landscape in challenging regions contribute to the development of neurodegenerative diseases. Purpose and Objectives NIH/CARD will continue to generate long-read sequencing data from patients with AD, FTD, LBD, and healthy subjects. This project will produce terabytes of data, which the Contractor will use pipelines for storing, analyzing, and harmonizing these large data sets on cloud-based computing platforms. The data pipeline shall include Oxford Nanopore PromethION sequencer software. The Contractor shall then use these datasets to identify DNA methylation changes and single nucleotide variants, both of which have been linked to normal aging and neurodegenerative diseases. The government will then use the dataprovided by the Contractor to evaluate how the epigenetic and genomic landscape in challenging regions contribute to the development of neurodegenerative diseases. 1) In the performance of the previous contract, the contractor developed algorithms to determine and phase single nucleotide variants and small insertions and deletions (indels) from long-read nanopore sequencing data. The results have been published. In the continuation of the project, the contractor shall refine this pipeline into a package that is easily usable by the CARD consortium, tune the algorithms to work with specifics of the data being generated by the consortium (for example, by training new models to account for changes in the base caller and/or chemistry of the sequencing), and assist in its running to generate results for the consortium. 2) In the performance of the previous contract, the contractor helped develop a novel algorithm for detecting structural variations in long-read sequencing data, creating the hap-dup pipeline (https://github.com/KolmogorovLab) specifically for CARD. This pipeline, novelly, is based on a de novo assembly method developed by the contractor, that allows it to characterize regions that are more structurally divergent from a reference genome. In the continuation of the project, the contractor shall further develop this pipeline and integrate it with the pipeline for determining small variants detailed in (1). The proposed combined pipeline will be able to produce phased structural variants and small variants in a consistent manner. The combined pipeline shall be published as part of this work. 3) In the performance of the previous contract, the contractor helped pioneer methods for the detection of methylation from long-read sequencing data. In the continuation of the project, the contractor shall provide its expertise in helping to develop robust methods for quantifying methylation and other base modifications within the CARD data. Ultimately, this information will be integraded into the pipeline described in (1) and (2) above. As the CARD project scales up its sequencing efforts, the contractor shall assist in the analysis of the long-read sequence results produced by the pipelines (described in 1-3) applied to CARD data. The contractor shall help in the interpretation by CARD researchers, helping to associate them to health and neurodegenerative phenotypes. CONTRACTING WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION As a result of the previous contract, and as the study project scales up, CARD needs supplemental support to continue the analysis of the long-read sequence results produced by the pipelines (described in 1-3 above) applied to CARD data. The contractor shall support in the interpretation by CARD researchers, helping to associate them to health and neurodegenerative phenotypes. In accordance with the terms of previous contract, the University of California Santa Cruz owns all of the algorithms resulting from the contract, including algorithms uploaded to GitHub. The NIH/CARD have unlimited rights to use the algorithms developed by the Contractor, including algorithms uploaded to GitHub. As in the previous contract, the contractor will retain the right to publish articles of data produced as a result of the requirements of the continued work. Other Important Considerations The contractor will continue to use algorithms earlier developed for this study, to analyze single nucleotide variants and methylation profiles in long-read sequencing data, as well as pipelines to harmonize and store long-read sequencing data shared between NIH and the Contractor on cloud-based computing platforms. The Contractor will upload all finalized algorithms for processing single nucleotide variants and methylation profiles to a GitHub repository maintained by CARD. The Contractor will then perform analyses for single nucleotide variant detection and methylation calling and upload these files to a shared cloud-based platform. The Contractor will also conduct laboratory work to generate long read sequencing data using Oxford Nanopore Technology. This work includes establishing and optimizing protocols for DNA isolation from blood and brain tissue, creating libraries for DNA sequencing, and operating the PromethION sequencer. The Contractor will work with and advise CARD on the finalized documents on cloud storage and GitHub. The contractor will assist in writing and publishing articles of data produced as a result of the performance of the requirements of the Statement of Work.