Research and development on many projects has continued in the division of molecular pathology.
Research and development on many projects has continued in the division of molecular pathology.
Research and development on many projects has continued in the division of molecular pathology. New clinical tests have been validated and implemented in the area of infectious disease, and development of additional tests has begun-such as the division’s rapid response to develop, optimize and implement a molecular assay for the H1N1 influenza outbreak of 2009. This effort was an important tool in the hospital’s triage of the sickest patients during the pandemic’s most crucial time. With the continued vital support from the Grant-A-Starr Foundation, progress on multiple projects was achieved including the following:
The project team will focus on shifting the scope of the project to DNA sequencing methodologies, including optimization of DNA/RNA extraction and sequencing methods for a variety of specimen types important in the diagnosis of sepsis, gastroenteritis and meningitis. At least three candidate pathogens of new human microbes/viruses will be identified, and approval of human studies protocols from the institutional review board will be obtained.
Discovery and development efforts will continue with the sequencing of a minimum of 100 clinical samples. Sequencing data analysis tools and algorithms will be developed, and a large scale hospital-based microbe/virus/pathogen sequence database will be established. Development will include the addition of specimen types vital to pneumonia and early-detection sepsis as well as the introduction of droplet PCR to boost throughput potential. By the end of Year 2, roughly 625 megabases of sequencing data (1 megabase equals 1 million bases) will have been produced, testing from a minimum of five specimen types will have been optimized, and the initial work will have been submitted for presentation at national scientific meetings.
Delivery of new diagnostic tests will begin in Year 3 with the introduction of the first next generation sequencing test in the inpatient pediatric setting. New tests will continue to be developed, and tissue samples will be added to the growing specimen optimization list. By the end of Year 3, the project will have produced 2.5 gigabases of sequencing data (1 gigabase equals 1 billion bases) from over 200 clinical samples, at least 1,000 microbe sequences will have been added to the sequence database, and the first journal article will be submitted for potential publication.
Implementation of new diagnostic tests continues through Year 4, with new tests continuing to be added to the development pipeline based on the discoveries made in the prior years. New specimen types for optimization will also be added at this time. By the end of Year 4, a total of 5 gigabases of sequencing data (1 gigabase equals 1 billion bases) will have been produced from over 400 clinical samples, and at least 1,500 microbe sequences will have been added to the sequence database. It is expected that a minimum of four new diagnostic sequencing applications will have been validated for use at Texas Children’s with at least six additional tests in development and 20 new candidate pathogens/microbes/viruses in the discovery/development phase.
The final year of the timeline includes continued progress in all three areas. By the end of Year 5, over 10 gigabases of sequencing data (1 gigabase equals 1 billion bases) will have been produced, with at least 2,000 sequenced microbes from 600 clinical samples added to sequence database. At least 30 new candidate pathogens/microbes/viruses will have been identified, and at least 10 new sequencing tests will be in development and moving towards implementation.