# Functional Annotation of Genomes via Phenotypic Convergence

> **NIH NIH R01** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2021 · $383,638

## Abstract

Project Summary
Of the multiple classes of functional elements encoded in the genome, non-coding RNA genes and
regulatory elements are some of the least functionally characterized in terms of their specific
contributions to the whole organism. While great strides have been made in identifying these elements
at the biochemical level, there is still much work to be done. Parsing them into specific functions will
greatly enable the biomedical community to use them to accurately diagnose genetic lesions and to
treat human disease. This project develops and applies novel computational tools to assign specific
biological functions to genes and regulatory elements based on their patterns of evolution among more
than 60 mammalian species. The tools will also be applicable to other model taxonomic groups with
sequenced genomes, such as insects, nematodes, plants, and fungi. The resulting functional
assignments will be invaluable to focus and prioritize experimental efforts and will reveal the pathogenic
effects of genetic mutations in patients. The project specifically develops and distributes programs to
analyze organismal traits (phenotypes) that show variation over evolutionary time. By exploiting their
variation within a large number of species, these programs identify those specific genetic elements
whose rates of evolution are associated with the trait. The first aim provides computational tools and
algorithms to study continuous trait variables, and applies them to identify genes accommodating long
lifespan in mammals. The second aim delivers a computational toolset to determine the functions of
regulatory regions and non-coding RNA genes, with specific applications to eye and ear development.
The resulting set of enhancers and promoters will be highly valuable for the identification of important
mutations in non-coding sequences of hearing- and vision-compromised patients. The final aim
distributes these programs to the public as code and through a user-friendly web-based interface. Any
biomedical researcher will be able to upload their trait/phenotype of interest across mammalian species
and rapidly retrieve genes and regulatory regions associated with their trait along with vital statistical
measures and tools for downstream analysis and visualization. To provide access to human and model
organism genes, the user will have access to pre-computed genome-wide datasets in mammals,
insects, nematodes, and fungi. The culmination of this research program will enable the rapid
identification of genes and regulatory elements underlying countless morphological and physiological
traits, thereby propelling experimental and medical genetics research with the power of evolutionary
biology.

## Key facts

- **NIH application ID:** 10170410
- **Project number:** 5R01HG009299-05
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** Maria D Chikina
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $383,638
- **Award type:** 5
- **Project period:** 2017-05-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10170410

## Citation

> US National Institutes of Health, RePORTER application 10170410, Functional Annotation of Genomes via Phenotypic Convergence (5R01HG009299-05). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10170410. Licensed CC0.

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