# An Integrative Bioinformatics Platform with Application in Single Cancer Cells

> **NIH NIH R01** · UNIVERSITY OF MICHIGAN AT ANN ARBOR · 2020 · $368,125

## Abstract

Project Summary
Human cancers are highly heterogeneous. However, due to the limit of technologies, the intercellular
heterogeneity was not detectable genome-wide at single-cell level until recently. New technologies such as
single-cell RNA-Seq and exome-Seq have revealed new insights and more profound complexity than what was
previously thought. In collaboration with Dr. Weissman's group in the Genetics Department at Yale University,
it is now feasible to perform multiple integrative assays from the same single tumor cell. However, rigorous
computational methods are still lagging behind, in order to solve the computational challenge and determine
true heterogeneity rather than noise. Here we propose a user-friendly bioinformatics platform that is optimized
to integrative multiple types of single-cell NGS data, in particular, transcriptome, exome and CpG methylome
data that are all obtained from the same cell. Specifically, in this study we will first construct and validate in
parallel three new NGS bioinformatics pipelines to enable single-cell based RNA-Seq, exome- Seq, and CpG
methylome data. We will then develop and validate an integration pipeline to analyze multiple types of high-
throughput data, exemplified by the RNA-Seq, exome-Seq and CpG methylome single-cell data. To test the
software suite, we will first obtain data sets from erythroleukemia cell line K562. We will then utilize this
bioinformatics suite to investigate heterogeneity in Myeloid Leukemia patient samples provided by
hematologist Dr. Stephanie Halene at Yale Stem Cell Center. Beyond deciphering tumor heterogeneity, this
user-friendly bioinformatics platform is expected to be used widely by the single-cell sequencing community.

## Key facts

- **NIH application ID:** 10004166
- **Project number:** 5R01LM012373-06
- **Recipient organization:** UNIVERSITY OF MICHIGAN AT ANN ARBOR
- **Principal Investigator:** Lana X Garmire
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $368,125
- **Award type:** 5
- **Project period:** 2016-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10004166

## Citation

> US National Institutes of Health, RePORTER application 10004166, An Integrative Bioinformatics Platform with Application in Single Cancer Cells (5R01LM012373-06). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10004166. Licensed CC0.

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