Official websites use .gov

A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS

A lock ( 🔒 ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Need Help

Statistical Methods for 3-Dimensional Spatial Transcriptomics: Design, Imputation, and Analysis

Award Number: R01HG014774
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/01/2026
PERIOD OF PERFORMANCE END DATE: 05/31/2030

Group Awards By:

View Award Description

Statistical Methods for 3-Dimensional Spatial Transcriptomics: Design, Imputation, and Analysis - PROJECT SUMMARY Moving from 2-dimensional (2D) to 3D spatial profiling represents a transformative milestone in biological research, offering unprecedented opportunities to enhance the understanding of tissue structure and pathogenesis. It also holds the promise to improve the diagnosis and treatment for various diseases, such as cancer and neurodegenerative diseases. However, the development of analytical infrastructures and computational tools has fallen seriously behind the technology advances, which present substantial analysis barriers that hinder biological investigations using 3D spatial transcriptomics (ST). The primary objective of this proposal is to address some of the most pressing analytical challenges facing designing and analyzing 3D ST data, including lack of robust strategy to guide the experimental design, lack of tools to recover the ST profiles for cells that are not covered by profiling technology within the 3D structure, and lack of methods to identify structures, microenvironments as well as cellular trajectory. The project is structured around three complementary research directions to overcome the hurdles. 1) We propose a robust statistical method to help identify the optimal number of 2D slides and locations to guide the experimental design for 3D ST profiling. This model works with preliminary or existing 2D ST data, providing cost-effective and statistically optimal designs based on bivariate P-spline based methods. 2) We aim to develop a statistical inference method that can accurately impute the unmeasured 3D spots together with a quantification of estimation uncertainty. This approach can effectively improve the sample size and data quality for downstream visualization and analysis. 3) We will create a 3D-aware dimension-reduction algorithm to detect tissue structure and cellular trajectories within the 3D landscape. The proposed methods will be applied to 3D ST data from gastric cancer patients at The University of Texas MD Anderson Cancer Center, as well as lymph node samples from published studies. Although initially motivated by cancer and immunology research, these statistical methods are broadly applicable for 3D ST profiling design and data analysis in other disease contexts and developmental biology studies. Once validated, all software packages developed in this project will be made available to the wider research community. Successful completion of these aims will dramatically enhance the quality and analytical power of 3D ST studies, facilitating the application of these cutting-edge technologies to translational and clinical research.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $2,759,668 )
2026	2026	THE UNIVERISTY OF TEXAS M.D. ANDERSON CANCER CENTER	1515 HOLCOMBE BLVD	HOUSTON	TX	77030	HARRIS	USA	Human Genome Research	000	1	7/6/2026	NEW	$2,759,668
														Subtotal = $2,759,668

Grand Total All Awards = $2,759,668

Top

All Categories

About

Search

Reports

Data Submission

Award Information

Statistical Methods for 3-Dimensional Spatial Transcriptomics: Design, Imputation, and Analysis

Award Number: R01HG014774

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 07/01/2026

PERIOD OF PERFORMANCE END DATE: 05/31/2030

Federal Websites

Department of Health & Human Services

HHS Operating Divisions

HHS Staff Divisions

Download A Document Viewer