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2022 05 Benchmarking Transcriptomics Methods Transcript Cell

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2022 05 Benchmarking Transcriptomics Methods Transcript Cell

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Benchmarking transcriptomics integration

methods for transcript distribution


prediction and cell type deconvolution

May 27 2022, by Zhang Nannan

The benchmark process of integrating spatial transcriptomics data with scRNA-


seq data. Credit: Li Bin et al

In a study published in Nature Methods, a research team led by Prof. Qu


Kun from the University of Science and Technology of China (USTC)
of the Chinese Academy of Sciences has benchmarked 16 spatial and
single-cell transcriptomics integration methods for transcript distribution
prediction and cell type deconvolution.

The spatial location of cells in tissues and organs plays a crucial role in

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performing its specific functions. In recent years, researchers have
developed various spatial transcriptomics approaches to detect whole-
transcriptome-level data in cells while maintaining accurate spatial
orientation. However, existing spatial transcriptomics approaches have
two deficiencies. The approaches based on next-generation sequencing
could not detect single-cell deconvolution of the spot. In addition, the
approaches based on in situ hybridization and fluorescence microscopy
are limited in the total number of RNA transcripts obtained.

In view of this, researchers have developed various integration methods


to combine spatial transcriptomic data with single-cell RNA-seq (scRNA-
seq) data to predict the spatial distribution of undetected transcripts
and/or perform cell type deconvolution of spots in histological sections.
These integration methods have undoubtedly promoted understanding of
spatial transcriptomics data and related biological and pathological
processes. However, due to diversified operating principles and
applicable scope, researchers had difficulty in selecting optimal
integration methods.

The research team led by Prof. Qu has been working on developing


analysis algorithms and software for biological big data for a long time.
In this study, the researchers presented benchmarking of 16 integration
methods using 45 paired datasets containing both spatial transcriptomics
and scRNA-seq data and 32 simulated datasets according to their
accuracy, robustness, and computational resources consumption.

According to the researchers, Cell2location, SpatialDWLS, and Robust


Decomposition of Cell Type (RCTD) were superior to other integration
methods for the cell type deconvolution of spots in histological sections,
whereas Tangram, gimVI, and Spatial Gene Enhancement (SpaGE)
showed excellent performance compared with other integration methods
for predicting the spatial distribution of RNA transcripts. Tangram,
Seurat and Linked Inference of Genomic Experimental Relationships

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(LIGER) had high computational efficiency and were suitable for
processing large-scale data sets.

This study concludes the attribute, performance, and applicability of


each integration method and the advantages of methods with high
efficiency. It helps researchers to further improve these algorithms.

The team also shares a benchmark process of integrating spatial


transcriptomics data with scRNA-seq data on GitHub to help researchers
select optimal integration methods to process their datasets.

More information: Bin Li et al, Benchmarking spatial and single-cell


transcriptomics integration methods for transcript distribution prediction
and cell type deconvolution, Nature Methods (2022). DOI:
10.1038/s41592-022-01480-9

Provided by Chinese Academy of Sciences

Citation: Benchmarking transcriptomics integration methods for transcript distribution prediction


and cell type deconvolution (2022, May 27) retrieved 3 November 2023 from
https://phys.org/news/2022-05-benchmarking-transcriptomics-methods-transcript-cell.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private
study or research, no part may be reproduced without the written permission. The content is
provided for information purposes only.

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