Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Innovations in Gene Expression Profiling: A Comparative Study

    Introduction to Multiplexed In Situ Technologies
    Researchers Hartman and Satija from the New York Genome Center and New York University have released a significant preprint entitled "Comparative Analysis of Multiplexed In Situ Gene Expression Profiling Technologies.” The study presents a comparative analysis of six in situ gene expression profiling methods.

    They assessed these technologies for their sensitivity, particularly in detecting unique molecules per cell, and for their specificity, focusing on the impact of off-target molecular artifacts. In addition, the researchers developed new metrics to control for these artifacts. Their findings highlight the variability among different in situ methods and emphasize the importance of considering molecular false positives in spatially-aware differential expression analysis.

    Technological Insights and Comparative Analysis
    This study focused on benchmarking various in situ spatial technologies used for multiplexed gene expression profiling, using datasets from full mouse brain sections. The technologies compared include Xenium (10x Genomics), MERSCOPE (Vizgen), Molecular Cartography (Resolve Biosciences), MERFISH, STARmap PLUS, and EEL FISH. The researchers aimed for a fair comparison by utilizing outputs provided by the dataset creators, which included gene-cell expression matrices and coordinates for each segmented cell.

    The initial analysis measured reproducibility and average counts and features identified in each cell. High reproducibility was observed across technologies. However, sensitivity varied, with no correlation found between the average number of transcripts detected per cell and total panel size. The study also assessed the ability of these technologies to categorize cell types in mouse brain sections, finding success in identifying broad cell groups but also noting non-specific expression of marker genes. Higher-resolution subsets were not benchmarked due to differences in panel size and composition across technologies.

    A comparison of molecular sensitivity between in situ technologies and scRNA-seq revealed that in situ methods generally showed higher molecular counts. However, this could be partly due to non-specific signals inflating gene expression counts. The study also observed a higher increase in molecular counts for lowly expressed genes from in situ techniques, suggesting the presence of a uniform background effect.

    Non-specificity was further examined through a 'mutually exclusive co-expression rate' (MECR), which varied across technologies. The study also explored potential sources of non-specific signals including off-target probe binding and the accuracy of molecular assignment to cells. Variations in cell segmentation quality across technologies affected molecular assignment accuracy. A uniform segmentation processing pipeline was applied to reprocess datasets, revealing significant differences in sensitivity and specificity.

    Further, the researchers examined how spatial location influences gene expression within a cell type. They found discrepancies in differentially expressed genes when comparing in situ datasets with scRNA-seq data, suggesting non-specific molecular signals and potential misassignment of molecules from in situ datasets. This was particularly evident in genes that appeared upregulated in certain cell types due to molecular misassignment.

    Main Findings
    • Vizgen's MERSCOPE datasets showed the best performance, with an optimal balance between sensitivity and specificity, and a large panel size of 483 genes.
    • Xenium technology, with a 247-gene panel, also performed well but had lenient segmentations that increased molecular detection at the cost of accuracy.
    • Resolve Molecular Cartography and MERFISH datasets showed similar sensitivity but differed in panel sizes (99 genes for Molecular Cartography and 1147 for MERFISH).
    • EEL FISH was the least sensitive technology, trading sensitivity for faster imaging time and reduced autofluorescence.
    • The study's limitations include its focus on mouse brain tissue and fresh-frozen samples, limiting its applicability to a single biological context.
    • Non-specific signals in imaging-based spatial transcriptomics is largely due to misassignment of molecules, necessitating improved segmentation and computational methods to address this issue.
    These findings highlight the strengths and limitations of each technology, guiding researchers in selecting the most appropriate method for their specific gene expression profiling needs. Hartman and Satija’s work provides pivotal guidance for the selection, processing, and interpretation of in situ spatial technologies in gene expression profiling, marking a significant contribution to the field.

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-28-2024, 06:12 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
74 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
85 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X