Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Development of a semi-automated method for tumor budding assessment in colorectal cancer and comparison with manual methods Tumor budding is an established prognostic feature in multiple cancers but routine assessment has not yet been incorporated into clinical pathology practice. Recent efforts to standardize and automate assessment have shifted away from haematoxylin and eosin (H&E)-stained images towards cytokeratin (CK) immunohistochemistry. In this study, we compare established manual H&E and cytokeratin budding assessment methods with a new, semi-automated approach built within the QuPath open-source software. We applied our method to tissue cores from the advancing tumor edge in a cohort of stage II/III colon cancers (n=186).

The total number of buds detected by each method, over the 186 TMA cores, were as follows; manual H&E (n=503), manual CK (n=2290) and semi-automated (n=5138). More than four times the number of buds were detected using CK compared to H&E. A total of 1734 individual buds were identified both using manual assessment and semi-automated detection on CK images, representing 75.7% of the total buds identified manually (n=2290) and 33.7% of the total buds detected using our proposed semi-automated method (n=5138). Higher bud scores by the semi-automated method were due to any discrete area of CK immunopositivity within an accepted area range being identified as a bud, regardless of shape or crispness of definition, and to inclusion of tumor cell clusters within glandular lumina ("luminal pseudobuds"). Although absolute numbers differed, semi-automated and manual bud counts were strongly correlated across cores ({rho}=0.81, p<0.0001). Despite the random, rather than "hotspot", nature of tumor core sampling, all methods of budding assessment demonstrated poorer survival associated with higher budding scores.

In conclusion, we present a new QuPath-based approach to tumor budding assessment, which compares favorably to current established methods and offers a freely-available, rapid and transparent tool that is also applicable to whole slide images.
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The categories of this paper are: systems
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The categories of this paper are: evolutionary
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The categories of this paper are: genomics
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The categories of this paper are: ecology
1
The categories of this paper are: bioinformatics
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The categories of this paper are: neuroscience
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The categories of this paper are: animal
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The categories of this paper are: toxicology
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The categories of this paper are: scientific
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The categories of this paper are: genetics
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The categories of this paper are: zoology
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The categories of this paper are: biology
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The categories of this paper are: microbiology
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The categories of this paper are: education
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The categories of this paper are: and
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The categories of this paper are: immunology