Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors
Abstract
:1. Introduction
2. Materials and Methods
2.1. Image Acquisition and Diagnostic Accuracy Comparison
2.2. Whole-Exome Sequencing
2.3. Targeted Sequencing of DNA and RNA Variant Calling
3. Results
3.1. MUSE Image Quality Compared to Conventional Histology
3.2. Preliminary Validation Studies
Reviewer 1 | Reviewer 2 | Reviewer 3 | |||||
---|---|---|---|---|---|---|---|
Tumor Type | Correct | Incorrect | Correct | Incorrect | Correct | Incorrect | Combined Accuracy |
Diffuse Astrocytic DA II, AA III, and GBM IV | 10 | 0 | 9 | 1 | 9 | 1 | 93% |
Oligodendroglial Oligo II, AO III | 4 | 0 | 4 | 0 | 3 | 1 | 92% |
Meningioma Grades I and II | 6 | 0 | 5 | 1 | 5 | 1 | 89% |
Metastatic | 3 | 0 | 3 | 0 | 3 | 0 | 100% |
Normal Anatomic Structures | 4 | 0 | 4 | 0 | 4 | 0 | 100% |
Combined Accuracy | 100% | 93% | 89% | 94% |
Reviewer 1 | Reviewer 2 | Reviewer 3 | |||||
---|---|---|---|---|---|---|---|
Tumor Type | Correct | Incorrect | Correct | Incorrect | Correct | Incorrect | Combined Accuracy |
Diffuse Astrocytoma Grade II | 5 | 0 | 5 | 0 | 5 | 0 | 100% |
Anaplastic Astrocytoma Grade III | 6 | 0 | 5 | 1 | 3 | 3 | 78% |
Glioblastoma Multiforme Grade IV | 10 | 6 | 9 | 7 | 10 | 6 | 60% |
Oligodendroglioma Grade II | 8 | 0 | 8 | 0 | 7 | 1 | 96% |
Anaplastic Oligodendroglioma Grade III | 2 | 0 | 0 | 2 | 0 | 2 | 33% |
Meningioma Grade I | 5 | 0 | 5 | 0 | 5 | 0 | 100% |
Meningioma Grade II | 4 | 1 | 0 | 5 | 1 | 4 | 33% |
Combined Accuracy | 85% | 68% | 66% | 73% |
Reviewer 1 | Reviewer 2 | Reviewer 3 | |||||
---|---|---|---|---|---|---|---|
Cellular Feature | Correct | Incorrect | Correct | Incorrect | Correct | Incorrect | Combined Accuracy |
Cellularity | 36 | 11 | 39 | 8 | 41 | 6 | 82% |
Atypia | 44 | 3 | 43 | 4 | 43 | 4 | 92% |
Mitoses | 38 | 9 | 34 | 13 | 33 | 14 | 74% |
Combined Accuracy | 84% | 82% | 83% | 83% |
3.3. Suitability for Downstream Molecular Analysis
4. Discussion
5. Patents
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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DNA ng/μL (Total Yield, ng) [260/280 Ratio] | RNA ng/μL (Total Yield, ng) [260/280 Ratio] | |||
---|---|---|---|---|
Sample | MUSE-Treated | Fresh Frozen | MUSE-Treated | Fresh Frozen |
39N | 28.7 (2009) [1.85] | 16 (1120) [1.91] | 49.2 (1968) [1.68] | 113.5 (4540) [1.86] |
53 | 113 (7910) [1.87] | 85.3 (5971) [1.87] | 195.4 (7816) [2.02] | 250.5 (10,020) [1.97] |
57T | 46.5 (3255) [1.85] | 30.8 (2156) [1.78] | 75.5 (3020) [1.92] | 101 (4040) [1.98] |
Sample 39N | Sample 53 | |||||
---|---|---|---|---|---|---|
Metric | Pass Metric | MUSE-Treated | Fresh Frozen | MUSE-Treated | Fresh Frozen | |
DNA | Mapped reads | ≥5,000,000 | 12,334,171 | 14,797,491 | 11,613,269 | 9,929,415 |
Mean read length (bp) | ≥75 | 115 | 114 | 112 | 112 | |
Uniformity (%) | ≥90 | 95.9 | 96.4 | 97.5 | 97.7 | |
Mean target coverage | ≥800 | 3703 | 4389 | 3426 | 2922 | |
On-target coverage (%) | ≥85 | 96.0 | 95.9 | 96.1 | 96.2 | |
C > T transitions (%) | <8.0 | 5.7 | 5.8 | 5.8 | 5.8 | |
RNA | Mapped reads | ≥500,000 | 969,724 | 764,965 | 1,302,634 | 1,207,136 |
Mean read length (bp) | ≥60 | 108 | 93 | 111 | 109 |
Sample 53 | ||
---|---|---|
Metric | MUSE-Treated | Fresh Frozen |
Mapped reads | 942,438,994 | 1,016,643,517 |
On-target reads | 457,723,211 | 479,992,813 |
On-target duplicate reads | 215,608,334 | 207,313,493 |
Mean target coverage | 939X | 989X |
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Lechpammer, M.; Todd, A.; Tang, V.; Morningstar, T.; Borowsky, A.; Shahlaie, K.; Kintner, J.A.; McPherson, J.D.; Bishop, J.W.; Fereidouni, F.; et al. Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors. Brain Sci. 2024, 14, 108. https://doi.org/10.3390/brainsci14010108
Lechpammer M, Todd A, Tang V, Morningstar T, Borowsky A, Shahlaie K, Kintner JA, McPherson JD, Bishop JW, Fereidouni F, et al. Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors. Brain Sciences. 2024; 14(1):108. https://doi.org/10.3390/brainsci14010108
Chicago/Turabian StyleLechpammer, Mirna, Austin Todd, Vivian Tang, Taryn Morningstar, Alexander Borowsky, Kiarash Shahlaie, John A. Kintner, John D. McPherson, John W. Bishop, Farzad Fereidouni, and et al. 2024. "Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors" Brain Sciences 14, no. 1: 108. https://doi.org/10.3390/brainsci14010108