FFPE tissue blocks were collected for each fresh-frozen tumor which underwent multiomic profiling and were used for pathology review, IHC (MYF-4, H3K7me3, S100, and Sox10) and additional molecular characterization [i.e., ploidy assay and multiregional whole-exome sequencing (WES)]. FFPE H&E slides from available blocks were reviewed by a pathologist to identify the block most representative (i.e., morphologically similar) to the frozen material which underwent multiomic profiling. These H&E sections were digitally scanned (40×) at each pathology hub by the Deep Lens Biomedical Imaging Team and uploaded to the VIPER digital pathology platform (Deep Lens, Inc.). Multiregional 500× exome sequencing was performed on 5 samples each from 36 FFPE NF1-related MPNST specimens to assess intratumor heterogeneity.
Protocol detail
Multiomics Profiling of MPNST Specimens
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Assay
Frozen
Heterogeneity
Lens
Mpnst
Myf 4
Pathologist
S100
Sox10
Tissue
Tumor
Viper
Corresponding Organization : Boston Children's Hospital
Other organizations : European Bioinformatics Institute, London Cancer, University College London, University of Alabama at Birmingham, Moffitt Cancer Center, Harvard University, University of Toronto, Mount Sinai Hospital, Washington University in St. Louis, Royal Marsden NHS Foundation Trust, Institute of Cancer Research, Wellcome Centre for Human Genetics, University of Oxford, Lifespan, Rhode Island Hospital, Huntsman Cancer Institute, University of Utah, Massachusetts General Hospital, Center for Neuro-Oncology, Princess Margaret Cancer Centre, Sinai Health System, Ontario Institute for Cancer Research, Hospital for Sick Children, SickKids Foundation, Royal National Orthopaedic Hospital NHS Trust, Nagoya University Hospital, NYU Langone Health, National Cancer Institute, National Institutes of Health, Center for Cancer Research
Top 5 similar protocols
Variable analysis
independent variables
- Multiomic profiling of fresh-frozen tumor samples
- Pathology review of FFPE blocks
- IHC staining (MYF-4, H3K7me3, S100, and Sox10)
- Ploidy assay
- Multiregional whole-exome sequencing (WES) on FFPE samples
- Morphological similarity between FFPE blocks and frozen material
- Intratumor heterogeneity in NF1-related MPNST specimens
- FFPE tissue blocks corresponding to each fresh-frozen tumor sample
- Digital scanning of H&E slides at 40x magnification
- Uploading of scanned slides to the VIPER digital pathology platform
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!