Catching up on 🧬 “Understanding #NGS and Interpreting Reports for Oncologic Pathology” with Dr. @sabahkadri and Dr. Cecilia Yeung at #CAP21@AMPath 👩🏻💻
📌 @Pathologists has NGS assay development tools regarding test design, validation, quality, and bioinformatics: cap.org/member-resourc…
📌 How much do you want to know? ➡️ what test is needed? (WGS vs WES vs targeted sequencing)
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🧬 NGS in a nutshell with Dr. Yeung
1️⃣ Library preparation (hybrid capture vs amplicon-based)
2️⃣ Sequence the fragments of DNA (cyclic reversible termination vs detection of chemical byproducts ⚡️ as single nucleotide is added)
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Other NGS techniques:
📌 Multiplexing samples: tag each library component from the same patient with indentical barcode ➡️ combine patient samples into one sequencing reaction ➡️ de-multiplex with #bioinformatics after sequencing
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🏷 Unique molecular identifiers (UMI)
📎Unique to each library component
📎 Allows you to distinguish noise from true variants (if all reads with same UMI have a change ➡️ likely true variant; if only some ➡️ likely noise)
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🔎 Analysis
1️⃣ Alignment to reference sequence
2️⃣ Variant calling and quality analysis
3️⃣ Annotation ✍️
4️⃣ Report
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📌 Tier I: strong clinical signficance (therapeutic, diagnostic, prognostic w level A or B evidence)
📌 Tier II: potential clinical signficance (⬆️ but w level C or D evidence)
📌 Tier III: unknown clinical signficance
📌 Tier IV: B9 or likely B9
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📌 How we convert data from sequencers into useful information for pathologists to interpret and pass along to clinical colleagues through our reports
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🌾 Problem scope: looking for a genomic anomaly (needle) in the whole genome (haystack) ➡️ but bioinformatics is your tool! (maybe a metal detector??)
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1️⃣ Determine the type of variant, 2️⃣ compare using databases (COSMIC, ClinVar), and then 3️⃣ filtering and ranking variants
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Thank you for this excellent talk Dr. @sabahkadri and Dr. Yeung!
⬆️ is just a brief summary of a few points - highly recommend viewing the full talk on @Pathologists@AMPath#CAP21, which also has great case studies to illustrate these concepts in action
But as someone who grew up in the desert ➡️ and then lived in TX 🤠 ➡️ if I can handle it, you definitely can too! (Just need to get yourself some good gear🧥🥾 - I’ve got suggestions!)
If you don’t want to go outside in the winter, Mayo Clinic & Rochester have tunnels & sky bridges connecting the med center w downtown, including from the parking ramps to the hospital 🏥
But personally, I’m excited for outdoor activities like snowshoeing & cross-country skiing!
🧬#MolecularPath “Selecting the Right Tool for the Job: Practical Considerations for the Application of Molecular Diagnostics Methods in SurgPath” with @LJTafeMD and Dr. Larissa Furtado
A few takeaways (just scratching the surface of this excellent talk!) ⬇️🧵#MolecularPath_CEJ