Scout Bug: Pinned Variant Not Recognized In ClinVar Submission

Hey guys! Ever run into a situation where your code just doesn't seem to recognize something that's already there? It's like when you're searching for your keys and they're right in front of you! We've got a similar head-scratcher in Scout, our clinical genomics tool, specifically related to how it handles pinned variants within oncogenic ClinVar submissions. Let's dive into what's happening and how to reproduce it.

The Problem: A Case of Mistaken Identity in Clinical-Genomics

The core issue lies in the Clinical-Genomics module of Scout. Imagine this: you've identified a variant that's oncogenic – meaning it has the potential to cause cancer. You've carefully pinned this variant within Scout, essentially marking it as important and relevant. Now, you're ready to submit it to ClinVar, a public archive of genomic variations and their relationship to human health. You go through the process of creating an oncogenic submission within Scout, making sure everything looks good, and the submission goes through successfully. Great! ...or so you think.

The kicker is that when you return to the case page in Scout, the system still prompts you to add the very same variant to a submission! It's as if Scout has completely forgotten that this variant is already part of a completed submission. This can lead to confusion, potential duplicate submissions, and a general feeling of, "Wait, did I actually submit this or not?"

This bug highlights the importance of robust data management and clear communication within software systems. If Scout isn't accurately tracking which variants are included in which submissions, it can undermine the confidence users have in the system. It's like having a librarian who keeps recommending you the same book you've already checked out – frustrating and inefficient! We need to ensure that Scout's internal logic is correctly recognizing and associating pinned variants with their corresponding ClinVar submissions. This involves a deep dive into the codebase, tracing the flow of data, and identifying where the disconnect is occurring.

Reproducing the Bug: A Step-by-Step Guide

Okay, so how can you see this bug in action for yourself? Here’s a step-by-step guide to reproduce the issue:

1. Pin an oncogenic variant: First, identify a variant within Scout that is classified as oncogenic. This means it's been determined to have the potential to contribute to cancer development. Use Scout's features to pin this variant. Pinning essentially marks the variant as important and relevant for further action.
2. Submit it to an oncogenic submission (in Scout): Now, initiate the process of submitting this pinned oncogenic variant to ClinVar directly through Scout. This involves creating an oncogenic submission within Scout and adding the variant to it.
3. Make sure submission has worked: Ensure that the submission process completes successfully. This typically involves checking for confirmation messages or status updates within Scout indicating that the submission has been sent to ClinVar.
4. On the case page, it still asks you if you want to add it to a submission: This is where the bug surfaces. After the submission is confirmed, navigate back to the case page in Scout. You'll likely see a prompt or notification suggesting that you add the previously submitted variant to a submission. This is incorrect behavior, as the variant should already be associated with the completed submission.

By following these steps, you can consistently reproduce the bug and demonstrate the issue to developers or other stakeholders. This helps in prioritizing the bug fix and ensuring that it's properly addressed. Think of it as providing a detailed recipe for the bug, making it easier for the development team to cook up a solution!

The Impact and Why It Matters

So, why is this bug more than just a minor annoyance? It actually has several implications for the accuracy and efficiency of clinical genomics workflows.

First and foremost, it creates confusion and uncertainty. If Scout is constantly prompting users to add variants to submissions that are already complete, it undermines their trust in the system. They may start questioning whether their previous actions were actually successful, leading to unnecessary double-checking and wasted time. Imagine constantly having to verify if you've sent an email because your email client keeps asking you if you want to send it – frustrating, right?

Secondly, it increases the risk of duplicate submissions. If a user, unsure whether a variant has been submitted, goes ahead and adds it again, this could result in redundant data being sent to ClinVar. This not only clutters the ClinVar database but also adds extra work for ClinVar curators who have to identify and resolve these duplicates. It's like sending the same birthday card twice – a well-intentioned mistake, but still a mistake.

Finally, it impacts overall workflow efficiency. The extra steps required to verify submissions and the potential for duplicate submissions slow down the entire process of variant curation and submission. In a clinical setting where time is often of the essence, these inefficiencies can have a real impact on patient care. Think of it as a small pebble in your shoe – it might not seem like much, but it can slow you down significantly over a long distance.

Potential Solutions and Workarounds

Okay, so we've identified the problem and understand its impact. What can be done about it? While a permanent fix requires a code update within Scout, there are some potential workarounds in the meantime.

One workaround is to manually track submissions. This involves keeping a separate record (e.g., a spreadsheet or a dedicated notebook) of which variants have been submitted to which ClinVar submissions. While this adds an extra step to the workflow, it can help prevent duplicate submissions and provide a clear audit trail. Think of it as creating your own