Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Using Copy Number Alterations detected in other studies for the same tumor cell line

    Hello everybody,

    It is my first time working with cancer genomes and I have some doubts. I found this study in which they provide a lot of different sequencing data for the cell line HCC1395, and I would like to use them to assess a new tool that we are developing for detecting Copy Number Alterations. Problem is, I'm lacking a ground truth. In this study, they provide a golden dataset for SNVs and short INDELS, but they do not provide info about the CNAs. I necessarely need a not simulated normal/cancer sample pairs from the same patient, and this is the only source I found so far whicjh is freely providing a lot of well documented sequencing data.

    Since the HCC1395 cell line was already studied before, I found some other studies providing the CNAs they found for it. My question now is: can I use those CNAs found in other studies on the same cell line as a ground truth to compare what I will find with our tool on the data I have?

    I don't have much biological knowledge and my doubts arise manly because, If I undersood well, those cells are usually grown independently in a laboratory setting for each study, so I am not sure if they are comparable, or if they could have different mutations occurring between the different studies.




    Thanks in advance!

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-28-2024, 06:12 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
74 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
83 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X