Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Complete Genomics User Group Meeting

    Just got back from the Complete Genomics User Group Meeting in San Francisco. Hopefully we'll start seeing some discussion of Complete data here on SEQanswers in the near future.

    I have yet to take a close look at our data back from Complete yet, but I now have a much stronger understanding of their bioinformatics and technical pipeline (you can get their biochemistry info from their white paper). Anyone else here get data from them or attend the meeting?

    I think CGA tools is very powerful for small variant detection. It looked from the data presented (again, preliminary) that their variant detection accuracy is on par or a little better than what is generally seen with Illumina or SOLiD whole genome data.

    Given the nature of their data, converting to BAM and doing alternative variant analysis may not be as powerful (this is something we users may have to try). This is because they do assembly over non-reference called positions in their data processing. It will be interesting to see how their variant detection performance compares to variants detected on other platforms and with other analysis platforms.

    They are just starting to produce CNV and SV calls. These data I'm not sure about yet, but it is good to see them diving into it with both feet because these variants are at least as important as small variants from a whole genome perspective.

    They are also heading towards in-house somatic variants analysis (comparing two genomes), which is pretty important for cancer genomics. It will be interested to see what is delivered there in the future. Right now, the CGAtools calldiff algorithm is used for this. I'd like to hear opinions on calldiff from people who've used it.

    Here's a pic of their machines in action:

    It's apparently 80% humidity and hot in that room. Yes, it's a dark room. This is because it's the optimal environment for the DNBs (DNA nano-balls) and for the picoliter quantities of reagents used at each cycle. (Later on, we had a rave party in there when the sequencers were on their lunch break!)

    Here's one of their slides:


    Complete Genomics may be a strong way to go in the near future for whole genome sequencing. I'd certainly consider it as an alternative to doing it in-house at this point, freeing up local machines for targeted pull-downs, exomes, non-human, RNAseq, ChIPseq, etc.

    I look forward to hearing from other Complete Genomics users in the future.
    Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
    Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
    Projects: U87MG whole genome sequence [Website] [Paper]

  • #2
    Reference dependence is the impression that Complete Genomics gives. Population level or cancer genomics could be problematic for that platform, which would be sad given that is the market they want. We will see after their cancer research grants.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Quality Control Essentials for Next-Generation Sequencing Workflows
      by seqadmin




      Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

      Nucleic Acid Quality Control
      Preparing for NGS starts with isolating the...
      02-10-2025, 01:58 PM
    • seqadmin
      An Introduction to the Technologies Transforming Precision Medicine
      by seqadmin


      In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
      01-27-2025, 07:46 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-07-2025, 09:30 AM
    0 responses
    65 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-05-2025, 10:34 AM
    0 responses
    101 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-03-2025, 09:07 AM
    0 responses
    79 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 01-31-2025, 08:31 AM
    0 responses
    45 views
    0 likes
    Last Post seqadmin  
    Working...
    X