Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Germine copy number variation detection?

    Hi all,
    I have the normal tissue of about 20 cancer patients with family cancer history. We would like to perform exome sequencing to identify germline mutations, especially germline copy number variations but have not much experience. A couple of questions:

    1) What will be a good "reference"/normal BAM file? Randomly selecting reads from BAM files of some normal people sequencing data?
    2) Assume we have such a BAM files in 1), can we just use public software tools such as VarScan2 to compare the patient's BAM with the reference BAM?

    Any input is greatly appreciated!

  • #2
    Originally posted by mrfox View Post
    1) What will be a good "reference"/normal BAM file? Randomly selecting reads from BAM files of some normal people sequencing data?
    You can use a program like CoNIFER or cn.MOPS to process the samples as a cohort. These programs each use a statistical method to consider all of the given samples in aggregate to determine the "expected" baseline for copy number inference.

    Alternatively, CNVkit works more like your proposal, where a reference copy number profile is initially constructed from a pool of normal BAM files and then reused to infer CNVs in individual samples. CNVkit can also operate without any normal-sample reference at all, but results will be slightly noisier.

    Originally posted by mrfox View Post
    2) Assume we have such a BAM files in 1), can we just use public software tools such as VarScan2 to compare the patient's BAM with the reference BAM?
    Yes, you could. Be careful to check that any recurrent CNVs you find aren't simply the result of having a region of unusually high or low read depth in your reference BAM.

    Most program for copy number inference will give you some indication of how the reference should be built and whether you should process one sample at a time or the whole cohort at once.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    24 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    25 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Working...
    X