Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Creating a customized reference genome for genome analysis?

    Hi everyone,

    I was just wondering something that I would like to discuss with experts - or at least those that are more expert in that area than myself as a newbie. I was not quite sure into what category to put that thread, so I opened it up here...

    So to my thoughts:
    We have a single reference genome that we use for our genome analysis, e.g. as used by the 1,000 genomes project. This reference had been assembled from a few individuals. If I think about all the populational differences, e.g. regarding different regions on earth or even between families, I somehow get the feeling that using this single reference genome for analysis is not sufficient as it does not represent those population-specific differences. Could it not be that we miss important genetic variations or identify some that actually are not one within that population?

    On the other hand, we have already access to population-specific variant data, e.g. from the 1,000 genomes project. So what comes to my mind now is: Why not using that data to construct a "customized" reference genome and use that for genome data analysis instead, i.e. using the general reference genome as basis and adapting it by particular genetic variants found in the majority of the data of a specific population? With that we could even create family-specific reference genomes, e.g. if we want to analyze a child's DNA by using its parents' DNA to customize the reference genome.

    I am wondering if that would be beneficial for genome data analysis at all, and if so what could be the theoretical challenges in combining those data? I mean, it will probably not be done that easily by just checking the genetic variants of a population and applying them to the reference genome at that position...?

    Would be great if we could discuss on that

    Best,

    Cindy

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X