Header Leaderboard Ad

Collapse

How to identify chromosomal translocation or deletions?

Collapse

Announcement

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

  • How to identify chromosomal translocation or deletions?

    I have a mouse cell line, which could have large-fragment deletion or translocation. I thought that the most affordable, efficient way to identify the translocation/deletion loci could be exome sequencing; at least I can identify which genes are lost in the mouse genome. I am not an expert on genetics or sequencing, so any comments or thoughts would be appreciated. Also, I welcome sequencing vendors to provide quotes about the possible project. Thanks.
    Last edited by spng; 07-22-2014, 08:34 AM.

  • #2
    If a large-scale event is heterozygous, I don't think exon-capture would be particularly useful; it does not give useful information about copy count because of the bias in bait efficiency. You MAY get some reads spanning a deletion, but then again, you may not; depends on whether the boundaries fall within the baited region. Also, some allegedly targeted exons will just not show up even though they are present.

    The cheapest way to look for large-scale CNVs is with an array chip. It won't give exact boundaries, but with a 3Gbp genome, a 1 million SNP chip should give a resolution down to around 3000bp. Also, this won't tell you anything about a copy-neutral translocation.

    Whole-genome sequencing is probably the most reliable method for finding novel junctions from translocations and deletions, though even then, discerning true translocations in large, repetitive genomes requires a substantial amount of skilled manual labor.

    Comment


    • #3
      First of all, how stable is the karyotype?

      Comment


      • #4
        Brian, thanks for your helpful suggestions. For my project I wish to get a clue about the genes responsible for the phenotype and then I will work on the gene candidates using wet lab techniques to rescue or recapitulate the phenotype. So I may not be so interested in the boundaries. I was also thinking about using RNA Seq, but that is not a direct and reliable approach to my aim, although I may get some clues about the downstream signaling. So I agree that your suggestion of using array chips is a better idea. And, I guess that array can work with heterozygous events (please correct me if not).
        To Joann: about the karyotype, I have to say I did not look into that; so it is good to know about this.

        Comment


        • #5
          Right, at some point I am hoping NGS will provide a simple assay mechanism to monitor these things that happen under tissue culture conditions like changes in chromosome number, which is a pretty macro event as well as other even harder to visually observe changes in chromosome structure, both qualitative and quantitative. In order to better validate results obtained with tissue culture models as well as to better understand cell division dynamics under cultured/immortalized conditions.

          Comment


          • #6
            Originally posted by spng View Post
            And, I guess that array can work with heterozygous events (please correct me if not).
            Arrays data I've worked with was able to indicate copy-count, since it's basically an analog measure of signal strength. The biggest disadvantage of arrays is that they are expensive and time-consuming to initially design and create, but for mouse they should already exist.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
              by seqadmin


              ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

              01-24-2023, 01:19 PM
            • seqadmin
              Introduction to Single-Cell Sequencing
              by seqadmin
              Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

              The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
              ...
              01-09-2023, 03:10 PM

            ad_right_rmr

            Collapse
            Working...
            X