Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How many SNPs are needed to perform haplotype analysis on close relatives?

    Hello!

    I need to haplotype a patient, their mother, and three or four of the (deceased) father's (living) siblings, so that we can deduce where the patient's (mutant) haplotype came from. We suspect a de novo SNV, only the patient has symptoms.

    Many years ago my group supposedly performed this type of haplotyping using 20 microsatellites (short tandem repeats) in a 1 Mbp window surrounding the SNV. STRs are very polymorphic which made the haplotyping possible (the haplotypes of 20 STRs were unique). For some reason we no longer have access to a lab that can perform this type of STR analysis, so I'm searching for alternatives. One alternative is a SNP array, its specifications suggest 300 SNPs per Mbp on average. Are 300 SNPs enough to perform this haplotyping on these ~5 individuals? I've no idea who to ask, so I ask here.

    Alternatively, are there better ways entirely to do this sort of thing?

    Big big thanks for any help!


    Masklin

  • #2
    Hi Masklin!

    Do you have a reference or link to the SNP array you were talking about using?

    I haven't done haplotyping yet, but I know some companies like Illumina have calculators to determine what type of coverage you need for each type of experiment. That may not be useful here, but it could be worth a shot.

    I used to know some good references for haplotyping, I just can't seem to find them now.

    Comment


    • #3
      Hello and thanks for replying!

      The SNP array I was thinking of is the one CentoGene offers, here is a pdf describing it:


      There are other options though, but many of them seem to accept only purified DNA, rather than blood, and we don't have the facilities to extract the DNA here, locally. CentoGene does all that for you, but the price... is vast.

      I'll see if I can find a calculator on Illumina's site, thanks!

      Comment


      • #4
        Thanks for the link. Let me look more into this panel and I will get back to you.

        Also, you said you didn't have the facilities to extract the DNA, but if you have access to a few things I think you might be able to make it work. Qiagen has a ton of kits that really only require a small centrifuge and some pipettes to extract genomic DNA from blood. There are also a lot of smaller biotech companies with cheap spin columns.

        I remember I used Qiagen's PAXgene Blood tubes for DNA extractions once and it was super easy and didn't require much stuff. Although if you don't have access to a few pipettes and a small centrifuge then it still won't work.

        Comment


        • #5
          Hello again,

          I asked my PI and apparently we have no lab equipment whatsoever, but he also said he's been thinking about starting a small lab, or a cooperation with an existing lab. I will urge him to realise this hypothetical, probably it will pay for itself in time...

          Comment


          • #6
            The computer analysis of APOL1 and single nucleotide polymorphisms in chronic kidney disease (CDK). Any help anyone can provide me with will be really appreciated. Thank you very much, everyone

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 07-19-2024, 07:20 AM
            0 responses
            28 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-16-2024, 05:49 AM
            0 responses
            41 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-15-2024, 06:53 AM
            0 responses
            46 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Working...
            X