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Questions related to SNP analysis

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  • aiguo li
    Dear all. I am trying to analyze my mapping 10K SNP data (5 tumor cell lines plus a standard cell line) using dChip. In array list file I created a list file
    Message 1 of 4 , Aug 4, 2004
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      Dear all.

      I am trying to analyze my mapping 10K SNP data (5
      tumor cell lines plus a standard cell line) using
      dChip. In array list file I created a list file as
      below:
      U251 (tumor)
      Standard
      --standard separate--
      Gli3AK (tumor)
      Standard
      --standard separate--
      Hs683 (tumor)
      Standard
      --standard separate--
      T98G (tumor)
      Standard
      --standard separate--
      S127 (tumor)
      standard
      --standard separate--

      Then I did 'analysis -> chromosome'
      The results I got from this analysis look strange
      because all the LOH are identical across 5 cell lines
      (see attached .ppt file). I exported the SNP call
      data and all the SNP calls across the cell lines are
      identical also. I am not sure there is a buy in the
      dChip or I did something wrong. Could somebody help
      me figure this out?

      In addition, the color schema in the LOH display has
      been changed. The menu said that the blue for LOH,
      Yellow for retention, gray for uninformative, white
      for no calls. Now in current display, there is no
      gray color, and I am not sure what the red color for.


      Thanks in advance,

      Aiguo Li



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    • Cheng Li
      Aiguo, You have to have paired normal and tumor samples from the same individual to do LOH analysis in dChip (normal first, then tumor). Is your standard
      Message 2 of 4 , Aug 4, 2004
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        Aiguo,

         

        You have to have paired normal and tumor samples from the same individual to do LOH analysis in dChip (normal first, then tumor). Is your “standard” sample from the same individual as tumor samples?


        Cheng

         

        -----Original Message-----
        From: aiguo li [mailto:li9212001@...]
        Sent: Wednesday, August 04, 2004 3:35 PM
        To: dchip@yahoogroups.com
        Subject: [dchip] Questions related to SNP analysis

         

        Dear all.

        I am trying to analyze my mapping 10K SNP data (5
        tumor cell lines plus a standard cell line) using
        dChip.  In array list file I created a list file as
        below:
        U251 (tumor)
        Standard
        --standard separate--
        Gli3AK (tumor)
        Standard
        --standard separate--
        Hs683 (tumor)
        Standard
        --standard separate--
        T98G (tumor)
        Standard
        --standard separate--
        S127 (tumor)
        standard
        --standard separate--

        Then I did 'analysis -> chromosome'
        The results I got from this analysis look strange
        because all the LOH are identical across 5 cell lines
        (see attached .ppt file).  I exported the SNP call
        data and all the SNP calls across the cell lines are
        identical also.  I am not sure there is a buy in the
        dChip or I did something wrong.  Could somebody help
        me figure this out?

        In addition, the color schema in the LOH display has
        been changed.  The menu said that the blue for LOH,
        Yellow for retention, gray for uninformative, white
        for no calls.  Now in current display, there is no
        gray color, and I am not sure what the red color for.


        Thanks in advance,

        Aiguo Li


                   
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      • aiguo li
        Dear Dr. Li, I did tried to use the standard sample first in array list, then the tumor cell line followed. However, it created a chromosome picture with all
        Message 3 of 4 , Aug 5, 2004
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          Dear Dr. Li,

          I did tried to use the standard sample first in array
          list, then the tumor cell line followed. However, it
          created a chromosome picture with all the lables as
          standards, i.e. each column in the heatmap is one
          standard cell line. I am trying to compare the tumor
          cell lines here and thought it makes more sense that
          the sample list in the chromosome picture to have all
          the tumor cell lines as labels. Am I right.

          It will be ideal to have blood DNA sample to compare
          with tumor tissue samples. The standard sample here
          is from Affy's reference DNA which they claimed as a
          healthy man's DNA.

          Thanks for your help.

          Aiguo Li
          --- Cheng Li <cli@...> wrote:

          > Aiguo,
          >
          > You have to have paired normal and tumor samples
          > from the same individual to
          > do LOH analysis in dChip (normal first, then tumor).
          > Is your "standard"
          > sample from the same individual as tumor samples?
          >
          > Cheng
          >
          > -----Original Message-----
          > From: aiguo li [mailto:li9212001@...]
          > Sent: Wednesday, August 04, 2004 3:35 PM
          > To: dchip@yahoogroups.com
          > Subject: [dchip] Questions related to SNP analysis
          >
          > Dear all.
          >
          > I am trying to analyze my mapping 10K SNP data (5
          > tumor cell lines plus a standard cell line) using
          > dChip. In array list file I created a list file as
          > below:
          > U251 (tumor)
          > Standard
          > --standard separate--
          > Gli3AK (tumor)
          > Standard
          > --standard separate--
          > Hs683 (tumor)
          > Standard
          > --standard separate--
          > T98G (tumor)
          > Standard
          > --standard separate--
          > S127 (tumor)
          > standard
          > --standard separate--
          >
          > Then I did 'analysis -> chromosome'
          > The results I got from this analysis look strange
          > because all the LOH are identical across 5 cell
          > lines
          > (see attached .ppt file). I exported the SNP call
          > data and all the SNP calls across the cell lines are
          > identical also. I am not sure there is a buy in the
          > dChip or I did something wrong. Could somebody help
          > me figure this out?
          >
          > In addition, the color schema in the LOH display has
          > been changed. The menu said that the blue for LOH,
          > Yellow for retention, gray for uninformative, white
          > for no calls. Now in current display, there is no
          > gray color, and I am not sure what the red color
          > for.
          >
          >
          > Thanks in advance,
          >
          > Aiguo Li
          >
          >
          >
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        • Cheng Li
          Aiguo, Since you don t have paired normal samples for each tumor, you may look into signal analysis instead: X Zhao, C Li, JG Paez, K Chin, PA Janne, TH Chen,
          Message 4 of 4 , Aug 6, 2004
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            Aiguo,

             

            Since you don’t have paired normal samples for each tumor, you may look into signal analysis instead:

             

            X Zhao, C Li, JG Paez, K Chin, PA Jänne, TH Chen, L Girard, J Minna, D Christiani, C Leo, JW Gray, WR Sellers, M Meyerson (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Research. 64:3060-3071.

             

            In this case you need >5 normal samples to serve as reference.

             

            Cheng

             

            -----Original Message-----
            From: aiguo li [mailto:li9212001@...]
            Sent: Thursday, August 05, 2004 9:51 PM
            To: dchip@yahoogroups.com
            Subject: RE: [dchip] Questions related to SNP analysis

             

            Dear Dr. Li,

            I did tried to use the standard sample first in array
            list, then the tumor cell line followed.  However, it
            created a chromosome picture with all the lables as
            standards, i.e. each column in the heatmap is one
            standard cell line.  I am trying to compare the tumor
            cell lines here and thought it makes more sense that
            the sample list in the chromosome picture to have all
            the tumor cell lines as labels.  Am I right.

            It will be ideal to have blood DNA sample to compare
            with tumor tissue samples.  The standard sample here
            is from Affy's reference DNA which they claimed as a
            healthy man's DNA. 

            Thanks for your help.

            Aiguo Li
            --- Cheng Li <cli@...> wrote:

            > Aiguo,
            >
            > You have to have paired normal and tumor samples
            > from the same individual to
            > do LOH analysis in dChip (normal first, then tumor).
            > Is your "standard"
            > sample from the same individual as tumor samples?
            >
            > Cheng
            >
            > -----Original Message-----
            > From: aiguo li [mailto:li9212001@...]
            > Sent: Wednesday, August 04, 2004 3:35 PM
            > To: dchip@yahoogroups.com
            > Subject: [dchip] Questions related to SNP analysis
            >
            > Dear all.
            >
            > I am trying to analyze my mapping 10K SNP data (5
            > tumor cell lines plus a standard cell line) using
            > dChip.  In array list file I created a list file as
            > below:
            > U251 (tumor)
            > Standard
            > --standard separate--
            > Gli3AK (tumor)
            > Standard
            > --standard separate--
            > Hs683 (tumor)
            > Standard
            > --standard separate--
            > T98G (tumor)
            > Standard
            > --standard separate--
            > S127 (tumor)
            > standard
            > --standard separate--
            >
            > Then I did 'analysis -> chromosome'
            > The results I got from this analysis look strange
            > because all the LOH are identical across 5 cell
            > lines
            > (see attached .ppt file).  I exported the SNP call
            > data and all the SNP calls across the cell lines are
            > identical also.  I am not sure there is a buy in the
            > dChip or I did something wrong.  Could somebody help
            > me figure this out?
            >
            > In addition, the color schema in the LOH display has
            > been changed.  The menu said that the blue for LOH,
            > Yellow for retention, gray for uninformative, white
            > for no calls.  Now in current display, there is no
            > gray color, and I am not sure what the red color
            > for.
            >
            >
            > Thanks in advance,
            >
            > Aiguo Li
            >
            >
            >
            > __________________________________
            > Do you Yahoo!?
            > Yahoo! Mail is new and improved - Check it out!
            > http://promotions.yahoo.com/new_mail
            >
            >
            > Yahoo! Groups Sponsor
            > ADVERTISEMENT
            > click here
            >
            <http://us.ard.yahoo.com/SIG=129opjeb0/M=295196.4901138.6071305.3001176/D=gr
            >
            oups/S=1705713159:HM/EXP=1091734524/A=2128215/R=0/SIG=10se96mf6/*http://comp
            > anion.yahoo.com>
            >
            >
            >   _____
            >
            > Yahoo! Groups Links
            > *      To visit your group on the web, go to:
            >      
            href="http://groups.yahoo.com/group/dchip/">http://groups.yahoo.com/group/dchip/
            >
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            an email to:
            >       dchip-unsubscribe@yahoogroups.com
            >
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            >
            > *      Your use of Yahoo! Groups is subject
            to the Yahoo!
            > Terms of Service
            > <http://docs.yahoo.com/info/terms/>
            .
            >



                       
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