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All theory, dear friend, is grey and the golden tree of life springs ever green,…

You are absolutely right, Mephistopheles. That’s why we uploaded exomes of a CEU Trio to the Demo account, so that you can play around with the new segregation filter! It is a well described Trio from the 1000 genomes paper: NA12787 is the daughter, NA12892 is the mother and NA12791 is the father. In the exome of the daughter we spiked in one somatic cancer mutation that’s causing melanoma and one rare homozygous mutation that is causing mental retardation and an elevated serum alkaline phosphatase. Now, try out the following:
Create a PED file for these three exomes (Manage Files -> Create Collection). Set parents to status “unaffected” and the daughter to status “affected”. Then go to the filtering menue. Here, VCF files with PED information will be listed separately. For these files the inheritance filter offers now the possibility for recessive and dominant segregation. Did you find the disease causing mutations?

Hint: you could also add a frequency cutoff and the GPI pathway gene set for finding the recessive mutation or the comprehensive cancer panel for the dominant mutation. 

2 Comments

  1. pablo says:

    Hi gene talk,

    that´s what i have found

    1 27121547 rs139073416 PIGV [Gene with OMIM Entry] C A/C A/C A/A missense

    Can we do the same for PCH?

    All the best

    Pablo

  2. Peter says:

    And the winner’s virtual ipad goes to Pablo! He solved the case! congratulations! It is indeed hyperphosphatasia syndrome with mental retardation, caused by a mutation in PIGV.

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