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From |
Neil Shephard <nshephard@gmail.com> |

To |
statalist@hsphsun2.harvard.edu |

Subject |
Re: st: Gene-incidence question/simulation |

Date |
Mon, 23 Mar 2009 13:06:49 +0000 |

On Mon, Mar 23, 2009 at 12:32 PM, moleps islon <moleps2@gmail.com> wrote: > Thanks for the input Neil. For my use I believe I can disregard the > genetic status of it all (ie recessive, dominant etc.,etc) and just > treat it as a risk factor, either you have it or you dont. I'm not > modeling the inheritance and we dont have anyone related in our > sample. That is implicitly a dominant model. However, you might observe a dosage effect in relation to penetrance. Someone who is heterozygous and carries one copy of the risk allele may have a penetrance that differs from someone who is homozygous for the risk allele (i.e. carries two copies). You often also find that there is a penetrance associated with the wild-type (i.e. zero copies of the risk allele) too. > We know our 217 patients have 11 cancers. What we dont know > is how many have the risk factor, but we know the general incidence of > cancer in people without the risk factor to be 6/100000. This is where molecular genetics steps into the arena, and you would be best served a) genotyping your samples yourself; b) searching public databases for estimates of the allele frequency in similar populations. > By simulating > a random number of random people in the sample having the riskfactor I > can compare the random allocation of the risk factor in the sample. > Next, by finding the random samples resulting in incidence rates of > 6/100000 in the risk factor negative group I can use those samples to > infer the incidence of the risk factor because the set has produced a > result within the constraints of the problem. That just seems like a circular reasoning to me, and it won't necessarily reflect the true allele frequency of the risk allele in the population as a whole. Regards Neil -- "The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data." ~ John Tukey (1986), "Sunset salvo". The American Statistician 40(1). Email - nshephard@gmail.com Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

**References**:**st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*Austin Nichols <austinnichols@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*Neil Shephard <nshephard@gmail.com>

**Re: st: Gene-incidence question/simulation***From:*moleps islon <moleps2@gmail.com>

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