From jldxt9 at umkc.edu Mon May 1 06:40:45 2006 From: jldxt9 at umkc.edu (Dembsky, Joshua Lyman (UMKC-Student)) Date: Mon May 1 13:30:34 2006 Subject: [Genetic-linkage] Quick Genetics problem help Message-ID: <01FF7FBD8A8F884CBF07D3B4AB6566FB50910A@KC-MSX2.kc.umkc.edu> Hello all! I am a graduate student in Kansas City. I have having some problems understanding a basic genetics concept that I am hoping one of you can help me with. If you have two chromosomes each with an area that has been identified as an area of linkage for a particular trait, what are some of the reasons you can have different lod scores? For example, if two academic groups have identified an area of linkage of a trait, one study found an area on chromosome 7 with a lod score of 6.00 and another study found an area on chromosome 13 with a lod score of 5.20, how do you explain the different linkage results? Your assistance is greatly appreciated! jldxt9@umkc.edu Josh Dembsky University of Missouri-Kansas City From wijsman at u.washington.edu Tue May 2 00:28:14 2006 From: wijsman at u.washington.edu (E. Wijsman) Date: Tue May 2 09:19:13 2006 Subject: [Genetic-linkage] Re: Quick Genetics problem help In-Reply-To: References: Message-ID: The magnitude of the lod score and where it is high vs. low depends on a number of factors: 1) Heterogeneity. There can be genetic heterogeneity, and even slight nuances in how a sample was obtained can affect ones ability to detect linkage at one site vs. another. Differences in the phenotype used to collect the sample would be one indicator of possible heterogeneity. 2) The "Suarez" effect. When there is heterogeneity, replication of a result often requires a larger sample size than the initial finding, because the initial report is the best of several possiblities, while replication requires a strong score in the same location. Are there any hints of positive lod scores at the second site across studies? 3) Bad luck or other "problems" with the analysis. One or both could be wrong. There are lots of ways one can end up with false positive results, some of which result from bad (naive) applications of the analysis methods, and some of which simply reflect badk luck. ************************************************************************ Ellen M. Wijsman COURIER DELIVERY ADDRESS ONLY: Research Professor Ellen M. Wijsman Div. of Medical Genetics and 1914 N 34th St., suite 209 Dept. Biostatistics Seattle, WA 98103 BOX 357720, University of Washington (Note: Use this address Seattle, WA 98195-7720 EXACTLY as given above, and phone: (206) 543-8987 use ONLY for courier delivery!!!) fax: (206) 616-1973 email: wijsman@u.washington.edu web page: http://faculty.washington.edu/wijsman ************************************************************************* On Mon, 1 May 2006, Dembsky, Joshua Lyman (UMKC-Student) wrote: > Hello all! > > I am a graduate student in Kansas City. I have having some problems understanding a basic genetics concept that I am hoping one of you can help me with. > > If you have two chromosomes each with an area that has been identified as an area of linkage for a particular trait, what are some of the reasons you can have different lod scores? For example, if two academic groups have identified an area of linkage of a trait, one study found an area on chromosome 7 with a lod score of 6.00 and another study found an area on chromosome 13 with a lod score of 5.20, how do you explain the different linkage results? > > Your assistance is greatly appreciated! > jldxt9@umkc.edu > Josh Dembsky > University of Missouri-Kansas City > >