[Genome] (no subject)

[Ann Zweig]

Hello Erika,

     The Recombination Rate Track displays data from three contributors: deCODE, 
Marshfield, and Genethon.  The following details are from the Recombination Rate 
track description (accessed by clicking on the hyper link in the track controls 
located under the browser display):

* The deCODE genetic map was created at deCODE Genetics and is based on 5,136 
microsatellite markers for 146 families with a total of 1,257 meiotic events.
Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., 
Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G., 
Shlien, A., Palsson, S.T., Frigge, M.L., Thorgeirsson, T.E., Gulcher, J.R., and 
Stefansson, K. A high-resolution recombination map of the human genome, Nature 
Genetics, 31(3), 241-247 (2002).

* The Marshfield genetic map was created at the Center for Medical Genetics and 
is based on 8,325 short tandem repeat polymorphisms (STRPs) for 8 CEPH families 
consisting of 134 individuals with 186 meioses.
Broman, K.W., Murray, J.C., Sheffield, V.C., White, R.L. and Weber, J.L. 
Comprehensive human genetic maps: Individual and sex-specific variation in 
recombination, American Journal of Human Genetics 63, 861-689 (1998).

*  The Genethon genetic map was created at Genethon and is based on 5,264 
microsatellites for 8 CEPH families consisting of 134 individuals with 186 meioses.
Dib, C., Faure, S., Fizames, C., Samson, D., Drouot, N., Vignal, A., Millasseau, 
P., Marc, S., Hazan, J., Seboun, E., Lathrop, M., Gyapay, G., Morissette, J., 
and Weissenbach, J. A comprehensive genetic map of the human genome based on 
5,264 microsatellites, Nature 380(6570), 152-154 (1996).


     Furthermore, each of the three contributors provides three sets of rates: 
Female Distances, Male Distances, and Sex Averaged Distances.  So for each row 
in the table, you will see nine rates listed.  Quite often, if you see a rate of 
0 for two contributors, you will see a small recombination rate for the other 
contributor.  For example in this location on chrX:74,000,001-75,000,000:

deCODE Sex-Averaged Rate: 0.0 cM/Mb
deCODE Female Rate: 0.0 cM/Mb
deCODE Male Rate: 0.0 cM/Mb
Marshfield Sex-Averaged Rate: 0.0 cM/Mb
Marshfield Female Rate: 0.0 cM/Mb
Marshfield Male Rate: 0.0 cM/Mb
Genethon Sex-Averaged Rate: 0.4 cM/Mb
Genethon Female Rate: 0.4 cM/Mb
Genethon Male Rate: 0.0 cM/Mb


     You will need to decide for yourself which set of data best suits your 
purposes, but because the data are calculated for adjacent markers, there would 
be no region in genome for which data are missing.  A value of zero represents 
no (or less than 0.1 cM/Mb) recombination observed in the data sets.

     I hope this helps you understand the data.  Please be sure to write back to 
the list if you have more questions.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Erika wrote:
> Dear colleagues at Santa Cruz Genome Browser,
> 
> I am interested in using the recombination data from the Table  
> Browser for Human Mar 2006, track =Recomb Rate , table=recombRate.
> 
>  From a previous posting on Jul 22, 2004 I noticed that UCSC  
> calculates a rate for all maps for all windows reported:
> For all other windows, we report a rate for all maps.  The absence of
> markers in a particular window does not affect our method of  
> calculation.
> A description of this method can be seen on the description page for the
> track.
> 
> However, I noticed that there are 1Mb intervals for which the rates  
> are indicated as zero.  I would like to know if this is a true rate  
> of zero i.e. there is no recombination in this interval or if this  
> indicates no data.
> 
> Thanks for your help clarifying this!
> - Erika
> 
> **********************************************************
> E.M. Kvikstad
> Academic Computing Fellow
> IGDP Genetics
> Center for Comparative Genomics and Bioinformatics
> The Pennsylvania State University
> 208 Mueller Lab
> University Park, PA 16802
> (814) 863-2185
> kvik at bx.psu.edu
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome