[Genome] Recombination Rate Track

Thu Mar 8 15:05:53 PST 2007

Hello again, Erika,

     I have checked the build document for this track.  Before we build this 
track, we always build the STS Markers track (where we align the marker DNA to 
the new assembly).  Then, to start this recombRate track, we *do* use the same 
set of marker files for each subsequent human assembly (e.g. decode markers). 
These files give us centiMorgan data between markers, which does *not* change.

     Because we align the marker DNA to the new assembly, the coordinates for 
the new assembly are taken into account.  That is, we do *not* just lift the 
data from the previous human assembly.

     Here is the beginning of the decode markers file (which we use for all 
human assemblies):

 > head -5 decode_all
D1S468  1       4       4.46    3.54
D1S2845 1       6.43    6.47    6.39
D1S2893 1       6.43    6.47    6.39
D1S2660 1       7.09    7.78    6.4
D1S2132 1       8.06    8.66    7.46

     Be sure to let us know if this doesn't fully answer your question.

     For some reason, your email did not make it through our mail list filters 
so although you should see this answer in the archives, the original question 
will not appear there.

Regards,

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

Erika wrote:
> Hi,
> Thanks for your help with my previous question regarding the 
> recombination track "recombRate".  I have another related question 
> concerning the description of the methods for the track:  it states that 
> rates are calculated according to the following:
> 
> http://genome.ucsc.edu/cgi-bin/hgTables
> Recomb Rate Track Description
> 
> "Each base is assigned the recombination rate calculated by assuming a 
> linear genetic distance across the immediately flanking genetic markers. 
> The recombination rate assigned to each 1 Mb window is the average 
> recombination rate of the bases contained within the window."
> 
> I am wondering if the liftover utility was used to get the rates for 
> hg18 from earlier genome builds, for example, the deCODE data originally 
> placed the markers on a data release of human from Aug 2001.  Or, if the 
> liftover utility was used to translate the coordinates of the markers 
> first and then the 1Mb window regression was conducted afterwards on the 
> hg18 data to get the rates.  This would take into account any movement 
> of the markers from genome build changes, while the former method would 
> not, and subsequent recombination rates would be affected.  
> 
> Thank you very much for your help answering this question!
> - 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 <mailto:kvik at bx.psu.edu>
> 
> On Dec 20, 2006, at 3:40 PM, Ann Zweig wrote:
> 
>> 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 <mailto:kvik at bx.psu.edu>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu <mailto:Genome at soe.ucsc.edu>
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> 
> 