Hello, Philip, I believe that your observation about the resolution of the FISH method gets to the core of the issue. These days we obtain the locations of the cytoBands from NCBI. The description of how the bands were determined is at the bottom of the details page for the cytoBands track:
http://genome.ucsc.edu/cgi-bin/hgc?db=hg18&o=160900000&t=164400000&g=cytoBand&i=q26 The track was built using BAC clones, but it is still a FISH experiment and the resolution is limited by the microscopy. I would not put too much faith in the exact basepair used as the breakpoint between bands. Some specific value must be chosen for the software to display, but you can see what level of confidence to have in the endpoints when you look at the details for 6p26: Item: q26 Position: chr6:160900001-164400000 Band: 6q26 Genomic Size: 3500000 In fact, the entire table is mapped only to 100-kb resolution, approximately the size of the LPA gene. If the actual gene has been FISH-mapped to 6p26 (&/or 27), especially if it has been reported more than once, then that seems to me to be a better estimation of the location. best wishes and thanks for being a Browser user, --b0b kuhn ucsc genome bioinformatics group On 1/19/2012 4:14 AM, Philip Haycock wrote: > Hello > > I am trying to clarify the chromosomal location of my gene of interest > - the lipoprotein A (LPA) gene, which is located at > chr6:160,872,505-161,007,397 (h18). The gene appears to straddle > 6q25.3 and 6q26. However, when the gene was originally mapped, in 1988 > using cDNA probes, it was mapped to 6q26-27 (Hum Genet (1988) > 79:352-356). Apparently the cDNA probes mapped most intensely to q26 > and q27 but binding was also observed at q25.3. So, I´m assuming that > their resolution was poorer than whatever method is used by UCSC for > their chromosomal band information? In every paper I read about this > gene, the location is given as 6q26-27, so I´m not sure which band > position I should cite - the one given by UCSC or by the paper that > mapped the gene? Do you know why there is a discrepancy? > > Name of assembly: hg18 > Track: chromosomal band > Location: chr6:160,872,505-161,007,397 > > Many thanks for your kind assistance! > > > Regards > Philip > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
