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Thursday, October 22, 2015

Cytogenetic band explained

This is a review of the basic concept of cytoband in molecular/cell biology.

See the original link by Strachan, T. and Read, A.P. 1999. Human Molecular Genetics, 2nd ed. New York: John Wiley & Sons.
Each human chromosome has a short arm ("p" for "petit") and long arm ("q" for "queue"), separated by a centromere. The ends of the chromosome are called telomeres.
Each chromosome arm is divided into regions, or cytogenetic bands, that can be seen using a microscope and special stains. The cytogenetic bands are labeled p1, p2, p3, q1, q2, q3, etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere.
For example, the cytogenetic map location of the CFTR gene is 7q31.2, which indicates it is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2. The ends of the chromosomes are labeled ptel and qtel. For example, the notation 7qtel refers to the end of the long arm of chromosome 7.

How to get the cooridnates of the cytobands?

You can find it in the UCSC database:
wget | gunzip
head cytoBand.txt  
chr1    0   2300000 p36.33  gneg
chr1    2300000 5400000 p36.32  gpos25
chr1    5400000 7200000 p36.31  gneg
chr1    7200000 9200000 p36.23  gpos25
chr1    9200000 12700000    p36.22  gneg
chr1    12700000    16200000    p36.21  gpos50
chr1    16200000    20400000    p36.13  gneg
chr1    20400000    23900000    p36.12  gpos25
chr1    23900000    28000000    p36.11  gneg
chr1    28000000    30200000    p35.3   gpos25
If you have a list of genes with cooridnates and want to see which band each gene reside in, you can use bedtools or bioconductor GRanges package to find out.
Someone has written scripts for this kind of task as well. see here

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