DAPI chromosome identification

Comments for chromosome identification scheme

General:

dashed boxes indicate groups of chromosomes with similar size or that might be particularly difficult to distinguish and should thus be classified by group

> or < chromosome arm greater or smaller than the one of an adjacent chromosome

Specific:

Chr. 1 Easy to identify, take care that the orientation is correct:

• end of the small arm lighter than the rest of the chromosome
• centromeric heterochromatin like an isosceles triangle with the base directed towards the long arm ()

Chr. 2 2nd largest chromosome (size similar to chr. 1), submetacentric

Chr. 3 3rd largest chromosome, metacentric

Chr. 4 vs chr. 5 same size

• chr. 4 darker than 5
• chr. 5 with light area at the end of the long chromosome arm

Chr. 6 darker long arm, lighter short arm with band/dots at the end.
(like "ears of a rabbit")

Chr. 7 3 distinct band visible, one at the short arm , two at teh long arm centromer slightly pronounced

Chr. X particularly difficult to distinguish from chr. 7 since it is almost of the same size. If the tumor or the normal genome originates from a male, the X-chromosomes usually shows a less intense fluorescence signal in the FITC and/or TRITC image (2 chr. 7 in the genomes compared to 1 X-chromosome)

Chr. 8 vs chr. 10 Both chromosomes particularly difficult to differentiate:

• chr. 8 usually darker than chr. 10
• chr. 10 show 3 bands on the long arm, in particular a subcentromeric band on the long arm comapred to 2 band on the long arm of chr. 8

Chr. 9 usually easy to identify:

• intense centromic heterochromatin (look for the suppression of the heterochromatin by the Cot1 DNA in the FITC and TRITC image)
• short arm of chromosome 9 is longer than the short arm of chr. 8 and chr. 10

Chr. 11 vs chr. 12 Chr. 11 show two bright dark band on the long and the short arm
(looks like a butterfly "papillon")
In contrast chr. 12 show only a distinct dark band on the long arm, the short arm of chr. 11 is longer than the one of chromosome 12
Chr. 8 to 12 are more or less of the same size, recommended order for classification (after chr. 6, 7 and X): chr. 11 chr. 12 chr. 9 chr. 8 chr. 10

Chr. 13 dark zone covering about 2/3 of the long arm

Chr. 14 vs chr. 15 difficult to differentiate from each other:

• the dark zone of chr. 15 extend more telomeric than the one of chr. 14
• Chr. 14 has a distinct band on the long arm ffollowed by a light zone before the telomeric chromosome end (chr. 15 may have a band too, however, there is usually no light zone distinguishible before the chromosome end)
• Chr. 15 shows a more prominent centromer (look for suppression in the FITC and TRITC image)

Chr. 16 easy to identify (smaller than chr. 9, greater than chr. 19, distinct centromeric heterochromatin, check orientation ("upside down")

Chr. 17 vs chr. 18 may be difficult to differentiate:

• Chr. 17´s short arm is longer than the short arm of chr. 18
• distinct band visible on the long arm and mostly on the short arm
• Chr. 18 darker than chr. 17, there are usually two distinct bands visible on the long arm

Chr. 19, chr. 20 difficult to differentiate:

• chr. 20 has a dark band on the short arm
• Centromeric heterochromatin of chr. 19 more pronounced than chr. 20 (look for suppression in the FITC and TRITC image)

Chr. 21, chr. 22 Together with Y-chromosome of similar size.

• Chr.21 has a more pronounced dark band on the long arm compared to chr. 22.
• The band takes the shape of a triangle compared to more distinct, rectangular-shaped staining pattern for chr. 22

Chr. Y usually easy to identify, carries a lot of heterochromatin almost the entire chromosome shows a suppression of the fluorescence signal in the FITC and TRITC image
the Y-chrosomsome is usually excluded from the evaluation of DNA gains or losses by CGH

CGH