How to read Cytogenetic Formulas after Array-CGH

Reading and understanding Cytogenetic Formulas after ARRAY-CGH may be complex.

DNA helix

Under normal circumstances each pair of chromosomes has individual characteristics: they have a specific size (length)which is measured in the number of basepairs and a specific distribution of genes within each chromosome. Chromosomes of the same pair have to be identical in their size and specific for each pair of genes. For example, the largest human chromosome – chromosome 1 – has 249 million basepairs (Mb). Like highways have mileposts, similar “mileposts” exist within each chromosome. Molecular cytogenetics is a method using specific probes to test for the presence (or absence) of these “mileposts”. As a result (if there are some abnormalities within the chromosome) these probes note the absence (or excessive presence) of several “mileposts”.

The automatic system checking each segment of the chromosome may show, for example, that a segment of the long arm of chromosome 13 between basepairs 106647859 and 107257158 is absent. The cytogenetic formula (see CDO database registry for examples) for such an abnormality will be “arr[hg 19] 13q33.2q33.3 (106647859-107257158)x1”. [13q33.2q33.3 in this formula shows which chromosome is affected and the cytobands within this chromosome]. “Hg 19” is a symbol indicating which version of the human genome [indicating the position of the genes] was used; “hg 19” (or CRCh37) is the most contemporary version.

Symbol “x1” indicates that only one copy of the genetic material of this segment is present in the testing sample. If a deletion affects the X-chromosome in males (they have only one copy of the X-chromosome) the symbol after the formula will be “x0”. The same symbol “x0” may also be seen if the patient has a homozygous deletion ( a deletion affecting both homologous chromosomes). If however any segment is present in 3 copies (instead of normal two) the symbol “x3” will be placed after formula; “x4” will be used if there are 4 copies of the specific segment.

Some patients may be mosaics usually having two clones: one normal and one with an abnormality. In such cases the index after the formula may indicate the percentage of an abnormal clone. Formula “arr[hg 19] 1p36.33p36.32 (834-3018)x 2.5” indicates that both normal and trisomic clones are present in equal ratios. The same formula with symbol “x2.2” indicates that the abnormal clone is present only in ~20% of the cells.

Sometimes a patient may have abnormalities in 2 chromosomes (or even more): for example deletions in different chromosomes. In that case the formula will look like “arr[hg 19] 1p36.33p36.32 (834-3018)x1; 13q33.2q33.3 (106647859-107257158)x1”. Two (or more) abnormalities within one chromosome are also possible. For example, the formula “arr[hg 19] 15q13.1 (29096386-29498094)x1; 15q22.31 (64242830-65570261)x3” means that the patient has a deletion in the segment 15q13 associated with a duplication in the segment 15q22.31.

Basically, a deletion or duplication of large segments presumes the involvement of a large number of genes, and as a result worse clinical consequences. However, the distribution of genes on chromosomes is very unequal: there are segments with numerous genes within a small segment (for example, the tip of the short arm of chromosome 16) and there are segments which contain very few genes (“gene deserts”). Moreover, not all genes are known to cause clinical problems.

Sometimes a very small deletion or duplication may be harmful, but in other cases a deletion in 1-2 Mb may be relatively benign.

The formula itself obtained upon examination does not include a list of duplicated (or lost) genes. However because each gene has a strongly predetermined position in the chromosome it may be concluded that, for example, a deletion in the long arm of chromosome 2 “arr[hg 19] 2q24.3q31.1 (164807751-170315525)x1” presumes the loss of the GALNT3, TTC21B, SCN1A, SCN9A, ABCB11, LRP2 and SCN2A genes.

It has to be noted that a loss of a gene does not guarantee that it will cause any abnormalities. Only some genes are related to human disorders (the so-called OMIM genes), and a significant part of the OMIM genes cause disorders only if both copies of the gene are affected. Most patients with chromosomal deletions have normal copies of the homologous genes on another chromosome. From another side sometimes we can see new publications showing a “morbid” status of some genes, previously not included in OMIM-list. The situation becomes even more complex when a gene is duplicated: currently there are only a few instances showing strong evidence of pathology caused by a duplication of a specific gene.

In all cases the clinical significance of any deletion or duplication should be discussed with a geneticist or genetic counselor.

Dr. Iosif Lurie, M.D., PhD Medical Geneticist, CDO Medical Advisor