Detailed chromosome analysis – array

The project aims to provide parents and doctors with more reliable information what to expect for a patient with chromosome 6 abnormalities. It therefore focuses on the effect of chromosome 6 deletions and duplications on the development, health and clinical features of an individual. In order to determine this effect as accurately as possible, we need the results of a detailed chromosome analysis.

What is detailed chromosome analysis?

Detailed chromosome analysis tells us the exact size of the deletion or duplication much more precisely than the older method, karyotyping, does.

Why can only patients with a detailed chromosome analysis participate?

Unfortunately, patients without a detailed chromosome analysis cannot participate. This is because we need this detailed genetic information to identify which parts of chromosome 6 are responsible for specific birth defects and developmental delays.

How are the different techniques for detailed chromosome analysis called?

There are a lot of names being used for detailed chromosome analysis. The most widely used are array-CGH, microarray, oligo array, SNP array, or whole genome array (WGA).

How can you read a chromosome analysis report?

You can find some information about interpreting the results of detailed chromosome analysis below.

What if you do not have a copy of the chromosome analysis?

If you don’t have a copy of the report, you can ask your geneticist or paediatrician for a copy using this template (example request). You can then join the study after you have received a copy of the detailed chromosome analysis.

What if a detailed chromosome analysis has not been done yet?

You can discuss the options with your own or your child’s general practitioner, geneticist or paediatrician. It may be possible to get a detailed chromosome analysis performed. However, a detailed chromosome analysis is not possible in all countries and it may not be paid for by your health insurance.

Understanding the results of detailed chromosome analysis

All array reports present the result in the same format, according to international guidelines. The formal results are likely to read something like the following:

arr [hg19] 6q25.1q25.3 (151,997,435-158,227,963)x1

Below we try to explain what those letters and numbers mean.

Arr      The analysis was done by an array (arr) technique; this can be, for example, an array CGH or SNP array.

hg19   ‘Human Genome build 19’. This is the ‘language’ in which the report is written. The number refers to the reference DNA sequence to which the DNA of your child was compared. As more information about the human genome becomes available, new ‘builds’ of the genome are made (the most recent is hg19 and in the future hg20/hg38 will be used). In some reports the old name Genome Reference Consortium (GRCh) is used; GRCh36 = hg18, GRCh37 = hg19. The different genome builds can be translated to the most recent genome build (hg19).

6q25.1q25.3

The chromosome involved is number 6, and the chromosomal bands involved are numbered 25.1 up to 25.3 in the long (q) (or short (p)) arm of the chromosome.

(151,997,435-158,227,963)x1

DNA is a long string of building blocks called base pairs. All the base pairs of a chromosome are numbered from the top of the chromosome, the top end of the short (p) arm, to the bottom of the chromosome, the bottom end of the long (q) arm.

In this example the DNA between base pairs 151,997,435 and 158,227,963 is only present one time (x1) instead of the normal two copies. This is, therefore, a deletion. In the case of a duplication, there are three copies (x3).

6.2 Mb

For calculating the size of the deletion, the lowest base pair number (see above) is subtracted from the highest base pair number. In this example the size is 6,230,528, or approximately 6.2 million base pairs, abbreviated as 6.2 Mb. This is the number of base pairs that are deleted (or duplicated if the results says x3).