DNA Analysis and OMICS data

Question 1

What does CGH array mean and when is it used?

Answer 1

CGH array= Comparative Genomic Hybridization

Using CGH array, a profile can be identified that classifies hereditary cancers for example. In short, it makes a special profile on chromosome level. You look at deletions, losses, gains in chromosomes. This is different than normal micro array. Micro array uses cDNA to look at gene expression whereas CGH uses DNA

Question 2

Can insertions and deletions in chromosomes lead to copy number variations (CNV)?

Answer 2

Yes because normally, there are 2 copies of genes, so if there is an insertion or a deletion of a gene, the CNV will change

Question 3

What tissue must be isolated from a patient with a lung tumor to detect deletions with ARRAY CGH, and what will be the reference

Answer 3

The tumor itself and a bit of (healthy) lung tissue has to be isolated. The normal/ healthy tissue will be the reference.

Question 4

How is the quantity of DNA compared to the samples while using CGH?

Answer 4

The DNA/ tissue is labeled with fluorescence (reg/blue/green) and then that can be compared with microarray to see a difference in gene expression

Question 5

What is the difference between homozygous- and heterozygous deletion

Answer 5

With a homozygous deletion, gene is from both chromosomes deleted whereas with a heterozygous deletion, the gene is from 1 chromosome deleted

Question 6

Can you validate CGH results with MLPA

Answer 6

Yes

Question 7

What is a Dotplot when when can you use it for

Answer 7

Dotplot is nice to visualize the single cell RNA sequence results and gene expression and cluster them. It gives info (by colour) for the average expression level across cells within the cluster and precentage (by size dot) of the cell express that gene within the cluster