Techniques

Question 1

How interpret vous from aCGH

Answer 1

Correct identification of VOUS can be adequately addressed through:

1) Choosing a level of resolution that balances sensitivity and specificity
2) Increased data sharing through the established database
3) Parental studies to determine whether CNV/s are de novo or inherited

Question 2

Advantages of using arrays over traditional karyotyping techniques

Answer 2

• Higher resolution detection
• Both CGH and SNP arrays detect amplifications and deletions, but SNP arrays have the ability to also detect mosaicism, extended regions of loss of heterozygosity, uniparental disomy, provide more accurate calculation of copy numbers and determine parental origin of de novo CNVs.
• DNA is extracted from uncultured cells therefore can be processed quicker (depend on lab workflow)
• Both array platforms and array analysis can be targeted, i.e., custom arrays or targeted arrays can be purchased depending on needs of the laboratory. Analysis of arrays can be targeted using software applications to consider only specific chromosomes or genomic regions. This would be increasingly important if using array analysis in parents of an affected proband as this approach would limit the chance of unexpected findings.
• Array files can be stored for quick retrieval and analysis in the future for consideration of newly identified genes
• Arrays iD cryptic del/dup in apparently balanced translocation using G-band analysis
• id new syndromes

Question 3

How many new syndromes detected by aCGH

Answer 3

• Many new microdeletion and microduplication syndromes have been identified in patients with DD; 211 microdeletion syndromes and 79 microduplication syndromes (Weise, A. 2012)

Question 4

How has the detection rate improved now using aCGH over g banding

Answer 4

Previous: 3%, now 15-20%

Question 5

Give brief overview of aCGH principal

Answer 5

Each array consists of thousands of immobilized DNA fragments adhered to a slide (array) surface, to allow the hybridization of complimentary sequences between these probes and target DNAs (patient and reference).
Test and reference DNA are labeled with different colors (Cy3 and Cy5) and hybridize competitively with the probes in the array. Differences in Cy3 and Cy5 fluorescence for each spot will indicate loss or gain of material in the respective chromosomal region. The log2 ratios of the test DNA (for example, Cy5) divided by the reference DNA (Cy3) are then plotted against the chromosome position.