Table 1.

Comparison between Multiplex Ligation-dependent Probe Amplification (MLPA) Assay and other methods for the detection of gene deletions/duplications.

Method	Advantages	Disadvantages
MLPA	Detects small rearrangements Up to 40 targets High throughput Low cost	Cannot detect copy neutral loss of heterozygosity. May have problems with mosaicism, tumor heterogeneity, or contamination with normal cells.
FISH	Detects balanced rearrangements Detects mosaicism Detects tumor heterogeneity Can quantify multiple copies	Cannot detect copy neutral loss of heterozygosity. Cannot detect small rearrangements (e.g., deletions <100 kb or duplications >500 kb). Limited number of targets and throughput.
Quantitative/Sq-PCR	Detects small rearrangements and even point mutations Can quantify multiple copies Low cost	Test optimization and efficiency is a concern. Limited number of targets. May have problems with mosaicism, tumor heterogeneity, or contamination with normal cells.
Southern blot	Detects small rearrangements Detects mosaicism	Cannot detect copy neutral loss of heterozygosity. Not quantitative. Laborious and time consuming Limited number of targets and throughput.
CGH array	Can detect very small rearrangements Can probe entire genome Low cost per data point	Cannot detect copy neutral loss of heterozygosity. Costly equipment and reagents Low throughput
SNP array	Can detect copy neutral loss or heterozygosity Can probe entire genome Low cost per data point	Cannot detect small rearrangements (e.g., deletions or duplications <100 kb). Costly equipment and reagents Low throughput