Using PamGene's 3-Dimensional, Flow-Through Microarray Platform we present a new format for MAPH: Microarray MAPH, using PMP22 gene dosage measurements in normal controls and CMT1A patients as an example.
We undertook high-resolution whole genome profiling using several Affymetrix microarray platforms to cross reference gene dosage, expression and DNA methylation changes in an isogenic, paired cell lines based on the human MDA-MB-468 breadenocarcinomanoma cell line [18], [22], [23].
In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A).
Statistical analysis of microarray data revealed a major gene dosage effect: for the three-copy genes as well as for a 2 Mb segment from mouse chromosome 12 that we show for the first time as being deleted in the Ts1Cje mice.
In addition to detecting changes in gene dosage, oligonucleotide-containing microarrays can also be used to determine whether a diploid strain is heterozygous or homozygous for a SNP (Gresham et al. 2008).
In summary, of the 15 chromosome 5q31.2 genes with detectable expression by microarray, none was consistently expressed out of proportion to gene dosage.
This is because variations in gene dosage can complicate the interpretation of microarray data and may also differentially contribute to the developmental or tumour phenotype [13].
The slightly lower gene dosage differences for the RT-qPCR and microarray analyses compared to the doubling time based estimates (cf. Figure 1 and 2 with Table 2) indicate an average replication speed that may exceed 1000 nt/s.
Using datasets on well established models such as worm and mouse, they reach the conclusion that apparent compensation of gene dosage differences between the X chromosome and autosomes may simply reflect an artifact of the microarray technique.
The microarray data has already been exploited to show that gene expression is a major determinant of the evolution of gene dosage [ 18].
