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Microarrays Make a Showing at European Society for Human Genetics Meeting

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The European Society for Human Genetics meeting, held May 25 to 28 in Strasbourg, France, was not just about karyotyping for single-gene disorders. Microarray-based research appeared to have penetrated numerous areas of genetics, with 18 different posters on a variety of topics using array technology. Following are summaries of several key abstracts:

• Researchers from Applied Bio-systems presented a poster that described a ligation/PCR-based assay, which uses a universal DNA microarray to identify products of SNP-specific assays. In this assay, sets of multiplex ligation probes that are specific to selected SNP loci interrogate the genomic DNA being analyzed, then the products are amplified in a PCR reaction. The assay uses about one nanogram of genomic DNA per SNP genotype, the researchers said. To demonstrate the assay, the researchers assembled multiplexes and tested them against 28 distinct samples from the CEPH (Center for the Study of Human Polymorphism) in France.

• A group from Leiden University Medical Center in the Netherlands and Dutch microarray company PamGene, of Den Bosch, presented a poster “Deletion/Duplication Detection In The 79-Exon DMD-Gene Using a Porous Microarray System.” The group used multiplex amplifiable probe hybridization to detect mutations in the DMD gene that cause Duchenne and Becker muscular dystrophy. This technique involves hybridizing probes to immobilized genomic DNA then recovering them with PCR. After amplifying the genomic DNA, the group hybridized the amplicons to probes on PamGene’s PamChip, a honeycomb-like microfluidic microarray where microchannels form the substrate for the probes. In this case, the probes were 60-mer oligonucleotides specific for exons of the gene being interrogated. The group fluorescently labeled the MAPH PCR products from controls and patient samples, then hybridized them to the array. By comparing the spot intensities between the patients and controls, they were able to detect deletions and duplications in both males and females, they said. Given the exon-specificity of the probes, the technique also detected one- and two- exon duplications missed by other techniques, the group said.

• Researchers from Otto-von-Guericke University, in Magdeburg, Germany, the University of Essen Medical School, in Germany, and Roche Diagnostics presented a study using Affymetrix microarrays to examine the role of the p53 gene in non-small cell lung carcinoma. Given that p53 is usually suppressed in this disease, the group wanted to see what would happen if they re-expressed it by adding wild type p53 to a cell-line of non-small cell lung carcinoma cells. They then interrogated these cells at different time points using Affymetrix arrays, as well as RT-PCR and western blots. They found that p53 actually arrested the cell cycle rather than inducing apoptosis, as previously thought. The changes in gene expression that resulted from this added p53 were reversible when the p53 was resilenced after 24 hours, but not after 48 hours.

• A group led by researchers at Germany’s GSF National Research Center for Environment and Health in Munich submitted a poster, “Expression profiling in patients with complex IV respiratory chain deficiencies.” The group designed a microarray with about 1,000 cDNAs thought to encode mitochondrial proteins. They then hybridized cDNAs from patient and control sample fibroblasts to the arrays. They were able to characterize expression patterns of these genes in nine patients with complex IV deficiencies, and to identify significant differences between the control and patient groups, as the patient group showed downregulation of mitochondrial protein synthesis and other genes. The researchers concluded that microarrays could help classify patients with mitochondrial disorders.

For additional information on the ESHG posters and presentations, go to http://www.medacad.org/ eshg/indexeshg.htm. — MMJ

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