New DNA chip improves prenatal diagnosis of genetic diseases

BY BIOCAT

Ever since the human genome was first published, there has been a constant influx of new discoveries regarding small chromosomal alterations that cause neurodevelopment syndromes with a bad prognosis, which were not previously detectable in prenatal tests but can now be diagnosed using new technology.

A joint research project conducted by the departments of Genetics, Gynecology and Obstetrics at the University Hospitals of Vall d’Hebron (Barcelona) and La Paz (Madrid) with Catalan biotechnology company qGenomics —a spin-off of the Center for Genomic Regulation in Barcelona and Pompeu Fabra University created in 2008— shows that DNA chips are significantly better for diagnosis than the current healthcare standard.

The study evaluated the technical reliability, detection, response time, and cost of the standard technology (cytogenetic karyotype) versus that of new technology like the MLPA (multiplex ligation-dependent probe amplification) or DNA chips. The study also looked at the level of acceptance of these new types of tests among a sample of 900 pregnant women (96%).

The results indicate that DNA chips are technically just as reliable as the current standard —with an error rate under 1%— and, moreover, can detect a higher percentage of disease-causing genetic alterations (6.2% of all cases), which is 34% higher than the current combination of karyotype and QF-PCR (4.6% of all cases). This detection rate is higher among high-risk patients (12.7%), but the high rate of alteration found in pregnancies that, according to current criteria, are considered low risk (4.2%) was surprising.

Overall, thus, the DNA chips are the most appropriate tool for diagnosing chromosomal alterations in a high-risk pregnancy.

The study, which was published on 6 October in the digital version of the international journal Human Genetics, was coordinated by Dr. Pérez-Jurado, professor of Genetics at Pompeu Fabra University and coordinator of the CIBERER, and funded by the Spanish National Healthcare Technology Evaluation Agency.

The current healthcare standard

According to data from the entities involved in this project, nearly one third of all pregnant women meet risk criteria (mother’s age, alterations on biochemical tests, family history, sonograms, etc.) for having a fetus with genetic alterations and are given an invasive test (amniocentesis or obtaining chorionic villi) to obtain and study the fetal chromosomes.

For more than 30 years, the established technological solution has been to carry out a cytogenetic karyotype (which in some communities is supplemented with a quick screening for alterations, called the QF-PCR), which consists of direct observation of tinted fetal chromosomes through a microscope. The karyotype is a slow and labor-intensive technique, which requires a great deal of highly trained human resources and, moreover, has a very limited resolution, which doesn’t allow for the detection of alterations of a considerable size (5-10Mb).