Mo Costandi

Reseachers will use DNA microarrays to probe for autism genes


Researchers at 11 institutions in Boston, including MIT, will use a new gene chip, or DNA microarray to probe the human genome for the genetic basis of autism.

DNA microarrays are powerful new research tools manufactured using an integration of techniques from robotics, chemistry,  molecular biology and semiconductor fabrication. The researchers involved in the study will use the GeneChip® Human Mapping 500K Array,  manufactured by Affymetrix, a company based in Santa Clara, California.  It was Affymetrix who pioneered the manufacture of DNA microarrays and first made them commercially available in 1994. 

A microarray consists of millions of spots, referred to as cells, each containing thousands of short oligonucleotide probes. Each gene being analyzed is represented by a set of probes; the sequence of the perfect match oligo exactly matches that of the target gene, while the sequences of mismatch probes differ by a single nucleotide.  The exact location of the oligos representing a gene is known; each oligo is bound to a molecule of biotin. 

To fabricate the chip, millions of oligos are synthesized directly onto a coated quartz wafer (in silico synthesis), using semiconductor-based photolithography and solid phase chemical synthesis techniques. Synthesis of the probes onto the quartz substrate is done by a robot. Other types of gene chips are ‘spotted’ with oligo probes that have been prefabricated by polymerase chain reaction.

After a DNA sample has been added, the chip is then placed into a hybridization oven, which can hold up to 64 chips, so that base pairing between the probes on the chip and DNA molecules from the sample can take place.

After hybridization with a sample has taken place, the chip is washed and stained with a fluorescent probe in a fluidics station. An Affymetrix GeneScanner machine is then used to analyse the binding of biotin-tagged probes to target DNA sequences; the intensity of the fluorescent signal provides data on the levels of each transcript in the sample being analysed.

“This project will allow us to study the genome with an unprecedented level of detail,” says Mark Daly of the Broad Institute, who is taking part in the work.

The study will involve the analysis of DNA from 3,700 autistics and members of their families. Using the Affymetrix GeneChip, the researchers will be able to simultaneously probe the entire genomes of the participants for up to 500,000 genetic variations called single nucleotide polymorphisms (SNPs). The identification of SNPs which occur more frequently in autistics than in unaffected people should enable the isolation of genes implicated in the condition, and provide a better understanding of its genetic basis.