DNA chips exploring the expression of thousands of genes in parallel are widely used in   research. However, as soon as the role of a small number of genes will be recognized in the   development of a given disease, in the resistance to a particular drug, in the prognosis of a   treatment, a new class of diagnostics chips, with a set of most representative biomarkers   (DNA and proteins), will be developed to become standard laboratory tests.
Development of   biochip assays for widespread diseases like papilloma virus, cystic fibrosis, colorectal cancer,   AIDS and leukaemia will appear sooner or later. These techniques offer obvious exciting perspectives for a personalised and more efficient medicine.
They however suffer from severely limiting factors, the first being cost: equipment for preparing and reading chips is well above 100.000 Euros and chips cost hundreds of euros. High costs are due to the sophisticated reading devices, with incompressible mechanical and optical complexities, to costly reagents, to a few monopolistic US firms, building upon a few broad patents. The second limiting factor is the lack of sensitivity and robustness of the biological reactions themselves, which, despite sophisticated filtering and normalisation methods, lead sometimes to questionable results. High cost and sophistication of techniques will clearly hinder a widespread usage of the diagnostic tests based on biochips. Only some central labs will be equipped and will perform tests for peripheral hospitals and clinicians. The advantage is the centralisation of the databases or results, useful for further research. The drawbacks are the delays and the problematic sample preservation during shipping.

The INDIGO project aims at widespread biochip use by developing the essential elements of complete disposable lab-on-a-chip, integrated from the injection of the biological preparation to the production of the final measurements1.
It is based on a miniature and highly sensitive fluorescence-based biosensor comprising (i) a disposable biochip monolithically integrated on a CCD or CMOS detector; (ii) an integrated and readyto- use equipment for biochip hybridisation and reading. The biochip architecture and its expected performances are at the heart of the project. It replaces the ordinary slide supporting the DNA spots, and the complex, large and expensive hybridization and reading system, by a sandwich of well defined chemical and optical layers grafted onto a CMOS or CCD sensor. The upper layer of the INDIGO biochip performs the biological function. Biomolecules (such as DNA, proteins, antibodies) acting as probes are chemically grafted on a cm-size array of spots. A liquid sample containing the target molecules to be recognized, for instance extracted from a patient and tagged with fluorescent labels wets the biochip. The analytes selectively attach to specific spots, thus providing molecular identification. The fluorescence induced by a light source is directly detected by the lower sensor part of the chip. In-between, we find a finely tuned sandwich of optical layers with various roles such as light guidance, or rejection of the excitation light.