Eli Lilly and Co. and General Electric Co. say they’ve made a breakthrough in cancer research that could help Lilly cut the size and cost of its clinical trials.

The two companies, based in Indianapolis and New York, respectively, said they have developed a new protein mapping technique that allows scientists to observe 25 different biomarkers produced by cancer tumors at one time.

Currently, scientists can see only one or two biomarkers in a cancer tumor.

Biomarkers are proteins made by human cells. As their levels rise or fall in a person’s body, these proteins can indicate the presence of a disease. For example, high levels of hemoglobin A1C indicate diabetes.

Lilly measures how biomarkers respond to its drugs as a shortcut to determining if the drugs are working or not.

The technology, developed over the last two years with GE, will help Lilly predict in advance which patients are most likely to benefit from an experimental drug. By screening patients with the new tool, Lilly can test a drug on fewer patients, saving time and money.

Lilly will apply the technology it developed with GE to its clinical trials in summer 2010. Lilly has 20 different cancer drugs in clinical trials, roughly a third of its entire experimental pipeline.

Lilly has been working feverishly to speed up and reduce costs on its clinical trials. As of December, the company said its average cost to bring a drug to market had fallen from $1.2 billion in 2007 to $1 billion. The company wants to have an average cost of $800 million.

It needs such savings because Lilly is trying to move 61 different drugs through clinical trials, an enormously costly undertaking.

It needs to bring new drugs to market because several of its top-selling drugs will lose patent protection from 2010-2014, which will sap more than 50 percent of Lilly’s current sales.

To date, the new technology has been tested successfully on colon and prostate cancer tissue samples. GE and Lilly scientists think it can be applied to all types of cancer.