WellPoint Inc.’s announcement of comparative-effectiveness research guidelines last week marks a new era for U.S. drugmakers.

The Indianapolis-based health insurer said it will use studies that compare the effectiveness of one drug against another as a complement to typical clinical-trial research that compares a drug against a placebo sugar pill.

Congress has also approved $4.1 billion in the past 15 months to fund comparative-effectiveness studies and a new agency that specializes in them. Now that private insurers like WellPoint are joining in, the United States could see a wave of head-to-head comparisons that have historically been rare in pharmaceuticals.

The goal of both the public and private initiatives is better health care at lower cost. WellPoint will use comparative-effectiveness research to help determine what percentage of the cost of a new drug it will pay for.

“Good comparative-effectiveness research study, along with clinical trial information and other peer-reviewed studies published in medical journals, can provide us the tools we need to help improve health outcomes and reduce costs for members of our affiliated health plans," Brian Sweet, WellPoint’s chief pharmacy officer, said in a statement.

Comparative-effectiveness research was a controversial topic during last year’s health reform debate, as many feared government and private health plans would use the information to intrude in the doctor-patient relationship.

But for pharmaceutical companies, it’s just the new reality, said Linda Heitzman, a life sciences consultant at Deloitte Consulting in Indianapolis.

“Just proving your product is better than nothing is not enough. You have to be able to demonstrate that your product is better than other products on the market,” she said, noting that the U.S. market is actually catching up to demands for comparative-effectiveness research already coming from government health plans in the United Kingdom and other European countries.

Heitzman said comparative-effectiveness research is both a challenge and an opportunity for drugmakers.

“Where comparative effectiveness hurts pharma companies is in broad-based treatments [such us cholesterol-fighters or blood pressure medicines]. Trying to have one more product in that market is a non-starter,” she said. “Companies are going to have to take a much riskier strategy.”

But drug companies can and are using blood and genetic testing to identify small groups of patients for which their drug is a big breakthrough in treatment. Proof of high effectiveness in a small group can get a drug market approval from regulators and favorable pricing from insurers like WellPoint.

Then, Heitzman said, drugmakers can build from there to get their drugs approved for more and more patients.