– The Mayo Clinic took one step closer to the brave new world of cancer treatments Tuesday but also strode squarely into a national debate over the spiraling cost of high-tech medical marvels.

The clinic unveiled a massive new building housing its proton beam therapy center, which will allow Mayo’s radiation oncologists to zap cancerous tumors with greater precision. Many researchers say the new therapy, projected to come online at Mayo in 2015, is an important tool to avoid the side effects of standard X-ray therapy in children with cancer and in adults who have tumors close to important structures like the spinal cord.

But the machines are so expensive that some medical centers have turned the beams on more routine and more common tumors, such as prostate cancer, to help pay for them. Mayo is building two proton therapy centers — one in Rochester and another at its campus in Arizona — at a cost of $380 million.

Exhibit A in what’s wrong

The two facilities were cited as “Exhibit A” in what’s wrong with American health care by Dr. Ezekiel J. Emanuel, chair of the University of Pennsylvania’s Department of Medical Ethics & Health Policy and a prominent health care commentator, in a 2012 column in the New York Times. Emanuel said there is no convincing evidence that proton beam therapy works better than cheaper treatments for more common cancers.

Dr. John Noseworthy, president and CEO of Mayo Clinic, responded in a letter saying the clinic built the facilities with its own money and philanthropic gifts to develop therapies that will provide more effective treatment without having to send patients outside of the Midwest. Mayo expects the Rochester center will treat about 1,200 patients a year.

The National Association for Proton Therapy says there are 14 operational proton centers and a dozen more in development.

Dr. Robert Foote, chair of Mayo’s radiation oncology department, said the clinic currently refers many people to centers in Massachusetts, Texas and Florida. But the therapy often takes a couple of months, and not everyone can afford to leave home for that long. Foote said his department sees 3,500 to 4,000 patients a year. “There’s a real need for proton beam therapy,” he said.

The centerpiece of Mayo’s center, called a Synchrotron, lies below ground in the Richard O. Jacobson Building, behind walls that are 8 feet thick. The blocklong building is named after an Iowa trucking, warehousing and packaging magnate who donated $100 million toward its construction.

The machine, built by Hi­tachi Ltd., creates a proton beam by splitting electrons away from hydrogen atoms. The protons are then accelerated using four 16-ton magnets up to about 60 percent of the speed of light, said Michael Herman, chair of Mayo’s division of medical physics.

The protons are fired down a tube that runs about the length of a football field. Along the way, more giant magnets bend the beam into one of four treatment rooms at a time. A 120-ton gantry hanging from the wall receives the beam and can be directed by radiation therapists, working in another room, at tumors inside the patient.

Painting tumor with radiation

The pencil-thin beam — the smallest of its type in the world — allows therapists to precisely “paint” a tumor with deadly radiation, killing the cells but not the surrounding tissue. Proton beam energy stops where it’s directed and does not exit the patient.

In contrast, X-ray therapy blasts tumors in a shotgun-like pattern, damaging surrounding tissue as well. It also passes through the body.

Proton therapy costs about 70 percent more than X-ray therapy, according to a 2012 study in the Journal of the National Cancer Institute. The study, using Medicare payment data for men treated for prostate cancer between 2008 and 2009, found modest advantages to proton therapy six months after surgery but no significant difference in postoperative side effects a year after surgery.

The lead author, Dr. James Yu, a radiation oncologist at Yale University, said Tuesday that he and his colleagues aren’t trashing proton therapy. “It would really be nice to have more comparative clinical data, is all we were trying to say,” Yu said. “It may be that truly transformative technologies are rolled out before we know 100 percent what to do with them.”

Under insurers’ scrutiny

Meantime, insurers are looking harder at proton therapy. Blue Shield of California cited the Yale study as the last straw in announcing last August that it would no longer pay for proton therapy in early-stage prostate treatments. Dr. Marcus Thygeson, a physician and chief health officer of the insurer, told the Los Angeles Times that expensive technologies were driving up the cost of health care when there’s no evidence of improved outcomes.

Minnesota’s largest insurer, Blue Cross and Blue Shield, said Tuesday that proton therapy is currently covered for treatment of localized prostate cancer and a few other clinical situations. But that may change. “We do want to point out that the National Comprehensive Cancer Network for Prostate Cancer currently takes the position that proton therapy is not recommended for routine use,” the insurer said.

Foote said the Yale study was limited by its use of Medicare data. “They don’t have real outcomes data. They just have bills,” he said.

The Yale study, he said, failed to consider the cost of treating secondary cancers that emerge sometimes years after surgery. Massachusetts General Hospital, which has had a proton therapy program for decades, found that proton beam therapy dramatically reduces the risk of radiation-induced cancers, Foote said.

“It does cost more to treat with radiation therapy,” Foote said. “We want to try to figure out what patients benefit, and where is it cost-effective.”