CHICAGO — A Naperville, Ill., doctor nationally known for offering alternative autism treatments has agreed to have her state medical license placed on probation for at least a year after state regulators accused her of subjecting two children to unwarranted, dangerous therapies.

Dr. Anjum Usman, whose treatment of a Chicago boy was featured in the Chicago Tribune’s 2009 “Dubious Medicine” investigation, will continue to practice but will take extra medical education classes and will submit 10 of her patients’ medical charts quarterly to Dr. Robert Charles Dumont, an integrative medicine physician who will assess them.

The Tribune investigation found that many alternative treatments for autism are unproven and risky, and are based on scientific research that is flawed, preliminary or misconstrued. The treatments, the Tribune found, amount to uncontrolled experimentation on vulnerable children. Some of these therapies were at the heart of the disciplinary case state medical authorities filed against Usman.

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The Illinois Department of Financial and Professional Regulation, which will oversee Usman’s probation, had alleged that Usman provided “medically unwarranted treatment that may potentially result in permanent disabling injuries” to the boy featured in the Tribune series and another child. In prescribing chelation, a hormone modulator and hyperbaric oxygen therapy, Usman subjected the Chicago boy to unproven treatments and demonstrated “extreme departure from rational medical judgment,” state medical regulators originally had charged.

Chelation leaches heavy metals from the body, though most toxicologists say the test commonly used to measure the metals in children with autism is meaningless and the treatment potentially harmful. Hyperbaric oxygen therapy involves encasing children in pressurized oxygen chambers normally used after scuba diving accidents. This unproven therapy is meant to reduce inflammation that experts say is little understood and may even be beneficial.

After years of legal wrangling over what constitutes ethical and appropriate care for children with autism — a disorder that mainstream medicine can’t fully explain or cure — state medical regulators softened the language they used to describe Usman’s care of pediatric patients.

In reaching a consent order with Usman, medical regulators alleged that Usman failed to disclose to her patients her financial interests in the company supplying the hyperbaric oxygen chambers and in the compounding pharmacy that filled prescriptions for her patients. The state said she also failed to obtain informed consent for the chelation therapy and did not keep adequate medical records for her patients.

Susan Hofer, a spokeswoman for the Department of Financial and Professional Regulation, said consent orders generally are more conciliatory than the state’s complaints. The consent order was approved in December.

Usman, who practices out of the True Health Medical Center in Naperville, neither admitted nor denied the state’s allegations in signing the consent order. She agreed to pay a $10,000 fine.

Usman attorney Jeff Levens, in an interview last week, said the consent agreement is good for Usman and her patients. “I commend Illinois because it realized that Dr. Usman is really a knowledgeable board-certified physician who has had remarkable success treating the medical issues that most autistic children have experienced,” he said. “They realized this and resolved this case in a way that won’t impact her ability to treat these patients.”

Levens noted that Usman suggested to the state the doctor who will be reviewing her charts.

“They’re not going to make judgments on the treatments or telling her how to practice medicine,” Levens said. “They’re going to make sure the files accurately reflect how the treatments are being done and that there are informed consents for every treatment.”

In earlier legal filings, Usman’s attorney said the charges were an abuse of the state’s police powers and that medical regulators should instead celebrate Usman as a visionary who is “willing to risk the disapproval of ‘mainstream’ medicine in order to afford parents options other than drugging their kids until they are old enough to institutionalize.”

Studies have shown that up to three-quarters of families with children with autism try alternative treatments, which can cost tens of thousands of dollars and are often not covered by insurance. Frustrated by mainstream medicine’s inability to help many children with autism, parents are drawn to these therapies based on online testimonials and presentations at conferences.

The state’s complaint against Usman alleged financial exploitation, which Levens denied. Medical regulators noted that Usman and the compounding pharmacy she owned together charged one girl’s parents $27,000 for care and treatments. Separately, Usman prescribed hyperbaric oxygen treatments.

Usman, the complaint alleged, told the girl’s father that her then-husband could sell him a hyperbaric oxygen chamber at a “better price,” and the child’s father did so. These arrangements “exploit patient R.S.’s parents for (Usman’s) own financial gain,” the state charged.

The Chicago boy whose treatment also was at issue in the state’s case was the subject of a bitter custody battle between his mother, who sought the therapies from Usman, and his father, who alleged the treatments harmed their son. The father, James Coman, filed a complaint with state medical authorities that prompted the case against Usman; he also sued Usman in Cook County Circuit Court in 2010 alleging she provided “dangerous and unnecessary experimental treatments.”

Coman’s attorney, David Wilzig, said he voluntarily dismissed the suit last year but intends to reinstate it at a later date.