For more on Maverick's story and the controversy surrounding organ donations and the disabled, tune in to "Sanjay Gupta, MD" at 4:30 p.m. ET Saturday and 7:30 a.m. ET Sunday.

(CNN) -- The mood in the room was somber as five doctors, a nurse, and a social worker pulled their chairs around the table and turned to address Autumn Chenkus and Charlie Higgs.

The couple's 5-month-old son, Maverick, was down the hallway fighting for his life, and the doctors explained there was nothing they could do to help him.

"Take your baby home and love him for the time he has left," Chenkus and Higgs say the doctors told them.

They asked how long their son had left to live. About six months, they remember the doctors telling them.

Higgs wept, but Chenkus felt like she'd cried enough in the past five months for a lifetime. She was like a rock now, and after the meeting with the doctors she went directly back to her son's room without shedding a tear. In a chair next to his hospital crib, she opened her laptop and hoped the Internet might have clues for how to keep her baby alive.

Maverick was born with a severe heart defect, and even after two surgeries was in heart failure. Doctors had discussed a heart transplant with Maverick's parents, but at the meeting they said he didn't qualify for a new heart because he had a rare genetic defect that put him at a high risk for tumors and infections. A heart transplant would be too risky, they explained.

As Chenkus did her research on Maverick's genetic condition, she couldn't believe her eyes. Not one of the studies she read mentioned anything about an increased risk for tumors or infections. She e-mailed one study's author, and he confirmed she was right.

Now they'll do the transplant for sure, she told Maverick's father excitedly. Our son doesn't have to go home and die.

But it didn't matter. The doctors still refused to give Maverick a new heart.

At first, Maverick's mother was confused, but then she said it dawned on her: This supposed propensity for infections and tumors was a smokescreen.

She felt the real reason the doctors were denying their baby a life-saving transplant was that children with Maverick's genetic condition grow up to have disabilities. They don't want to give Maverick a heart because he won't grow up to be "normal," she thought.

At another meeting, she looked one of the doctors in the eye.

"You're discriminating," she said.

"That's ridiculous," she remembers the doctor responding.

"You don't want to waste a heart on him," Chenkus replied. "You're trying to play God, and you're lying to me."

What happened next is the subject of a federal investigation and has pitted a family against the very doctors who were supposed to save their baby's life.

"They're blowing smoke up my butt"

There are few hard and fast rules to guide doctors as they select who will get a transplant, effectively selecting who will live and who will die.

And there's no question some will die. Last year in the United States, 321 people, including 19 infants, lost their lives while waiting for a new heart. Right now, some 3,500 people await a heart transplant, and the situation is only getting more desperate as the waiting list grows but the number of donors remains about the same.

In the face of such scarcity, doctors try to select the patients most likely to get the longest life, and the highest quality of life, from a new heart.

"We have to be stewards of a very valuable resource. We want hearts to go to people who we think will benefit the most from them," said Dr. David Taylor, immediate past president of the International Society for Heart and Lung Transplantation.

These decisions are, to some extent, subjective, as doctors sometimes disagree with each other about who should get an organ. Over the years, medical ethicists and patient advocates have accused transplant physicians of discriminating against one group in particular: the disabled.

"We absolutely know this happens. It's a huge problem," said David Magnus, director of the Center for Biomedical Ethics at Stanford University. "It's real people sitting in a room making these tough decisions, and it's not surprising their own prejudices and biases influence them."

He points to the case of Amelia Rivera, a New Jersey girl with disabilities who was denied a kidney transplant last year, and to a survey he conducted in 2008 showing that more than four out of 10 pediatric transplant centers say they always or usually consider a child's neurodevelopmental delays when making a transplant decision, even though studies have found children with these delays fare just as well medically after a transplant as other children.

In the past when transplant doctors rejected patients with disabilities, they were often explicit about why.

"We do not feel that patients with Down syndrome are appropriate candidates for heart-lung transplantations," doctors wrote in 1995 to a patient named Sandra Jensen, according to a newspaper article at the time. An uproar ensued and Jensen got a new heart.

Now families and advocates say to avoid adverse public reaction, doctors are shrouding their transplant denials in medical excuses that some say are outright lies in order to avoid transplanting patients who will never be "normal."

Karen Corby said doctors have given her one reason after another for refusing to give a transplant to her son, Paul, 24, who has autism, and she doesn't believe any of them.

Corby, who reached out to three hospitals for a heart transplant for her son, said doctors have told her Paul wouldn't be able to manage the complicated drug regimen after his transplant. Corby, 47, explained that she lives with her son and directs his care, and if anything were to happen to her, he has "Team Paul," his sister and six aunts and uncles.

She was also told transplant medications could have potentially harmful interactions with Paul's psychiatric medications. She responded that Paul's psychiatrist said he could easily switch to other drugs.

Doctors also said they worried Paul might not be able to let anyone know if he felt sick after the transplant. Karen replied that her son, who graduated from high school and has taught himself to program computers in several languages, is completely verbal and had alerted her a few years earlier to subtle symptoms that ended up being a stroke.

"To be blunt, I feel like they're blowing smoke up my butt," she said.

Ari Ne'eman, president of the Autistic Self Advocacy Network, agreed that doctors sometimes "blow smoke" at patients with disabilities.

"Doctors give faux medical reasons. On further scrutiny, they don't stand up," said Ne'eman, who wrote a policy brief on the issue. "When someone with a disability is looking for a transplant, discrimination is the norm."

Transplant doctors said they don't discriminate against people with disabilities, but that disabilities need to be considered when making transplant decisions.

For example, Taylor, a heart transplant cardiologist at the Cleveland Clinic, said physicians must weigh whether a patient -- any patient -- is willing and able to follow complicated post-transplant medication directions. If the patient doesn't follow doctors' orders, the body could reject the new organ.

"If I were to go in front of the transplant committee, they'd want to stop and see if I'm some pompous doctor who's not going to listen to instructions," he said. "That has to be taken into account."

Maverick's story: New York

Early in her pregnancy, Chenkus and her boyfriend, Higgs, sat on the floor of a Barnes and Noble store poring through baby name books, unable to agree on a boy name.

Higgs suggested "Maverick," like Tom Cruise's fighter pilot character in the movie "Top Gun." Chenkus balked and kept searching.

But after a while, she warmed up to the unusual name and it was settled: Maverick Banks Higgs, his middle name for the street in the rural South Carolina town where Chenkus, now a hairstylist, and Higgs, now a lawyer, met when they were 12 years old.

At an ultrasound a few months later, Chenkus was grateful they had chosen a fighting name for their son. The scan showed he had a severe heart defect, and doctors gave the couple three options: terminate the pregnancy; give birth to Maverick and let him die, which would happen within days or weeks; or give him a series of three surgeries.

Maverick's parents chose the surgeries and met with doctors at New York-Presbyterian Hospital in Manhattan. At first they enjoyed a good relationship, but then, as Chenkus put it, things got ugly.

The couple said they wanted the hospital to talk to CNN about Maverick and agreed to waive their son's privacy rights, but a spokeswoman for New York-Presbyterian said it would be inappropriate to comment on Maverick's case.

The hospital issued this statement: "New York-Presbyterian's transplant teams have evaluated thousands of patients for lifesaving transplants over the past 40 years. These evaluations are conducted with compassion, and include the input of physicians, nurses, social workers and psychiatrists who bring the best ethical, medical and scientific principles to the process."

On September 29, 2012, Maverick was born with hypoplastic left heart syndrome. He had his first surgery when he was 4 days old at Morgan Stanley Children's Hospital, a part of the New York-Presbyterian system. The surgery didn't go as well as the doctors had hoped. By Christmas, Maverick was in the intensive care unit.

As Maverick's condition worsened, doctors decided to perform a second surgery several months ahead of schedule. That surgery didn't work, either.

Maverick was running out of options.

On March 18 of this year, the medical director of the hospital's transplant program sent Chenkus a letter saying Maverick was "an eligible transplant candidate." Maverick's parents were elated.

But two days later, everything changed.

On March 20, the doctors called Maverick's parents into a hospital conference room and told them they had just received the results of a genetic test showing Maverick had Coffin-Siris syndrome. Chenkus said the doctors went into detail about how because of this syndrome Maverick would grow up to have intellectual disabilities and developmental delays.

According to a recent study, babies with Coffin-Siris sit, walk, and speak later than other children on average. They have cognitive delays ranging from mild to severe and are often small for their age and have difficulty feeding, vision problems, and other issues. Fewer than 100 cases of Coffin-Siris have been reported worldwide, according to the report.

Two days later, the doctors convened another meeting and said Maverick was no longer a candidate for a transplant. According to Chenkus, they said children with Coffin-Siris have compromised immune systems and are at a high risk for tumors and infections. After the transplant, he would have to take drugs to suppress his immune system even further, making the transplant too risky, they said.

His medical record includes a note about the meeting, signed by Dr. Linda Addonizio, medical director of Presbyterian's pediatric cardiac transplant program.

"His genetic defect is associated with increased infections and tumors, which would be greatly magnified combined with the immunosuppression involved in transplantation," the note said. "I discussed that this does not mean we are giving up on Maverick, but trying to improve his heart failure as best as possible and get him to gain weight."

Chenkus disputes that version. She said during the meeting the doctors offered no hope at all for Maverick, telling his parents to love him for the time he had left.

According to Chenkus, the doctors never proposed a treatment plan to get her son's heart better, and for the rest of his stay at Presbyterian he didn't gain weight and remained in heart failure.

The doctors confirmed their decision with a letter.

"After careful completion of Maverick's medical history, it was determined that he does not qualify to be a heart transplant candidate at our institution at this time," Addonizio wrote. "This decision was based on the medical implications of his Coffin-Siris syndrome, which would limit his survival and potential benefit from transplantation."

The doctors gave Maverick's parents information about Coffin-Siris, which cited a study by Dr. Gijs Santen at Leiden University Medical Center in the Netherlands. Maverick's mother e-mailed Santen and asked if it was true that children with Coffin-Siris have compromised immune systems.

No, he wrote back, they don't.

"There is no objective problem with the immune system (in children with Coffin-Siris)," Santen wrote to Maverick's mother. "It is difficult to use infection risk as a reason not to perform a heart transplant."

CNN interviewed Santen and five other experts on Coffin-Siris, who explained that while some children with the syndrome have been reported to have frequent infections, that's not uncommon among children in general, even in ones without genetic disorders.

The six Coffin-Siris experts said children with the syndrome do not have suppressed immune systems or increased risk of infection or tumors and that in their opinion, Coffin-Siris isn't a valid reason to deny a patient a transplant.

"I've never seen a child with Coffin-Siris who was immune compromised," said Dr. John Carey, a pediatrician and geneticist at the University of Utah School of Medicine who has been studying the genetic syndrome for 36 years. "I don't think it's a valid reason to deny a transplant."

"(Coffin-Siris) is not a reason to say no to a transplant," said Dr. Grange Coffin, who first identified the syndrome in 1970, along with his colleague at the University of California, Dr. Evelyn Siris. "I would say it's wrong to do so."

Chenkus told her son's geneticist what she'd learned from Santen, hoping she'd change her mind and offer Maverick a new heart.

But she said the geneticist dismissed the Dutch doctor as a "junior researcher."

Dismayed, Chenkus asked Santen to reach out to Maverick's geneticist in New York directly. Santen sent the geneticist an e-mail saying the reason for denying Maverick the transplant "is not based on solid evidence," and that a more senior colleague of his agreed.

Presbyterian still wouldn't budge. They insisted they would not give Maverick a transplant, emphasizing that he had a compromised immune system.

On April 12, Chenkus called for another meeting with Maverick's doctors, thinking she might have one more chance at getting her baby a new heart.

She repeated what she'd learned from the Coffin-Siris experts, and asked them a question. Maverick was now 6 months old and had spent nearly his entire life in the hospital, a well-known source for germs, and he'd had multiple invasive procedures that would have given those germs a good opportunity to invade his body. If he had a compromised immune system, why had he never had a single infection, not even a case of the sniffles?

She said the doctors didn't answer her question, said they had another meeting to attend and walked out the door. Chenkus sat in the room, sobbing.

"I can't f***ing believe this," she thought to herself.

"The more I fought, the less they listened," she said. "But I knew that going home to die was not his fate."

Maverick's story: Philadelphia and Cleveland

Chenkus and Higgs realized they didn't have a chance of getting Maverick a transplant at New York-Presbyterian. They knew they had to move fast.

The couple reached out to three well-respected heart transplant centers: Children's Hospital of Philadelphia, the Cleveland Clinic and Boston Children's Hospital.

But they were to meet with only more disappointment.

On May 6, according to Maverick's mother, two of Maverick's doctors walked into his hospital room and said the doctors in Philadelphia had refused to give him a new heart for the same reason: that his Coffin-Siris syndrome meant he had a suppressed immune system.

But Chenkus said when she got on the phone with the Philadelphia doctor, he told a different story. According to her, he said Maverick's genetic problems played very little role in their decision making. He said they wouldn't give her son a transplant because of "the big picture."

Chenkus said she asked the doctor several times to explain what he meant by "the big picture," but she said his answers were vague, and he repeated that at a surgical conference a team of physicians had unanimously agreed that Maverick wasn't a candidate for transplantation. Chenkus asked the doctor to send her a copy of the written report from that conference.

Children's Hospital of Philadelphia declined to comment for this story about Maverick's case, but sent CNN a statement about their transplant policies in general.

"The Children's Hospital of Philadelphia does not disqualify potential transplant candidates on the basis of intellectual abilities, and, in fact, has transplanted many children with a wide range of disabilities, both physical and intellectual. CHOP is deeply committed to providing the best possible medical care to all children, including those with any form of disability," according to the statement.

"Patients with certain complex conditions display a predisposition to serious illnesses, which can be exacerbated by transplant-related care, such as immunosuppressive drugs, which are necessary to prevent rejection after transplant. These serious co-morbidities are severe impediments to organ transplant success. For some patients, transplantation simply serves to replace one serious medical situation with another," the statement continued.

"When faced with such significant countervailing negative medical risks, the transplant evaluation team must sometimes make the difficult decision to recommend against transplant at CHOP, despite knowing how devastating such decisions can be for any family who has come to us for help."

Two hospitals had now refused to give Maverick a new heart for completely different reasons, neither of which made sense to Maverick's parents. They continued to feel that their son's disability was the real reason for the denials, and they felt powerless to do anything about it.

Maverick's parents watched their son's health deteriorate, his heart function getting worse and worse. They pinned their hopes for their son's life on the Cleveland Clinic and Boston Children's Hospital.

A few days later, they received an e-mail from Dr. Gerard Boyle, medical director of pediatric heart failure and transplant services at the Cleveland Clinic, saying his hospital wouldn't give Maverick a transplant, either.

The doctor said Maverick was at "the highest risk of early death post-transplant" because he'd had two failed surgeries for his hypoplastic left heart syndrome. He e-mailed Chenkus a study saying one year after transplant, 70% of babies like Maverick were still alive, compared to the most successful group of babies, who had an 89% survival rate.

In addition, Boyle noted that Maverick had a gastronomy tube in his stomach for his feedings, considered a risk for infection, and they could close the tube, but then they would have to replace it after the transplant.

Chenkus wrote back hoping Boyle might reconsider, but once again her hopes were crushed.

"Transplantation in a child with a genetic defect is frought (sic) with uncertainties," the Cleveland Clinic doctor wrote to her. "We in the transplant community are charged with protecting a precious resource, a donated heart. We must do our best to assure this precious gift has the best chance of success in bringing a full life to its recipient."

He said the hospital "would be happy to offer management of his heart failure and to optimize his medical care to provide him as long a life as we are able," but he was adamant that Maverick was not a transplant candidate.

Boyle added he had heard through Maverick's cardiologist in New York that Chenkus was meeting with a physician at Boston Children's Hospital.

"I applaud you for that initiative," he wrote to Chenkus.

"We are obviously not alone in this determination as (Presbyterian) has made this clear and I assume Boston has as well knowing them as well as I do," he wrote.

He added that the Boston doctor was a "friend and colleague" of his. "It is my understanding that Boston has a similar stance on the question of transplant that I have outlined. That is no coincidence as we are all a small community of pediatric transplant specialist (sic) and are all aware of the current data and literature," he added.

Angie Kiska, a spokeswoman for the Cleveland Clinic, declined to comment for this story because Maverick was never a patient there. In an e-mail, Boyle said he is "not interested in participating in this story."

Time was now more critical than ever. Maverick's parents drove from New York to Boston Children's Hospital to save their son's life.

Maverick's story: Boston

Finally, in Boston, Chenkus and Higgs heard what they'd been hoping for. The doctors agreed to accept Maverick as a patient, and while they couldn't promise he would be eligible for a heart transplant, they didn't rule one out as the other hospitals had done.

On May 18, Maverick was taken by ambulance from New York to Boston, where for the next three weeks doctors tinkered with his medications. He responded quickly: His blood pressure, once sky high, went down more than 30 points and the level of oxygen in his blood, once dangerously low, rose dramatically.

Maverick, who had been lethargic and sleeping 18 hours a day toward the end of his hospital stay in New York, became more lively. He gained a pound in one month in Boston, after gaining no weight in his last three months in New York.

"He was a completely different baby," Chenkus said.

It was ironic, she thought, that as she watched the Boston doctors improve her son's health, she received the surgical discussion summary she had asked for from Children's Hospital of Philadelphia. It said they had no hope for her son.

"We regret that we do not have an intervention to offer Maverick that is more likely to help than harm him at this time," she read.

On June 7, Maverick's Boston doctors called a meeting. Once again, a group of physicians in white coats gathered around a conference table and turned to face Chenkus and Higgs. But this meeting was far different from the one in New York 11 weeks earlier.

The doctors reported that Maverick was doing so well he didn't need a transplant after all and could go home in a few weeks -- not to die, but to live.

They added that Maverick might need a heart transplant in the future, and if he did, his Coffin-Siris syndrome wouldn't stand in the way. He wasn't immune compromised and he didn't have a high risk for tumors.

After fighting for her child for so many months, Chenkus put her head down on the table and cried. It was her 32nd birthday, and it was the best present she could have received.

As Chenkus walked out of the meeting, she thanked hospital geneticist Dr. Amy Roberts and gave her a hug.

"I felt like the weight of the world had been taken off my shoulders," she said.

On June 21, Maverick was discharged from Boston Children's Hospital. He has been back a few times for short stays, but Chenkus said that he's thriving.

He turned 1 on September 29, can sit up by himself and can stand and jump if someone holds his hands. He loves to play with toys (a baby-sized keyboard is his favorite) and grabs his bottle.

Like other children his age, he's a social baby, interacting with those around him, and he shows particular affection for his parents and others who are close to him. He knows what he likes and doesn't like: He chows down on applesauce and mashed bananas, but spits his carrots back out at his mother.

A few weeks ago, he said his first word: "Mama."

Chenkus said she thinks the Boston doctors figured out a way to get her baby out of heart failure simply because they were willing to put forth the effort, even though he'll likely have disabilities.

"The difference between Boston and all the other hospitals is the way they cared -- the fact that they cared," she said.

'Maverick amazes me constantly'

In August, the U.S. Department of Health and Human Services' Office for Civil Rights agreed to investigate a complaint against New York Presbyterian Morgan Stanley Children's Hospital, Addonizio, and Dr. Wendy Chung, a geneticist at New York-Presbyterian. The complaint charges Maverick's civil rights were violated and that he was discriminated against based on his disability.

CNN reached out to both doctors for comment. Presbyterian Hospital spokeswoman Christina Stolfo declined to respond specifically to the complaint, and referred us back to the hospital's previous statement.

In the complaint, filed April 16 by Maverick's father, he recounts how the hospital refused to give their son a transplant and "then told us to take our son home and wait for him to die."

"The hospital first said the decision was based on Maverick being at a heightened risk for tumors and infection. We later learned that this was false information and that Maverick is not at a heightened risk for tumors or infection," Higgs wrote in the complaint.

"The real reason the hospital is refusing to list our son or consider him for a transplant is the hospital's perception that Maverick will be mentally and/or physically delayed. It is clear that the hospitals (sic) decision to deny Maverick a transplant is based on nothing more than this illegal discrimination," Maverick's father concluded.

Today, Maverick's mother starts to cry when she looks at her son and remembers how seven months ago his doctors said he had had about six months to live.

"I'm glad I didn't give up and I'm glad I didn't lose hope, and I'm glad I didn't listen to the doctors," she said. "Maverick amazes me constantly."