The federal government issued a major study Wednesday on the fates and sufferings of thousands of Native American children who were sent to more than 400 federal- and church-run boarding schools.

But among the report’s hundreds of pages, there’s not a word about what happened to Mary Kininnook.

The Tlingit girl died three days after her 14th birthday in a hospital bed at the Carlisle Indian Industrial School in Pennsylvania.

She remains missing. And her family in Alaska continues to look for her. They suspect she may lie among more than a dozen “unknowns” buried in the school cemetery, on the grounds of what is now the Army War College in Cumberland County.

“We’re missing her,” Eleanor Hadden, 69, Kininnook’s great-niece, said in a phone call from Alaska on Wednesday. “Mary, I’ll talk to her on occasion, let her know we’re trying to get to her.”

The new Interior Department study identified at least 53 marked and unmarked burial sites of students who died at the schools, which were defined by their effort to force Native children to assimilate into white society. Death brought on by disease, overwork, and hard labor was common.

The Carlisle school — the Carlisle experiment to “Kill the Indian, save the man” — hovers over the report, first mentioned on page one.

Included is a photo of the Carlisle student body and superintendent’s house, taken in about 1885 by John N. Choate, that has become the iconic image of the boarding-school era and of the modern demand for acknowledgment and accountability.

Another 1880s photo lends insight into how Carlisle operated, showing Chiricahua Apache children soon after they arrived.

Carlisle administrators often took before-and-after photographs of the students, the second depicting girls in dresses and boys in shirts and ties, their hair shorn, to show the school’s progress in turning Natives into white people.

At Carlisle and across the country, children were taken far from their families, banned from speaking their languages and cut off from their culture, a legacy that continues to torment tribes and families today.

Many children never returned home. The Interior Department identified more than 500 deaths at 19 schools, though that figure is doubtless a vast undercount.

About 180 children are buried at Carlisle alone, and a smaller but unknown number of students are interred in communities across central and eastern Pennsylvania. They were buried where they died, after Carlisle leaders placed them into domestic and farm service for white families under the school’s “outing” program.

The Interior Department said the ongoing count of deceased children could climb into the thousands or higher.

A second volume of the study will seek to examine what are often poorly maintained burial sites, the federal government’s financial investment, and the schools’ continuing impact on Indigenous communities, the department said.

On Wednesday Hadden dived into reading the report, saying the simple fact of its existence proved times were changing.

“People weren’t ready to hear the message of missing children, of children who didn’t return home,” she said. “Now to have the world hearing what’s going on is very encouraging.”

The federal government ran some schools itself and provided funding to Catholic, Protestant, and other churches to operate others, backing the system with laws and policies intended to “civilize” Native Americans.

The schools were part of a twin U.S. policy to assimilate Native Americans while taking their land. Providing basic education at schools like Carlisle was considered the cheapest and safest way of subduing Natives and helping whites acquire desirable property.

In releasing the study, Interior Secretary Deb Haaland, who is Laguna, called the family separation and intergenerational trauma inflicted by the schools both “heartbreaking and undeniable.”

School rules were “often enforced through punishment,” which included solitary confinement, flogging, withholding food, whipping, and slapping, the study said. The schools sometimes made older children punish younger children.

In modern America, it’s rare to find a Native family that wasn’t touched by boarding schools.

Haaland announced the inquiry last June, following the discovery of hundreds of unmarked graves at former schools in Canada. Her agency identified 408 schools known to have operated in 37 states or territories.

The seed of that system was planted in Pennsylvania, where former cavalry officer Richard Henry Pratt opened the nation’s first federally run, off-reservation boarding school at an old Army barracks in 1879.

For 40 years, his school worked to “civilize” American Indian children by eliminating their names, languages, religions, customs, and family bonds, forcing them to speak English and teaching them rudimentary job skills.

Beatings were common punishment, and epidemics killed boys and girls. More than 10,000 children passed through Carlisle before it closed in 1918.

During the last five years, tribes have traveled to Carlisle to retrieve the remains of their lost children, carrying them back to their ancestral homelands for reburial.

Those disinterments have bolstered allegations that the original burials were sloppily handled, that white administrators cared little for Native students.

In July, after years of research and effort, the Rosebud Sioux claimed the remains of nine tribal boys and girls and escorted them home to the vast grasslands of their South Dakota reservation.

That disinterment produced disquieting findings.

A second set of remains was found in the same grave as Maud, also called Little Girl, the 16-year-old daughter of Chief Swift Bear. The Army said another grave contained an additional second vertebra, a bone that sits high in the neck.

That meant four cemetery disinterments had produced three unidentified sets of remains.

In 2017 a Northern Arapaho child, Little Plume, was missing from his grave. Buried there instead were two unknown remains, which were reinterred. Little Plume’s remains were later located and returned to his family in Wyoming.

The Interior Department said it was difficult to account for the whereabouts of deceased children, because records weren’t always kept.

Native leaders have asked: How could schools lose track of children?

At Carlisle, original, wooden grave markers rotted into the ground. In 1927 the cemetery was moved to its current location near the campus front gate.

Hadden, an Alaska Native, believes Mary Kininnook may lie under one of the stones marked “Unknown.”

The school took children from everywhere. The Alaskan children generally sailed 700 miles to a Pacific port like Seattle, then moved 2,700 more miles by train to Carlisle.

Kininnook came to the school in 1903. Records show she died on Dec. 28, 1908, and was buried there, though none of the headstones bear her name.

Hadden continues to push the Army for answers, and believes a formal effort to identify the “unknown” children could begin in 2024.

Hadden’s mother, who died recently, first began searching for Mary in 1967. Hadden too has spent years looking, making multiple trips from Alaska to Pennsylvania.

“My mom did all she could while she could,” Hadden said on Wednesday, “and I’m trying to finish it.”

The Associated Press contributed to this article.