Amid the many emotional reactions that followed was one particularly painful question: What should be done with the juvenile remains in the ground?

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A few years ago, an amateur historian shook Ireland with a ghastly allegation: Hundreds of bodies of young children appeared to have been buried in an abandoned septic system by Roman Catholic nuns who for decades had managed a home for unwed mothers and their offspring in the County Galway town of Tuam.

Early last year, investigators confirmed that many commingled human remains had been found in just a single corner of the 7-acre site, where a subsidized-housing project had long since replaced the old mother-and-baby home.

Amid the many emotional reactions that followed was one particularly painful question: What should be done with the juvenile remains in the ground?

Last month, a team of forensic experts assembled by Katherine Zappone, Ireland’s minister for children, issued a report that presented several possible answers, but not before noting the “unprecedented” challenges.

“The group has not identified any directly comparable cases, either nationally or internationally, that involved the complexities of commingled juvenile human remains, in significant quantities and in such a restricted physical location,” the report said.

Then, in technical language devoid of emotion, the report listed five options, including the estimated cost. The least intrusive choice would be to do little more than erect a memorial on the site and leave things as they are. The most ambitious would be to conduct a forensic exam of most of the site, including its parking lot and grassy playground; exhume all relevant human remains; and do exhaustive DNA testing for possible identification.

Even in its no-nonsense prose, the report revealed the complexities of the matter that the Irish government faces — a matter touching on the profound influence of the Catholic Church on national policy, the subjugation of women, respect for the dead and proper redress for human-rights abuses.

The report’s suggestions have offended the likes of Peter Mulryan, who spent the first few years of his life in the Tuam home and was eventually handed over to a foster father who beat and exploited him. He learned, only recently, that he had a half sister who died at the home in 1950s and that her remains, presumably, are commingled in the site’s unconsecrated ground.

“Awful, insulting,” Mulryan said last week. “How would any of those doing the report like it if one of their siblings was being treated like that?”

The scandal began when Catherine Corless, an amateur historian, dug into the history of the old mother-and-baby home in Tuam that was managed by the Sisters of Bon Secours from 1925-1961. It was one of more than a dozen homes throughout Ireland that were often run by Catholic religious orders, but were funded and supposedly regulated by the government.

Corless came across the death certificates for nearly 800 children who had died at the home, often of contagious disease. But there were virtually no burial records, an absence in the public record that neither the Bon Secours nor the local government could explain.

After further sleuthing, she wrote an article in the local journal in 2012 that strongly suggested that the remains of hundreds of children, all born to unwed mothers and all baptized in the Catholic faith, had not been buried in consecrated ground, but in parts of a disused septic system dating to when the home was a 19th-century workhouse.

Those suspicions were confirmed last March by forensic investigators working for the Commission of Investigation Into Mother and Baby Homes, which had been established by the chastened government in response to Corless’ work. The commission is charged with examining the social and historical reasons for these institutions, to which Irish society had long relegated vulnerable, unwed mothers and their children.

Zappone, meanwhile, dispatched a panel of technical experts who eventually developed the five options. They reported that the considerable complications included the amount of juvenile remains and their commingling, which would make individual identifications difficult, and the potentially limited yield of DNA tests. The experts emphasized the importance of communicating “realistic expectations,” given the need to match extracted samples with those of living relatives and the likelihood that samples taken from infants would be of poor quality.

Mulryan, chairman of a group called the Tuam Home Survivors Network, listed a series of “appropriate actions,” including complete excavation and exhumation, thorough DNA analysis for individual identification and an inquest into the cause of death of each child.

“The DNA should be done at all costs,” he said. “In a war situation, look at the extremes we take to find out where our relations are. And here they’re all in a small area. They don’t have to go digging in different sites around the country. It can all be gone over with a fine-tooth comb and the remains taken out of there.”

Corless agreed, and wondered whether the government was leaning toward the cheapest, quickest way past this national embarrassment. “First of all, the remains are in a septic tank,” she said. “They cannot be left there.”

Zappone said she understood the raw feelings, especially after having been to Tuam and having met some of the survivors. “So many of them, for so long, have traveled this journey alone,” she said. “I want to accompany them as much as I can in my ministry, and I genuinely mean that.”