A former Middlesex Township man serving a long prison sentence after being found guilty of sexual assault charges in Butler and Allegheny counties in 2014 is challenging his convictions in both counties.

Ralph Skundrich, 59, whose last address was in Greensburg, is seeking post-conviction relief by challenging the computer software that linked his DNA to both sexual assaults, which police said took place seven weeks apart 2002.

In the Butler County case, Cranberry Township police charged Skundrich with burglary, rape, terroristic threats, indecent assault and two counts of involuntary deviate sexual intercourse for entering a township woman’s home June 6, 2002, and raping her several times under the threat of killing her sleeping 11-year-old daughter. He wore a mask and told the woman he had a knife, according to testimony and court documents.

A jury convicted him on all charges in June 2014, and he was sentenced in November that year to serve 31 years and 10 months to 63 years and eight months in prison. His sentence was made consecutive to any sentence he already was serving at the time.

In Allegheny County, Pittsburgh police filed similar charges against Skundrich for breaking into the third-floor Shadyside Apartment of an 18-year-old college student at 2:30 a.m. July 25, 2002, threatening her with a gun, demanding money and then forcing her to have sex while he was wearing a mask.

A jury convicted him of all 13 charges in January 2014, and he was sentenced April that year to 65 1/2 to 131 years.

Skundrich was identified as a suspect in both cases after a DNA match was made from a national database in 2010.

Post-conviction relief petitions filed in both cases were appealed to Superior Court after being dismissed by common pleas court judges in both counties. In the Butler County case, the appeals court vacated the orders dismissing two petitions and remanded the petitions back to common pleas court. In the Allegheny County case, the appeals court reversed the dismissal of a petition and remanded the petition back to common pleas court, where the case remains pending.

On Tuesday, April 28, Butler County Common Pleas Judge Maura Palumbi held an evidentiary hearing on the petitions. The hearing lasted about six and half hours, but was continued until sometime in May to allow a prosecution witness to testify.

Skundrich filed a post-conviction relief petition in December 2014 arguing ineffective assistance of counsel, and attorney Stephanie M. Noel filed an amended petition in September 2023 questioning the DNA evidence. Noel and attorney Kenneth Haber represented Skundrich at Tuesday’s hearing, with Haber questioning witnesses.

Attorney Jose Hernandez Cuebas, who was Skundrich’s trial attorney, testified remotely, saying the “elephant in the room” is the computer-generated identification of Skundrich as the suspect.

During the trial, Mark Perlin, chief scientific and executive officer at Cybergenetics, of Pittsburgh, testified about using the firm’s TrueAllele software to identify Skundrich based on a report from the state police crime lab that found DNA tests inconclusive, Hernandez Cuebas said.

He said he didn’t obtain a defense expert to challenge the identification. He said he discussed it with Skundrich, and he didn’t think he could afford to hire an expert and wanted the case to proceed.

In addition, Hernandez Cuebas said he didn’t understand the algorithms Perlin talked about in explaining his computer analysis of the DNA test results, and he didn’t want to risk boring the jury with technical testimony. He said he did not try to obtain the source codes used to create TrueAllele.

Hernandez Cuebas said there was no witness identification of Skundrich and no physical evidence implicating Skundrich, and the DNA computer analysis report was the only evidence tying him to the alleged crime. The TrueAllele software held up in peer review studies, he added.

He said he believed the lack of physical evidence was more compelling that Perlin’s testimony, but he tried to discredit Perlin and TrueAllele. In his closing argument, he said he called Perlin “magic Mark” and called his computer analysis “voodoo.”

He said he learned through discovery that the information from the crime lab report was run through TrueAllele a number of times and produced different results each time, but he didn’t present that to the jury.

Hernandez Cuebas said he doesn’t remember if he knew that a run on the report of a facial swab taken from the woman excluded Skundrich as a suspect, but he would have used that information in the trial if he knew about it and thought it was admissible.

He said Skundrich’s defense attorney in the Allegheny County case was aware of the differing results, but it didn’t help, and he knew Perlin’s findings would be admitted as evidence in the Butler County case.

Hernandez Cuebas said he visited Skundrich in jail twice a week over three months before the trial to discuss the case.

The next witness was Nathaniel Adams, a systems engineer with Forensic Bioinformatics of Ohio.

He said a thorough examination of TrueAllele is needed to measure its accuracy.

Adams said TrueAllele is “probabilistic genotyping” software that interprets data in DNA profiles. That type of software is used when laboratory analysis doesn’t find answers, he said.

He said he reviewed some of TrueAllele’s source codes for a federal case, but was not given access to the entire program. Numerous “bugs” were found in the software, but Cybergenetics corrected those issues, he said.

TrueAllele and other probabilistic genotyping software is used in other courts and crime labs, he said.

No probabilistic genotyping software is flawless and “all software has bugs,” Adams said. Crime labs using probabilistic genotyping software produce unreliable results, he said.

Adams said people who have purchased and licensed TrueAllele say it is reliable.

TrueAllele has undergone a peer review, Adams said.

The hearing was continued to allow Assistant District Attorney Andrew Calve to call a prosecution witness. The continued hearing has not been scheduled yet.