But records show that the SBI performed crucial, confirmatory tests on the clothing three times, and all tests were negative for blood.
A review of the case against Allen, which was built in large part on the work of the SBI, is a window into one of more than 200 criminal files across North Carolina in which the state agency's blood analysis work is in doubt.
A blistering audit made public Aug. 18 says that SBI lab agents misstated or overstated blood test results from 1987 until 2003, when their methods changed with new testing procedures.
Further, a series of reports in The News & Observer in early August showed that lab analysts have bent rules and pushed past the bounds of accepted science to deliver reports that bolstered prosecutors' cases.
The newspaper reports and the audit have jolted the state's justice system, raised the possibility of constitutional violations against defendants and prompted court officials to begin reviewing dozens of homicide, rape, assault and other cases.
The questioned lab work doesn't mean that suspects, including Allen, are innocent. But it could undermine how convictions were won or guilty pleas reached. In some cases it likely affected the types of charges leveled and the punishments handed down.
Allen's case, which 12 years ago grabbed headlines for months, will likely receive fresh scrutiny.
Allen, who was 19 at the time, had always maintained he was innocent of the sensational crime, telling the police, the toddler's family and a newspaper reporter that he never hurt the child.
A week ago, outside his cell, Allen shut his eyes tight and barely moved when he was first told that the stains that played a significant role in upending his life were now in question.
"I'm just happy the truth might come out," he said, finally.
Allen said that he welcomes the new attention to his case, though he refused to discuss the details of what happened to the child on the advice of his lawyer. "I never wanted to accept that plea," he said.
His current court-appointed lawyer, Lisa A. Williams of Durham, and the elected Durham district attorney, Tracey Cline, both declined to comment on the ramifications of the blood analysis in Allen's case.
Cline, who has prosecuted many sex crimes, said only that she wants justice in every case.
Beyond the blood work, there are other fundamental concerns about the handling of the case against Allen, based on interviews, court documents, and other records. )
Suspect from the start
Police suspected Allen had hurt Adesha Artis almost from the moment that he called 911 dispatchers at 2:29 p.m. on Feb. 9, 1998, and asked that an ambulance come to an apartment complex off Garrett Road in southwestern Durham.
"All I knew, um, I got her out of the tub... putting her clothes on... and she passed out," he told a dispatcher that afternoon.
The child's mother had gone to work that morning and left the child in her apartment with Allen and a woman described as her cousin.
The mother, Diane Jones, told police the cousin was in charge of the bright toddler, who had been learning her ABCs and loved dogs. Her bed sheets were covered in dogs from "101 Dalmatians."
Four minutes after the first call to 911, Allen dialed again and said the girl wasn't breathing. Allen told paramedics at the scene a variation of the same story, that he was either giving her a bath or had just given her a bath and the girl passed out.
Paramedics took Desha, as she was called, to Duke Hospital, where she was pronounced dead.
A doctor at Duke examined the girl and noticed a vaginal tear and some blood in that area. The doctor told police it was evidence of a sexual assault, reports show.
Then, a nurse noticed something she said was unusual: As Allen and the mother held the child's body in mourning, Allen lifted a sheet and tried to look at the girl's "private" areas, according to a police report.
Later, when officers first interviewed Desha's mother, she said that she did not suspect that Allen did anything to the girl and that, the night before, she had applied Vaseline to the child's bottom because of a scab that was bleeding. She at first gave police a different name for Allen.
And Allen at first gave police his younger brother's name and birthday, then later acknowledged that he told a lie because he had pending warrants on charges of driving without a license. His record also included a charge of assault against his mother, and he acknowledged frequently smoking marijuana.
When he was confronted with the doctor's opinions on a possible sexual assault, Allen asked for immediate testing, according to police.
"He stated that he wants us to check him, check his hands, his blood, whatever we need to prove that he did not sexually assault the baby," a police investigator wrote. Police charged him with assault that night.
Police also swabbed his hands and clipped all 10 fingernails.
Two days after police submitted the items to the SBI for testing, Allen wrote to the child's mother from jail. At the time, the only charge against him was sexual assault.
"You and your child are the world to me," he wrote. "Baby, you don't got to believe me! But you'll believe that test! And I promise you that your family and the police are wrong. Just wait, you'll see."
Desha's grandmother declined to comment. Diane Jones could not be reached.
By all accounts, the cousin, Zakia A. Ward, was at the apartment with Allen until she was picked up by a relative about 2 p.m. - a half hour before the 911 call.
The day of death
The next day, Ward described for police an unusual morning in which Allen disciplined the child several times as part of toilet training. The child's mother would later tell police that her practice during potty training was to "pop" the child's bottom or arms, using her hand. Allen has said that he followed her methods on that day.
The child at one point during the day seemed to go into a seizure, according to statements both Allen and Ward gave to police.
Ward said it was 12:30 p.m. or 1 p.m., after Allen was with the child in the bathroom, cleaning her and scolding her.
Ward told police the toddler came out of the bathroom in Allen's arms. She was shaking and had her head down.
Ward said the baby stopped shaking within minutes. Shortly after that, she said, while she was on the phone, she heard a banging sound, "like maybe two heads bouncing together."
She also said he changed her underwear a couple of times that day and seemed protective of the child.
Ward's ride arrived at 2 p.m., according to her and phone records. She said she gave Desha a hug and the girl felt "stiff" but that she responded with two- and four-word sentences to a couple of questions and was last seen "chillin' " on a bed.
When paramedics arrived at 2:39 p.m., the child was unconscious and lifeless, medical reports show.
An autopsy found the cause of death to be shaken baby syndrome a violent shaking of the child. Almost a month after the death, Allen was charged with first-degree murder.
The state's evidence against Allen was outlined in court on the day of his guilty plea. Durham prosecutor Freda Black read Ward's statement to police almost verbatim, adding that after Ward left the apartment at 2 p.m., "no one but Derrick Allen knows what happened."
The prosecutor told the judge that investigators also seized a number of items from the apartment.
"The most significant item they found there," Black told the judge, "was a pair of bloody panties on the floor of the bathroom."
She noted the vaginal tear and said in court that blood was found "near" that same spot on the pajamas that Desha wore to the hospital.
"He never was able to give an explanation about why the child had a tear to her vagina or why she had blood on her pajamas or on her underwear," Black said, according to a transcript of the hearing. "So Derrick Allen was arrested very shortly thereafter for the sexual offense."
Allen has said he can't explain any evidence of sexual assault because he didn't do it.
Faulty blood work
SBI records and the recent critical audit of the agency show the blood analysis that was crucial to the sexual assault charge was faulty.
When police submitted the evidence to the SBI for testing, the lead investigator wrote a memo outlining the case and suspicions about the evidence. That practice has come under criticism recently as an example of how the SBI lab takes cues from law enforcement instead of following the science.
Research has shown that giving lab analysts information about a crime or investigation can introduce bias in tests, producing results consistent with the provided information, according to a 2009 National Academies report on forensic science.
SBI forensic agent Jennifer A. Elwell tested 20 items in the Allen case for blood, records show.
Elwell wrote in a three-page lab report that her blood analysis resulted in "chemical indications for the presence of blood" on five of the items: Two pajama outfits, two pairs of panties and a T-shirt.
But her report didn't reflect the truth.
The positive results came from a preliminary test that is prone to give false positive answers. (A negative result on that first test is considered reliable and, typically, no further testing is then done.)
The records show Elwell performed more conclusive, confirmatory testing on four of the items - and those tests came back negative, according to the lab reports. The recent SBI audit, which was authored by two former FBI agents, also identified the Allen case as one in which the blood analysis was in question.
One of the negative tests was on the panties that were seized from the bathroom floor, which Elwell wrote in her notes had a "very dilute" stain on them and were negative "x2" in confirmatory testing - a direct contradiction of what prosecutor Freda Black would later say in court.
The same confirmation test was also negative on the pajamas recovered from the child at the hospital.
Those negative findingsweren't documented in the SBI's final laboratory report.
From the court files, it appears that Elwell's rough notes were available to Allen's lawyers, and to Black, before Allen's plea deal. But the notes that show the negative results are far more obscure than the official written lab report that indicated positive results.
No one raised objections about the results prior to the plea.
The SBI analysis did not find any semen or sperm on any of the evidence that was seized. There was no evidence found on Allen's fingernails.
The only place blood was confirmed was on a paper towel and on a bath towel. Blood stains on both those items were "very dilute," according to the SBI lab notes. In the 911 call, Allen had said there was blood coming from Desha's nose.
The SBI did not perform any DNA testing to determine whose blood was on the items.
In 2004, citing a then relatively new state law that gave inmates the ability to seek DNA testing on evidence in their cases, Allen filed a request from jail to get that done. Black objected in a court hearing during which Allen again proclaimed his innocence.
There is no record in his files of any DNA tests being performed.
Reached by telephone, Black - a prosecutor for years in Durham - said she would not comment on any of the new information because she is running as a candidate for a judgeship in Durham on the November ballot.
Black at first said that Jim Hardin, a former district attorney, handled the plea, though her name is on all the plea documents. She also was the prosecutor who interacted with police, and she outlined the case at the plea deal.
"It would be inappropriate for me to say anything," Black said.
Elwell could not be reached to discuss the case. She still is employed at the SBI, but has been removed from lab work.
Accepts plea, not guilt
Allen accepted the plea deal 11 years ago last week, but did not admit guilt in a maneuver, known as an Alford plea, that allowed him to acknowledge there was probably enough evidence against him to convince a jury. His lawyers from the time could not be reached.
For the sexual assault, Allen was sentenced to a minimum of 24 years in prison.
For the murder, he got a minimum of almost 20 years.
Shortly after getting to prison, Allen started filing letters with the court, seeking the state's entire files against him.
Slowly, he got some. Then, in 2004, he filed motions from prison raising questions about the length of the punishment he received and alleging neglect by his court-appointed lawyers, arguing they spent more time persuading him to admit guilt than they did in building a case to defend him.
The state Court of Appeals agreed that he had grounds for an argument and sent the case back to Durham for a hearing.
After long delays, Allen went before Superior Court Judge Orlando Hudson in March, and Hudson allowed Allen to withdraw his guilty pleas.
The case would start from scratch.
As a result, Allen was released from a state prison and sent back to Durham - where he has been in jail awaiting a new trial. He is being held in lieu of $250,000 bail on the original charges of murder, sexual assault and felony child abuse.
His next court date, on a procedural issue, is scheduled for after Labor Day. Hudson, the senior judge in Durham, said he would likely oversee the case going forward and declined further comment.
One of Allen's appeals lawyers, Kevin P. Bradley, wrote to prosecutors in 2009 that "this is literally a 'shaken baby' case, the then-19-year-old Allen ignorant of the injury that would be inflicted by violently shaking the two-year-old girl." In one court motion, he said the state's evidence supports "excessive corporal punishment or accident ... rather than malice and/or premeditation."
As to the possible sexual assault? He wrote, before the SBI's role was ever in question, that it was a mystery.
Staff writer Joseph Neff contributed to this report.
