It was in May 2020, on a Sunday COVID afternoon. I was in Pittsburgh, with testimony looming that week in the capital case of California v. Manuel Lopez. Zooming from home with Santa Clara Deputy Public Defender (DPD) Kelley Kulick, trying to solve a crazy DNA mystery.
So much evidence making so little sense. Weeks of transcripts from many witnesses nagged by DNA discrepancies—conflicting rectal swabs, immaculate mother, battered child. Something was missing, and we needed an answer soon.
Toddler Apollo Torres died in January 2016. He was 2 years and 10 months old. There were bruises to his face, genitals and rectum. An autopsy revealed brain swelling, skull fracture, cheek bruises and asphyxia. The boy's rectal swab showed semen that matched the defendant’s DNA.
Manuel Lopez was accused of the crime. He was the new 22-year-old boyfriend of Samantha Torres, the victim's mother. They lived together in a crowded messy house filled with friends, relatives and children—and a lot of stuff. A house stuffed with people's DNA.
The county crime laboratory analyzed DNA from 97 house and victim evidence items. They generated autosomal short tandem repeat (STR) data. The DNA mixtures of 2, 3 and 4 people were hard—or impossible—for them to interpret.
The lab reported 43 DNA matches, found 1 unknown person, and gave up on many "inconclusive" items. Their matches lit up boyfriend Lopez (Figure A). The lab found his DNA on 10 items, including clothing, bedding, fingernails and in the toddler's rectum. There was no DNA from Apollo's mother.
Semen in a dead toddler’s rectum from a defendant accused of rape and murder is virtually a death sentence. You can explain away many other facts—witness testimony, DNA items, forensic evidence, but not that semen. A prosecutor will build a story around the child's rectal DNA that forces a jury to convict. There is no workable defense.
Kulick had successfully defended against state DNA evidence before. In 2012 she acquitted Lukis Anderson of homicide, undermining apparent touch DNA evidence as innocent DNA transfer. Co-counsel DPD Michael Ogul postponed his retirement to defend Lopez, whom he strongly believed to be innocent.
I had worked with the Santa Clara District Attorney's Office earlier that year on a different case. They charged Alejandro Benitez with the rape and murder of a 16-month-old toddler at his babysitter’s home. Cybergenetics technology connected Benitez' DNA to 7 evidence items, leading to a guilty plea. The prosecutors saw Lopez as another Benitez. Their view was that defendant Lopez raped and killed a 2-year old boy who lived in his house.
LR results from the (A) county crime laboratory and (B) Cybergenetics TrueAllele. One of three DNA match table pairs is shown. Rows are for evidence, columns for references. Darker colors mean stronger LR match values, ranging from 1 to 30 powers of 10. Gray is an inclusion, without a statistic. A blank entry indicates no match result.
Public defenders Kulick and Ogul had a different perspective. They saw a messy house, a long history of brutally violent child abuse, a potentially culpable mother, and a recent boyfriend wrongfully accused of a capital crime. Their view was that a severely physically abused toddler had died. And that defendant Lopez had nothing to do with the boy's death. They saw an innocent man facing the death penalty.
Kulick reached out to Cybergenetics, requesting our usual free probabilistic genotyping (PG) screening of the Lopez DNA evidence. We processed over a hundred case items using our pioneering TrueAllele system, which easily unmixed the DNA mixtures. It found 76 informative evidence items and discovered 6 unknown people. Comparing the evidence genotypes with reference DNA from the 6 known and 6 unknown people produced 128 likelihood ratio (LR) match statistics. The defense asked us to report everything.
Cybergenetics' computer-derived matches (Table B) revealed more DNA connections than the lab's data review (Table A). Our PG computer found 3x as many DNA matches as the county lab. It tripled the number of matches to defendant Lopez. Whereas the lab's data analysis found just 1 match to 1 unknown person, we found 42 matches to 6 unknown people—and Apollo's mother Samantha wasn't on any item.
TrueAllele fully mapped the crime scene, comparing six dozen evidence items against a dozen people. The computer unmixed the mixtures to reveal whose DNA was on which items for a complete forensic DNA landscape.
The DNA results posed two confounding puzzles:
1. Rectal swabs taken at different times gave conflicting results. At the hospital, Apollo's initial rectal swab showed Lopez's DNA. But in a later autopsy, Lopez wasn't in the victim's rectal swab sperm fraction. How does DNA magically vanish?
2. Apollo's mother was his primary caretaker. She fed, dressed, changed and held him. How could her immaculate DNA not be on any item?
That Sunday, over Zoom, Kulick and I scrutinized witness transcripts, including the pathologist testimony and what the mother told the jury.
Suddenly I asked, "Was that really her testimony?" I just had the strangest idea...
To be continued in Part 2 on Wednesday
DNA Matters, an exclusive Forensic column, discusses cases that have been aided by the power of computer software in DNA analysis. It is authored by Dr. Mark Perlin, M.D., Ph.D., chief scientist, executive and founder at Cybergenetics. Twenty years ago, Perlin invented TrueAllele probabilistic genotyping for automated human identification from DNA mixtures. His company helped identify victim remains in the World Trade Center disaster, and has helped exonerate 10 innocent men. He is a Scholar in Residence at Duquesne University’s Forensic Science and Law program, and a Fellow of the American Academy of Forensic Sciences. © Mark Perlin 2025