A couple were gunned down by an intruder in their North Carolina home in the early hours of Feb. 4, 2012. The teenaged daughter had seen the hooded gunman, when he had briefly held a knife to her throat, but she could apparently not describe him to cops.

The attacker left several drops of blood on a handrail as he fled, apparently self-inflicted from his blade.

During the first year of the investigation into the murders of Troy and LaDonna French, detectives swabbed more than 50 people for DNA, including the daughter’s boyfriend. The trail of evidence went cold for months, and then years.

But it was a series of small revelations in the genetic information – including those from the use of DNA phenotyping by Parabon NanoLabs – in those few blood drops which led police to a suspect, who was hidden in plain sight. The information, released by the company this week, follows the sentencing of the killer this past summer to two life sentences without parole.

Blood drops on a handrail

Police immediately turned to DNA to try and crack the case.

“We swabbed a lot of people,” said Capt. Tammi Howell, of the Rockingham County Sheriff’s Office, who led the investigation. “Early on, if there was a remote chance someone could have been connected to the crime, we asked for a swab.”

Those swabs produced no hits. And they did not include the real killer.

At first, DNA told investigators there were no matches with known friends or family of the Frenches – and the killer was not in any of the public databases. Further analysis then indicated that the daughter’s boyfriend, John Alvarez (who had given a swab), could be related to the killer. But it was only a possible relationship, since the STR did not definitively say whether the killer and the boyfriend shared ancestry.

The partial DNA matching led to a Y-STR analysis. The short-tandem repeat on the Y chromosome shows paternal links between fathers, sons and brothers, and has produced huge breakthroughs in cases like the Los Angeles serial killer Lonnie Franklin, Jr., infamously dubbed the “Grim Sleeper.” But in the Sleeper and other cases used “familial searching,” or “FS,” a painstaking and somewhat controversial process of combing large state and national databases like CODIS to find partial DNA matches eventually leading to a suspect. FS was not used in the Rockingham County case, where they had a limited pool of suspects.

That Y-STR analysis appeared to eliminate two close relatives of John Alvarez, both Jose Alvarez Sr., and Jose Alvarez Jr. The police continued their investigation, but without a focus on the three Alvarez men. Since the three appeared to be related by blood, the single Y-STR analysis was thought to exclude all three, according to reports.

Phenotyping a face

Detectives had heard about the vaunted technology of DNA phenotyping. Parabon NanoLabs, headquartered in Virginia, has been the foremost company on the market with its program called Snapshot. It produces a facial image estimated to resemble that from an unknown person’s genome, based on hair color, skin tone, and other characteristics – all determined by genes.

The Rockingham Sheriff’s Office contacted the company in early 2015, around the third anniversary of the crime.

From approximately 30 nanograms of DNA, the software genotyped approximately 850,000 single-nucleotide polymorphisms, or SNPs, at a call rate of 98.9 percent.

In this case, the blood showed the killer to be someone with mixed ancestry – apparently someone with one European and one Latino parent.

Shockingly, the picture looked like someone right in the mix of initial suspects, but later put aside based on other DNA tests: the boyfriend’s brother.

“The Snapshot ancestry analysis and phenotype predictions suggested we should not eliminate Jose (Jr.) as a suspect, despite the Y-STR results,” said Det. Marcus Marshall, the lead investigator on the case. “The likeness of the Snapshot composite with his driver’s license photograph is quite striking.”

The detectives requested DNA samples from both Jose Alvarez Sr. and Jose Alvarez Jr. Both agreed.

Two revelations, one killer

The DNA revealed two things.

First: Jose Alvarez Jr.’s matched the blood on the handrail at the crime scene.

Second: Jose Alvarez Sr. was not Jr.’s biological father, so his Y-STR had gone unnoticed in the investigation up until the Parabon sketch had placed emphasis again on the younger Alvarez as a suspect.

Jose Alvarez, Jr., was the killer, authorities said.

He was arrested in August 2015 and charged with two counts of capital murder. He later pleaded guilty to killing the Frenches, and was sentenced to two consecutive life sentences without the possibility of parole in July 2016.

Parabon touted its tool’s ability to complete the investigative picture at the exact right time to narrow down the police focus.

“Snapshot analysis helps investigators in many ways,” said Ellen Greytak, the company’s director of bioinformatics. “In this case, it helped focus the investigation onto a suspect who might have been logically discounted because of results from another type of DNA analysis.

“Interestingly, both analyses were correct,” she added. “It was the surprising relationship between the DNA sources that provided the twist in this case.”

The police said in a statement through the company, months after the successful sentencing of Alvarez, that the tool had made the difference.

“Now that I have seen SnapShot in action, I am a believer,” said Howell, the sheriff’s captain.

Jose Alvarez Jr. (Department of Corrections)