Inside the 15-year manhunt to find Boston's serial rape suspect

Investigators from the linked a attorney to a series of violent rapes in Boston after tracking down his relative's DNA on a commercial genealogy database.

Matthew Nilo, 35, was arrested last week on suspicion of raping three women and sexually assaulting a fourth in 2007 and 2008.

Police took samples from the , in Boston, at the time of the incidents and processed the glove of a fourth victim who poked her assailant in the eye while wearing the garment.

All three matched the same profile, leading officers to believe that the same man committed each of the assaults.

The FBI confirmed 15 years later that the DNA belonged to Nilo after comparing the samples to one from a glass he drank from at a corporate event, but there were multiple hurdles they had to first overcome.

Matthew Nilo, 35, denied attacking four women in Boston in 2008 and 2007 during his appearance in Suffolk Superior Court on Monday

Police took samples from the three women who were raped in Terminal Street, in Boston, at the time of the incidents and processed the glove of a fourth victim who poked her assailant in the eye while wearing the garment 

The investigation initially stalled because the DNA obtained from each of the women failed to flag any potential matches on the federal CODIS system. 

Officers kept the case open, using the Sexual Assault Kit Initiative - a federal program designed to help process a backlog of rape kits - to reinvestigate the incidents.

Boston Police Department doesn't have a backlog of rape kits but has instead used the initiative and a $2.5million federal grant to re-examine 'unsolved cases that present the greatest threat to public safety.'

Cops requested the DNA be cross-referenced by the FBI using 'forensic investigative genetic genealogy' in October last year. 

Officers from the BPD submitted the DNA samples obtained from the three women to GEDMatch and Family Tree DNA, two of the only genealogy websites which allow law enforcement access to their databases.

Because the databases are so small, the FBI could only search 'about two million people', meaning they had to either 'get lucky or be really skilled.'

Consumers using the sites must consent before their information is shared with law enforcement, and they use the sites to trace their ancestry or locate other relatives.

GEDMatch and Family Tree DNA then provide a list of relatives and the percentage of DNA they share with the sample submitted by the police - which led them to Nilo in April this year.

The FBI confirmed 15 years later that the DNA belonged to Nilo after comparing the samples to one from a glass he drank from at a corporate event

His fiance Laura Griffin was seen gripping rosary beads during his court hearing in Suffolk Superior Court on Monday

Pictures from Nilo's Facebook page show how he would have looked at the time of the assaults in 2007 and 2008

Unlike police DNA databases, those of commercial genealogy companies can search for up to one million DNA markers (using single-nucleotide polymorphisms, not STRs), creating a much wider pool of relatives to sift through.

Historically law enforcement had to rely on federal and local DNA databases, which contain the profiles of people previously arrested.

If a suspect had not been apprehended before, then their DNA would not be in the CODIS system, and they could not be identified.

Once a suspect is identified through the genealogy companies, who provide names and how strong the match is, police then attempt to take a DNA sample to confirm a direct match.

However, this often takes place surreptitiously, with officers tracking Nilo in New York for at least a month when he was identified as a suspect in April. 

Court documents show that the FBI was able to 'obtain various utensils and drinking glasses they watched the defendant use at a corporate event.'

They obtained a DNA profile from one of the glasses, which they say matched the profile of the three rapes on Terminal Street.

After obtaining a match from the glass, they then tested a sample found on the glove of the fourth woman - and 'determined that this profile was 314 times more likely to belong to Matthew Nilo than to any other male in the population'

His fiancée gripped the religious beads throughout the hearing but did not say anything as she exited the court 

Once a suspect is identified through the genealogy companies, who provide names and how strong the match is, police then attempt to take a DNA sample to confirm a direct match PIctured: Nilo (center) with friends 

After obtaining a match from the glass, they tested a sample found on the glove of the fourth woman - and 'determined that this profile was 314 times more likely to belong to Nilo than to any other male in the population.'

In the past 15 months, Boston Police Department has arrested six people for alleged rapes, using a $2.5 million federal grant to re-examine 'unsolved cases that present the greatest threat to public safety.'

Former State Street Bank vice president Ivan Cheung was one of those arrested - with cops obtaining his DNA from a cigarette butt he discarded at South Bay Center.

He is charged with raping two children and two women at knifepoint between 2003 and 2006.

Irving Pierre was also arrested over the alleged rape of a 16-year-old girl and a woman in Roslindale in 2007 and 2013.

They have also charged William Mancortes with attacking women while pretending to be a ride-share driver in 2017. 

Demetrius Wilson has been charged with two rapes, and Ali Abdallah-Muhammad is accused of a 2014 rape.

In the past 15 months, Boston Police Department has arrested six people for alleged rapes, using a $2.5 million federal grant to re-examine 'unsolved cases that present the greatest threat to public safety'

Prosecutors said that all three women underwent a sexual assault examination, which yielded a DNA profile which matched the male in each attack

Nilo, who once lived in the North End, was arrested at his home in Weehawken, New Jersey, on Tuesday, more than 15 years after he allegedly terrorized four victims 

Experts say that DNA from sexual assault kits are very reliable, even if they are 15 years old. 

FBI agents used a kit that was 38 years old to identify a former police officer as the Golden State Killer.

Barbara Rae-Venter, an investigative genetic genealogy consultant, told the Boston Globe that people who are identified by the websites 'have no record' and are 'not on anybody's radar.'

'That is what is so amazing about investigative genetic genealogy.

You are able to identify people who you otherwise would not be able to identify,' she said.

Genetic genealogy has also been used to identify murder victims, with the FBI confirming the identity of 'The Lady of the Dunes' - which had left law enforcement puzzled for nearly 50 years.

Nilo on Monday pleaded not guilty to three counts of aggravated rape, two counts of kidnapping, one count of assault with the intent to rape and penipu one count of indecent assault and battery

Nilo, who was linked to the crimes by DNA, was supported in court by family members and Griffin who was present when FBI officers swooped at their home 

He was handcuffed and appeared in court wearing a blue shirt and jeans and looked emotional as he pleaded not guilty to the charges

Nilo is accused of assaulting the four women in or around Terminal Street in Charleston on 18 August 2007, 22 November 2007, 5 August 2008 and 23 December 2008 

His bail was posted at $500,000, and if he able to post that amount, he must submit to GPS monitoring and stay away from his alleged victims and the scene of the crime.

At the time of the alleged rapes, Boston Police Department issued a warning that a man was attacking women after offering them rides home.

According to a police affidavit, a dozen FBI agents and Boston Police officers arrested Nilo at his luxury apartment complex.

They lured him down to the lobby under the pretense that 'a large package had been delivered to him that did not fit in the ...

lockers where the residents pick up packages.'

He was with his fiancée, Laura Griffin, at the time of his arrest, and immediately invoked his Miranda rights.

Nilo is accused of assaulting the four women in or around Terminal Street in Charleston on 18 August 2007, 22 November 2007, 5 August 2008 and 23 December 2008.

A 23-year-old woman claims she was approached by a man in his 20's after leaving a friend's home in the State Street area in the early hours.

She said she thought she knew the man, who offered her a ride to help her look for her vehicle before driving her to Terminal Street.

According to a police affidavit, a dozen FBI agents and Boston Police officers arrested Nilo at his luxury apartment complex 

Nilo is accused of assaulting the four women in or around Terminal Street in Charleston on 18 August 2007, 22 November 2007, 5 August 2008 and 23 December 2008

Nilo then allegedly told her to 'shut up' or he would kill her, claiming to have a weapon before raping her on a grassy area near railroad tracks, according to court filings.

The second attack allegedly took place in November 2007, when a woman, 23, was leaving a bar on State Street after attending a high school reunion.

Documents say that she got into Nilo's car, thinking it was a taxi, before giving him the address of an ATM near her apartment.

She claims that the man flashed a knife at her after she told him he missed the address, driving her to Terminal Street where he ordered her out of the car before raping her.

The third assault took place in August 2008, after Nilo allegedly approached a 36-year-old woman on Boston Common, promising her money if she went to Charlestown with him.

When they exited the car at Terminal Street, he allegedly 'tackled her to the ground, held a gun to her back' and raped her repeatedly.

The final assault took place in December 2008, where a 44-year-old woman was attacked as she was jogging in the area of Terminal Street.

Court documents claim that he approached her from behind, tackled her to the ground and sexually assaulted her.

The man, who was later allegedly identified as Nilo, repeatedly told her 'I have a gun' before she managed to escape by poking at his eyes while wearing a glove.

Nilo's lawyer Joseph Cataldo claimed that he has received 'no indication' that a search warrant was obtained before they collected Nilo's DNA samples.

Speaking outside court, he said: 'My educated guess is there are no search warrants.

Obtaining DNA and analyzing it without a warrant based on probable cause, I posit that is unconstitutional.'