Genetic Mapping

[gt6267a]

it would be nice if there was a way to get the information while remaining anonymous and not entered in a database. i suppose that will never be possible.

what about the harmony test used for trisomy? do they run a full test and only report a small piece of information? or is this a case like 11.4 seems to be advocating where only a specific test is completed? i ask because most people are skipping invasive tests to discover down's. in the process of picking a less invasive test, are all those new babies catalogued for life ... not just for down's but everything thing about them? if so, 23andme would look like a little tiny snack of data compared to the millions of parents taking the harmony test. they would have the DNA on both mother and child. yikes.

When you're submitting DNA for specific genetic testing you are also providing the material to get a DNA identity. --11.4

so is everyone who has taken a harmony test in a database with a DNA identity?

[joosttx]

I'm glad they caught the guy, but it's a slippery slope. My mom wanted to buy my sister and I those 23 and me kits and both of us politely declined.

I remember in grade school there was string of thefts happening at school. What felt unrelated the police department and the school offer free fingerprinting to kids marketing it as if you get kidnapped maybe the cops can find your fingerprints and save you. Turned out they had fingerprints of the theif and wanted to match them to a student which they did under the afore mentioned ruse. The cops and the teachers let it be known what they did to catch the theif. Kinda bummed me out that cops and teachers lied to us. I lost a lot of trust in teachers and cops after that.

[j44ke]

I remember in grade school there was string of thefts happening at school. What felt unrelated the police department and the school offer free fingerprinting to kids marketing it as if you get kidnapped maybe the cops can find your fingerprints and save you. Turned out they had fingerprints of the theif and wanted to match them to a student which they did under the afore mentioned ruse. The cops and the teachers let it be known what they did to catch the theif. Kinda bummed me out that cops and teachers lied to us. I lost a lot of trust in teachers and cops after that.

There is likely a pretty strong civil liberties case there, don't you think?

Re: the test. My cousin found out her dad was not her dad, and now her mom isn't talking to her. But my cousin was able to get enough out of the few living members of the family who knew bits and pieces, found who her father was (now deceased) and found a half-sister she didn't know she had.

This recent Golden State sociopath will make people pause a bit though. Opens up can of worms people didn't realize was there.

[gt6267a]

I remember in grade school there was string of thefts happening at school. What felt unrelated the police department and the school offer free fingerprinting to kids marketing it as if you get kidnapped maybe the cops can find your fingerprints and save you. Turned out they had fingerprints of the theif and wanted to match them to a student which they did under the afore mentioned ruse. The cops and the teachers let it be known what they did to catch the theif. Kinda bummed me out that cops and teachers lied to us. I lost a lot of trust in teachers and cops after that.

my elementary school also fingerprinted anyone who might volunteer. they gave a similar reason. i don't recall any thefts but remember thinking there was something not kosher. elementary school aged gt6267a declined to provide fingerprints even after much encouragement. i remember thinking it unwise to provide identifying information for no reason.

[joosttx]

There is likely a pretty strong civil liberties case there, don't you think?

Re: the test. My cousin found out her dad was not her dad, and now her mom isn't talking to her. But my cousin was able to get enough out of the few living members of the family who knew bits and pieces, found who her father was (now deceased) and found a half-sister she didn't know she had.

This recent Golden State sociopath will make people pause a bit though. Opens up can of worms people didn't realize was there.

Texas in the 1980s wasn’t much about civil liberties. Although I owned a gun when I was seven. How about them rights.

[j44ke]

Texas in the 1980s wasn’t much about civil liberties. Although I owned a gun when I was seven. How about them rights.

[Too Tall]

Small world Lane. A very good family friend works for National Advisory Council for Human Genome Research Project.

I'd avoid this like the plague. My first cousins just recently descended from the trees. That's all anybody needs to know.

[sk_tle]

Re: the test. My cousin found out her dad was not her dad, and now her mom isn't talking to her. But my cousin was able to get enough out of the few living members of the family who knew bits and pieces, found who her father was (now deceased) and found a half-sister she didn't know she had.

I read somewhere that according to statistics for 1 kid out of 5 the legally registered father is not the biological one. Those were stats from Germany but I don't think it is much different elsewhere. That can amount to a lot of unknown fathers and siblings.

[dgaddis]

So I'm still not exactly sure how they tracked this guy down. Am I correct in thinking this is what happened:

They uploaded his DNA (recovered from a crime scene) into the database and found relatives of his.
They then looked into the relatives (were the relatives contacted? how did they work thru the family tree? birth records or something?), and figured out who they were related to that fit the profile (age, location, job, etc), which narrowed it down to him.
They then followed him, found some of his DNA he left somewhere (like a hair or saliva on a cup or something?) tested it, it matched the DNA from the crime scene, and they arrested him.

Is that right?

[steve garro]

So I'm still not exactly sure how they tracked this guy down. Am I correct in thinking this is what happened:

They uploaded his DNA (recovered from a crime scene) into the database and found relatives of his.
They then looked into the relatives (were the relatives contacted? how did they work thru the family tree? birth records or something?), and figured out who they were related to that fit the profile (age, location, job, etc), which narrowed it down to him.
They then followed him, found some of his DNA he left somewhere (like a hair or saliva on a cup or something?) tested it, it matched the DNA from the crime scene, and they arrested him.

Is that right?

Yes.

They found a near relative who gave the bio-hackers all their family's info and, based on the DNA you can tell if a person shares the same parents, grandparents, etc - from there, you ask if the relative is male and lived in Sacramento in the 70's - 80's - they know the person would be a cop or armed services, both of which he was based on activities and skills - they told them what they were up to, and the family gave up the info willingly when told their member may be the perpetrator.

Then, anything you throw away is public property and can be tested at will - they said they tracked him to his home, so I assume this to be the case.


Dude can gargle trucker cum in hell for eternity.


- Garro.

[MarkC]

I read somewhere that according to statistics for 1 kid out of 5 the legally registered father is not the biological one. Those were stats from Germany but I don't think it is much different elsewhere. That can amount to a lot of unknown fathers and siblings.

10-30% is a popular myth. Interestingly, when asked what people think rates might be, many folks will guess 10-20%. But non-paternity rates are not that high (in western countries). 1-3% is a figure supported by genetics studies. My experience (coupled with that of colleagues) supports that estimate and collectively spans thousands of families, trios and sibling pairs. Legitimate adoptions and such also happen and are easily detected and not included in those estimates.

Leaving one to wonder why when asked to guess at the possible rates, people go with 10-20%. Oh my cheating heart...

An interesting change in genetic testing is due to the tremendous drop in whole genome sequencing costs. In the old days (10-15 years ago), you would only test for the suspected event. Perhaps by sequencing a gene or two or other methods. This stuff was hard and expensive. In the real old days, sequencing was not in the picture and we were reliant on southern blots and protein polymorphisms. A lot has changed in 30 or so years.

With NGS costs dropping, even if the test question is for a single or small number of genes, its become more cost effective to simply sequence the entire genome, call all the variants but only report back on the gene(s) of interest. What that means in context of the thread is that pretty soon most everyone who undergoes a genetic test will have a full genome sequence somewhere. This is basically the model of Invitae and some other less known companies. 23 and me, Ancestry.com and others have a long game of wanting to be health providers and drug discovery companies. The ancestry, country of origin and other things are loss leaders to get individuals to join their programs and give them access to genetic and longitudinal health data. Nothing wrong with that but not 100% transparent to participants.

Invitae Hopes To Become The “Amazon Of Medical Genetics”

23andMe wades further into drug discovery | Nature Biotechnology

That data has high value if coupled to patient records and longitudinal data as it could help us understand biology of disease (and health), potentially find new drug targets, enable prediction and prognosis. These are very exciting frontiers about to be breached by sequencing technology and social constructs. There are also going to be some vexing ethical conundrums - many of which we will get right and some of which we'll get wrong.

My perspective is not to be fearful or worry about conspiracy theories but definitely read the consent very carefully if you engage in genetic testing for either medical reasons, fun or simple curiosity.

Hope the was entertaining...

-Mark

[11.4]

it would be nice if there was a way to get the information while remaining anonymous and not entered in a database. i suppose that will never be possible.

what about the harmony test used for trisomy? do they run a full test and only report a small piece of information? or is this a case like 11.4 seems to be advocating where only a specific test is completed? i ask because most people are skipping invasive tests to discover down's. in the process of picking a less invasive test, are all those new babies catalogued for life ... not just for down's but everything thing about them? if so, 23andme would look like a little tiny snack of data compared to the millions of parents taking the harmony test. they would have the DNA on both mother and child. yikes.

When you're submitting DNA for specific genetic testing you are also providing the material to get a DNA identity. --11.4

so is everyone who has taken a harmony test in a database with a DNA identity?

The test for trisomy is a simple cytological test -- they stain some cells and look at them under a microscope. You count the number of chromosomes and pair them up (there are supposed to be 23 pairs in a female, 22 pairs plus an X and a Y in a male). It's pretty simple and as a test has been around for most of a century. There's no DNA sequencing involved in that, though inexpensive DNA sequencing will make it easier to do an assay specifically for that chromosomal duplication instead of cytology.

There's a hunger for individual patient data across all parts of business and government these days. It's used for identification (as with the capture of a mass murderer), for insurance exclusion, for insurance fraud, for military exclusion, for racial/gender discrimination, you name it. And it can come from a blood sample, from waste in your garbage (a bloody menstrual pad or a used condom is all one needs, for example, or just a piece of dental floss or a used bandaid), and so on. Your computer keyboard can reliably generate skin flakes with DNA. Let's not even discuss a bib shorts chamois. In short, if someone seriously wants the data in a directed search (as in a criminal search), they have plenty of ways to get it at work, home, or somewhere in between. The bigger risk (for those of us not on the FBI Most Wanted) is in becoming part of a database used for insurance or employment purposes. To get into such a database you pretty much have to give permission at some point, because they have to be collecting samples en masse and they run up against all kinds of legal impediments if you don't give permission. If you give blood for a basic blood chemistry, be sure you aren't giving it for anything more. Ditto for any hospital procedures, and so on. Read all that small print and don't allow your doctor's office to extend their information sharing or data collection disclosures (you sign those when you go to a physician) to any DNA sample, retained samples of fluids or tissues, or any material intended for current or future sequencing. You can write an exclusion into the documents on the clipboard your doctor's office gives you, and take a photo with your phone (or better, ask for a copy from the front desk so they absolutely know what you've done).

It's a new world and our traditional concepts of privacy and individuality are probably going to disappear. With so much information available and the efficiencies it offers in law enforcement, insurance, whatever, there's no way that isn't going to happen. Rather than going nuts over it, I'd just be cautious and acknowledge that the world is changing. Pretty soon we're going to be getting medical tests like the wealthy buy houses ... through our own personal LLC's.

[vertical_doug]

The problem is if your mom, aunt, sibling do up their DNA I reckon there is predictive analytics to predict genetic issues with you.

How an Unlikely Family History Website Transformed Cold Case Investigations - The New York Times

and we have a winner

[j44ke]

I read somewhere that according to statistics for 1 kid out of 5 the legally registered father is not the biological one. Those were stats from Germany but I don't think it is much different elsewhere. That can amount to a lot of unknown fathers and siblings.

The macabre side of German genetic testing is that there are likely to be a concentrated group of ~73 year old Germans with Russian genetics.

[sine]

The macabre side of German genetic testing is that there are likely to be a concentrated group of ~73 year old Germans with Russian genetics.

Maybe not specifically Russian.....but yes, it was brutal being ethnic German in the east.

Lebensborn program is another horrible case.

[j44ke]

Maybe not specifically Russian.....but yes, it was brutal being ethnic German in the east.

Lebensborn program is another horrible case.

Referring to the fall of Berlin and afterwards in the Soviet zone from about 1945 to 1948. The estimates of the number of sexual assaults is mind-boggling.

[davids]

Referring to the fall of Berlin and afterwards in the Soviet zone from about 1945 to 1948. The estimates of the number of sexual assaults is mind-boggling.

Nothing unusual about this. The brutality humans inflict on each other spans the globe.

[j44ke]

Nothing unusual about this. The brutality humans inflict on each other spans the globe.

But in terms of genetic mapping, genetic evidence becomes almost like the fable of King Midas' ears. It won't stay buried.

[vertical_doug]

Police Are Increasingly Taking Advantage of Home DNA Tests. There Aren’t Any Regulations to Stop It. – Mother Jones

Police Are Increasingly Taking Advantage of Home DNA Tests. There Aren’t Any Regulations to Stop It.
“This stuff is being used, and I don’t think people are really thinking about the implications.”

Madison Pauly March 12, 2019 6:00 AM

CeCe Moore knew that she could find serial killers. But she wasn’t sure that she should.

By the time authorities in Sacramento, California, announced an arrest in the Golden State Killer case in April 2018, Moore had spent years uncovering family secrets for hire as a self-taught expert in DNA and genealogical research. Using consumer genetic tests, she reconstructed family trees for adoptees and helped the children of American soldiers in Vietnam identify their half-siblings in the US. She rediscovered the identity of a man with amnesia. And she went on TV—Dr. Oz and 20/20 and Finding Your Roots—spreading the gospel of genetic genealogy, the name for the investigative technique she and other “citizen scientists” had developed.

Law enforcement officials had long been asking Moore to apply genetic genealogy to crime scene DNA. Each time, she said no. “I just didn’t feel I could ethically do it,” she says. “I’ve encouraged thousands, maybe hundreds of thousands or more people to take consumer DNA tests. I didn’t want to then go and use their DNA in such a way that might seem like a betrayal.”

Then, police announced that they had identified a suspect in the decades-old serial rape and murder case with assistance from an amateur genetic sleuth using techniques like Moore’s. First, investigators asked the FBI to sequence crime scene DNA they believed came from the perpetrator. They uploaded the results to GEDmatch, a popular free database where anyone can share their DNA profile after taking a consumer test. After identifying distant cousins on GEDmatch, investigators used public records and social media to construct those cousins’ family trees, tracing the branches to a man the right age, in the right place, with the right amount of shared DNA: Joseph DeAngelo. When they compared a swab from his car door handle against DNA from the crime scenes, it matched. He’s now accused of at least 13 murders and dozens of rapes.

Details of the case soon plastered newspaper front-pages and international media outlets—igniting broad discussion over many of the same ethical concerns Moore had been struggling with. At the heart of the debate was how, without explicitly consenting to a police search, a single user of a consumer DNA test could unknowingly cast legal suspicion on hundreds of family members. “Three hundred people, most of whom you do not know and have probably never met, can illuminate your genetic information,” biologist Rori Rohlfs and bioethicist Stephanie Fullerton wrote in an op-ed last year in Leapsmag, a science magazine funded by Bayer. “There is nothing that you can do about it, no way to opt out.”

The arrest changed everything for Moore. While the public was mostly cheering the breakthrough, GEDmatch changed its privacy agreement to state clearly that law enforcement was using the database. That “opened the door” for Moore. Within days of DeAngelo’s arrest, she said yes to working a cold case. Moore identified her first suspect, she says, within two hours of receiving results on GEDmatch.

But while Moore has come to peace with her qualms over law enforcement using genetic genealogy, academics, legislators, and Washington bureaucrats are just now starting to grapple with the same issues. While that debate continues on, nearly a year after the Golden State Killer arrest provided a template for investigators all over the country, regulation governing how and when cops can use the technique is nonexistent. The result is a law enforcement free-for-all, with police and allies digging into consumer DNA databases with little law or policy to guide them.

Since Moore decided to go all-in on assisting police, the genetic genealogy slice of the forensic industry has grown rapidly. Shortly after the Golden State Killer arrest, Moore was hired to lead a team at Parabon NanoLabs, a biotech company known for creating forensic sketches based on DNA sequences. It has since emerged as the go-to contractor for police departments across the country hoping to crack cases with genetic genealogy. News of such arrests now breaks almost weekly: On February 15, in Alaska, state troopers announced that findings from Moore’s team helped them to identify and arrest a man for sexually assaulting and killing a fellow student at the University of Alaska-Fairbanks in 1993. On February 20, in Orange County, California, authorities announced that with Parabon’s help, they’d found and charged a man with the 1973 murder of an 11-year-old. As of mid-February, Moore estimated that her team has identified 36 suspects using crime scene DNA, including some individuals who were deceased. Three have pleaded guilty.

Other labs are now starting to get in on the game: The largest forensic DNA company in the US, Bode Technologies, announced last month it was launching its own team. Law enforcement officers are also increasingly looking for training from self-taught genetic genealogists, Moore says, and the FBI has started its own unit dedicated to the practice.

Meanwhile, the prospect of finding hits in public databases continues to grow, thanks to the mainstreaming of consumer DNA testing. More than 200,000 profiles have been added to GEDmatch since last May, Wired reported in December, bringing its total to about 1.2 million. On January 31, Family Tree DNA confirmed that it allows law enforcement to search its database of more than a million entries. Researchers recently told BuzzFeed that between those two services, police can now likely link almost all Americans with European heritage to at least a third cousin.

As genetic genealogy spreads, of course its risks do too. One fear is its potential to place innocent people under police suspicion. In her book Inside the Cell: The Dark Side of Forensic DNA, New York University law professor Erin Murphy warns that the practice of searching for genetic relatives could cast wide nets of suspicion over families, and lead cops to test a person’s DNA despite no independent evidence linking them to a crime. Victims could be pressured not to report crimes, she writes, “for fear of implicating their own relatives in other offenses.” And by examining family trees, police could expose secrets of people uninvolved in the crime in question, including infidelity, incest, and abandoned children

Just consider that California investigators, before they arrested DeAngelo last year, collected DNA samples from at least two other men in connection with the Golden State Killer case, including a 73-year-old Oregon man in a nursing home whose daughter had uploaded her genetic profile to Ysearch.org. After police determined that the man had an uncommon genetic mutation they were looking for, the judge permitted authorities to obtain his DNA by force if necessary, according to the Los Angeles Times. And in a separate case in 2015, a partial match in an Ancestry.com-owned database led police to suspect a New Orleans filmmaker, Michael Usry, of a 1996 murder. In both cases, the men were ruled out as suspects after police compared their DNA samples to the crime scene using traditional DNA testing. But that confirmation process is far from bulletproof; years of investigations have revealed how contamination, mistakes, and fraud can lead to false DNA matches and wrongful convictions.

Skeptics have raised other concerns too. Steve Mercer, a Maryland defense attorney specializing in DNA and forensic science, told Bloomberg that police would inevitably want to apply genetic genealogy not just to rapes and murders, but also to minor crimes like trespassing. And computer scientists at the University of Washington published a working paper that outlines how criminals could manipulate investigators with fake or modified DNA profiles.

Legislatures, city councils, and attorneys general offices have all historically played a role in regulating the way police can use DNA to scrutinize families. Since the 2000s, amid advances in DNA technology, some states have debated the use of so-called “familial searches” in CODIS, the FBI’s national DNA indexing program, which contains profiles taken from convicted offenders, as well as people arrested for violent crimes or burglary. CODIS profiles consist of 20 genetic markers—significantly fewer than the hundreds of thousands of data points used in consumer testing and by genetic genealogists. They’re good for finding exact DNA matches but bad at locating even close relatives, the FBI has determined.

Nevertheless, a handful of states have decided to allow familial searches in CODIS since 2006, when then-FBI director Robert Mueller first authorized them. Some compromised; California and Virginia, for instance, opted to permit familial searches only in cases when all other investigative leads had been exhausted. Maryland and Washington, DC, went the other way, banning familial searches altogether, in part due to concerns that the overrepresentation of people of color in law enforcement DNA databases would amplify police suspicion of minority communities.


..... go to the link on motherjones to read the rest. No pay wall.

https://arxiv.org/pdf/1810.02895.pdf link to working paper on Distant Relative Matching in Consumer Genetic Databases.

In Europe, because of GDPR restrictions, a person living in the EU should be able to sue the company providing the data if they have any EU presence.