Wednesday, 25 September 2019

US Department of Justice Interim Policy on Forensic Genetic Genealogical DNA Analysis and Searching

The US Department of Justice have issued an Interim Policy on Forensic Genetic Genealogical DNA Analysis and Searching. The press release can be found here:

https://www.justice.gov/opa/pr/department-justice-announces-interim-policy-emerging-method-generate-leads-unsolved-violent

Here is a direct link to the policy statement: https://www.justice.gov/olp/page/file/1204386/download

The announcement was made by Ted Hunt, Senior Advisor to the Attorney General on Forensic Science at the Department of Justice, during a talk given at the International Symposium on Human Identification in Palm Springs, California.

Investigative genetic genealogy or forensic genealogy is a powerful tool which can help to solve crimes and identify missing persons but, as with any such tool, it needs to be used responsibly. Earlier this year I wrote an article for Forensic Science International on Using genetic genealogy databases in missing persons cases and to develop suspect leads in violent crimes. I explain in the article how the methodology works but I also discuss some of the privacy implications and the need for ethical and regulatory oversight. These new guidelines from the DOJ are long overdue and this document will be a good starting point for further debate but there are a number of important issues that have not been addressed and which I will discuss briefly below.

Informed consent
The following sentence in the report is highly misleading: "The FGG [forensic genetic genealogical] profile is... compared by automation against the genetic profiles of individuals who have voluntarily submitted their biological samples or entered their genetic profiles into these GG services (‘service users’).

FamilyTreeDNA changed their terms of service in March this year. All European Union customers who tested prior to the change were automatically opted out of law enforcement matching. Going forwards, all customers, including all EU users, were automatically opted in to law enforcement matching. New settings were introduced so that customers could opt out. Previously if you didn't want to share your results with law enforcement you had to switch off matching altogether, thus losing all the benefits of the genetic genealogy database. While FTDNA customers have voluntarily uploaded their samples for their family history research, because of the automatic opt in they cannot in any way be considered to have given consent to have their profiles matched with law enforcement kits. The DOJ perhaps doesn't realise that FTDNA has an international database. There are international conventions on the transfer of DNA data for people in criminal databases (eg, through Interpol or the PrĂ¼m Convention in Europe). Innocent people in genetic genealogy databases should expect similar protections if their data is to be used by law enforcement agencies in foreign countries. I would like to see the DOJ make a requirement that, at the very least, DNA profiles of non-US citizens can only be used if the customers have given explicit informed consent. Ideally they should insist that FTDNA follows the standard convention and adopts an opt in policy for everyone.

GEDmatch customers have voluntarily uploaded their profiles to the database and, following the decision in May this year to require all users to opt in to law enforcement matching, anyone who has exercised this option has given their consent to have their data used for law enforcement investigations.

Proportionality
The DOJ guidelines include the following criteria which must be met before a genetic genealogy search can go ahead:

Before an investigative agency may attempt to use FGGS [forensic genetic genealogical DNA analysis and searching], the forensic profile derived from the candidate forensic sample must have been uploaded to CODIS, and subsequent CODIS searches must have failed to produce a probative and confirmed DNA match.

The investigative agency with jurisdiction of either the crime or the location where the unidentified human remains were discovered (if different) must have pursued reasonable investigative leads to solve the case or to identify the unidentified human remains.

Proportionality is a key concept in the criminal justice system and priority should always be given to the most effective and least intrusive methods. It is notable that in a number of the forensic cases where genetic genealogy databases have been used, the police have failed to use existing and well proven methods.

In some cases, the suspect had already had prior contact with the police or had even been in prison but the police had failed to get a DNA sample. See for example herehere and here. Jerry McFadden was identified through genetic genealogy as the murderer of Anna Marie Hlavka. But McFadden was executed in 1999 without having his DNA taken.

If matches are to be found in the CODIS database then surely it makes sense to ensure that all convicted offenders are in the database. Yet, according to a report from Forensic Magazine in 2017 there is a big backlog of prisoners who have not been tested:
...seven states hold prisoners whose DNA had not been collected, and who were not in CODIS. Most often, these states had no retroactivity conditions in their DNA laws, which were generally enacted in the 1990s and were never extended into the past to include criminals already locked up. But there are other cases where prisoners refused to give samples, or authorities simply didn’t get the testing done for logistical reasons. For others, there were simply collection delays.
There is also a huge backlog of untested sexual assault kits in the US. Astonishingly it's not even possible to determine the size of the backlog but there are probably tens of thousands of kits which still haven't been tested. The End The Backlog website keeps track of the problem.

I cannot understand why these backlogs have been allowed to develop. There must be many victims of crime who have yet to receive justice and potentially many innocent people who could be exonerated if this testing were done.

Familial searching has far fewer privacy implications than genetic genealogy because the people whose DNA is being searched have already committed a crime and can therefore be considered as having forfeited the right to privacy. Familial searching involves a search of the police database to identify people who are first-degree relatives of the suspect (eg, the parent, child or sibling). It works on the basis that crime tends to run in families so, even if the perpetrator himself is not in the database, it's quite possible that he could be identified through a match with another family member.

Some of the cases where genetic genealogy has been used could have been solved much earlier if familial searching had been used. A number of the suspects, including the Golden State Killer, had a brother who already had a criminal record but sadly his DNA was not in the police database.

Familial searching is currently only done in a handful of states such as California, Texas and Colorado. The practice is banned in Maryland and in Washington DC. Familial searching could potentially produce tens of thousands of useful investigative leads. The Florida Department of Law Enforcement have set an excellent example by adopting a policy whereby genetic genealogy is only used if a familial search has produced a negative result. It would be good to see the DOJ updating their policy to follow Florida's example and insist that genetic genealogy should only be used after an unsuccessful familial search.

The National DNA Index System (NDIS), the federal CODIS database, has over 16 million DNA profiles. DNA searches in the national database would probably produce valuable leads in thousands of cases. For some reason the FBI has resisted allowing the use of NDIS for familial searching. However, if the DOJ is happy for genetic genealogy databases to be used then the FBI's position is clearly untenable and familial searching should be introduced as a matter of priority.

Ethical oversight
The policy makes no provision for ethical oversight. Genetic genealogy searches are left to the discretion of the investigative agencies and the prosecutors. Agencies are required only to use companies which "provide explicit notice to their service users and the public that law enforcement may use their service sites". Law enforcement and prosecutors are necessarily going to want to push for the use of genetic genealogy. There is an urgent need for some form of independent oversight to provide balance in the system. Again, Florida is setting an excellent example. Because genetic genealogy is only used in Florida when familial searching has been unsuccessful, all searches must be approved by a Familial Search Review Committee. I would like to see other states follow this example.

Mechanics of genetic genealogy searches
The policy recommends that "The investigative agency shall, if possible, configure service site user settings that control access to FGG profile data and associated account information in a manner that will prevent it from being viewed by other service users." At GEDmatch kits can be uploaded as research kits which means that the user will receive a list of matches but will remain invisible to the people on the match list. At FamilyTreeDNA law enforcement kits appear in the match list of everyone who has not opted out of law enforcement matching. They are not distinguished in any way from those of ordinary users. I understand that some people are trying to encourage FTDNA to adopt a similar system to GEDmatch so that the law enforcement kits cannot be seen. The DOJ missed a big opportunity here and could have insisted that the police only use companies which restrict matching in this way which would put pressure on FTDNA to adopt best practices.

The report discusses the procedures for target testing which is sometimes done when the matches are more distant. Testing someone who is potentially a second cousin to the suspect helps to narrow down the search and confirm that the investigators are pursuing the right line.  The report says that "An investigative agency must seek informed consent from third parties before collecting reference samples that will be used for FGGS". However, they do not discuss the tricky subject of incidental findings, such as the discovery that a target tester is not related to his or her presumed biological family in the expected way.

I am sure that there is much more I could write but I just wanted to set down a few initial thoughts about the areas which I think are the most important.

Further commentary

Sunday, 15 September 2019

New DNA and subscription bundle from Findmypast for UK subscribers

Findmypast are offering a free DNA kit to new UK subscribers for a limited time only. Findmypast have a partnership with Living DNA and the test on offer is the Living DNA test packaged under the FindmypastDNA brand name. Note that the test offered in this bundle is an autosomal test only. If you wish to have the Y-DNA and mtDNA haplogroup reports, which are included with the standard Living DNA test, you would need to upgrade.  

Full details of the offer are included in the following press release from Findmypast which I received on 4th September 2019.  As far as I'm aware this offer is still available. It is restricted to the UK market. I do not know if there are any plans to extend the offer to other countries.
FINDMYPAST ANNOUNCES NEW DNA & SUBSCRIPTION BUNDLE FOR UK MARKET
 
  • While stocks last, all 12 month Pro or Plus subscriptions now come with a free Findmypast DNA kit worth £79
  • New offering allows users to combine cutting-edge science with Findmypast’s archive of more than 9 billion historical records
Leading family history website, Findmypast, has announced that as of today, any UK customer who purchases a 12-month Plus or Pro subscription will receive a Findmypast DNA kit worth £79, completely free of charge whilst stocks last. 
The new bundle combines cutting edge science and traditional family history research methods, allowing family historians to explore their past in more depth than ever before.
Launched in partnership with fellow British brand, Living DNA in November 2018, this first of its kind service uses Living DNA’s unique test employing cutting-edge science to provide a breakdown of 21 regions across Britain and Ireland, connecting family history enthusiasts with the records they need to bring their ancestors’ stories to life. 
Those looking to take advantage of this incredible offer can choose from: 
  • A 12-month Plus subscription priced at £120 – covering all record categories, perfect for expanding your family tree and adding colour to your research
OR
  • 12-month Pro subscription priced at £156  - providing full access to everything Findmypast has to offer, including the largest online collection of British & Irish newspapers
AND…
  • They will receive a Findmypast DNA kit completely FREE plus free delivery (normally £79)
Once you have purchased your Plus or Pro Subscription, or upgraded from a starter sub, simply claim you free kit by visiting /www.findmypast.co.uk/subscribe?dnaoffer=true.  All free kits must be claimed no later than 30 days after the subscription purchase.

Wednesday, 10 July 2019

MyHeritage enters the genetic health testing market


MyHeritage announced the launch of a new Health and Ancestry test on 20th May this year. The launch occurred at a busy time of the year and I've only just got round to investigating it. On doing so, I discovered that the test is on special offer with 40% off the recommended price until 15th July so I decided to take the plunge and order a kit. I already have a MyHeritage DNA account but I have not tested direct at MyHeritage DNA. Instead I transferred my raw data file from AncestryDNA in order to participate in the genetic genealogy matching database. I received various e-mails from MyHeritage about the new health test but none of them mentioned a discount or special introductory offer and the 40% discount does not show up when I log into my existing MyHeritage account. I don't know if this special offer is available to everyone in the UK or if a similar offer exists in other countries so you will need to check for yourself. Make sure you log out of your MyHeritage account first. There was an additional charge of £9 for shipping so the test cost me £114 in total, a saving of £74.


MyHeritage is now using the Illumina Global Screening Array (GSA) for their Health and Ancestry test. This has a different range of markers (SNPs) compared to the AncestryDNA profile I uploaded to my other MyHeritage account. Having two accounts at MyHeritage will allow me to do comparisons to assess the effectiveness of the relationship predictions with the two different chips.

Included with the cost of the test is a free 12-month subscription which will allow me to receive all the new genetic risk and carrier status reports as they are released. The health subscription also includes all of the advanced DNA features for genealogy (such as viewing family trees of DNA matches, viewing shared matches and "ethnicities", and shared ancestral places), all of which previously required a MyHeritage site subscription. The health subscription will normally cost £89. However, I am somewhat concerned that the subscription is automatically renewed at the end of the year. In order to place my order I had to authorise MyHeritage to use my PayPal account for future payments.
I don't like the idea of having subscriptions automatically renewed so I have set myself a reminder to review the situation prior to the renewal. I have also discovered that there is an option buried deep in the settings to switch off the auto-renewal.

If you are ordering a test from MyHeritage there a few things to watch out for from a privacy perspective. As part of the order process you need to provide information about your date of birth. There is of course no requirement that you have to provide the correct date but you need to be aware that with the default privacy settings your "general age" (eg, thirties, forties, fifties) is automatically displayed to other MyHeritage members. MyHeritage also automatically creates a profile for you and by default this is publicly displayed. The default settings are shown in the screenshot below. 



Note that it is not possible to buy a MyHeritage kit as a standalone health test. Also you need to be aware that anyone who orders the Health and Ancestry test is automatically opted in to the relative matching feature and to the sharing of "ethnicity" reports and matching segment data. If you do not wish to opt in to these features you will need to adjust your settings in the My Privacy section under DNA Preferences. MyHeritage probably ought to review some of these default settings for their European Union customers because they are counter to the basic principles of GDPR (General Data Protection Regulation) which requires explicit informed consent.

I recommend checking your MyHeritage settings immediately after placing an order to make sure you are only sharing information that you wish to share.

The MyHeritage Health and Ancestry test currently offers 14 genetic risk reports including reports for haemochromatosis, Alzheimer's, late-onset Parkinson's disease, coeliac disease and hereditary BRCA cancers. There are 13 carrier status reports including cystic fibrosis, sickle cell anaemia and a number of other conditions, most of which I have never heard of. You can see a full list of the health reports here.

There have been concerns about false positive health reports with microarray testing. One study reported a 40% false positive rate though this was based on a small sample of just 49 people and included reports from third-party tools as well as direct-to-consumer genetic testing companies. According to the MyHeritage blog, the company takes additional steps to avoid false positive results and to ensure that the results are accurate. For any condition where a person has a significantly increased genetic risk, MyHeritage will double-check the results with Sanger sequencing.

You can watch the video below for an overview of the new MyHeritage Health and Ancestry test.

If you are in the US you should watch the US version of the video. MyHeritage have partnered with PWN Health, a private American network of doctors and genetic counsellors. US reports are reviewed by a doctor and you are referred, if necessary, to a genetic counsellor. The US price is $199 which works out at about £160 so it appears that American customers are paying a small premium equivalent to about £19 to cover the costs of the medical service. They do not have the option of ordering a test without clinical oversight.

You need to be over 18 to order the MyHeritage Health and Ancestry test. It is available in most countries of the world. It is currently not on sale in the following countries: Israel, France, Germany, Austria, Switzerland, Iran, Libya, Sudan, Somalia, North Korea, Lebanon and Syria. US residents living in the states of Rhode Island, New Jersey and New York are also not able to purchase the test. The price will vary in different countries depending on local taxes and exchange rates.

Direct-to-consumer genetic health tests are also provided by 23andMe, but they only sell their test in a limited number of countries. They are also not able to provide health reports in many of the countries where they sell their test. MyHeritage's entry into this market will now make health reports available to a much wider international consumer base. It will be interesting to see what the take up rate is and if there will be any international regulatory implications. The UK Parliament's Science and Technology Committee has just launched an enquiry into consumer genomics and the effects on the National Health Service. We will need to wait and see what recommendations emerge from this enquiry.

Once I've returned my kit it should take about four to six weeks to get my results and I will report back on what I learn and how the results compare with my 23andMe reports. There are proposals in England to have a paid for NHS genome sequencing service whereby healthy people will serve as "genomic volunteers" who will pay through the NHS for their genome to be sequenced and share the data. In the long run, I am probably likely to get more benefit from a UK-specific service which can be integrated with my health records as part of the NHS Genomic Medicine Service. However, such plans are in their infancy and, even if the service does eventually get off the ground, it will be useful to have data from other sources to serve as a comparison.

For further information about the MyHeritage Health and Ancestry test or to order a kit go to: https://www.myheritage.com/health

Further reading

Thursday, 4 July 2019

Updated genetic communities at AncestryDNA

On 19th June AncestryDNA rolled out over 225 new communities for people with ancestry from Australia, New Zealand, Canada, the United Kingdom and "French North America". These new communities are in addition to the 92 regions in Ireland that were introduced in January this year.  If you have taken a DNA test with AncestryDNA and have ancestry from any of these places you will probably find that your results have been updated and that the regions are now more granular.


I previously had just one genetic community for Southern England with South-East England as a sub-region. I am now in the Central Southern England community and have two sub-regions: (1) Dorset and Somerset; (2) Gloucestershire, Wiltshire and West Oxfordshire. Here is a screenshot of my updated results.


My dad previously had two communities: (1) Southern England with East Anglia and Essex as a sub-region; (2) Wales and the West Midlands. My dad now has three communities: Central Southern England, Devon and Cornwall, and East of England. He does not yet have any sub-regions. Below is a screenshot of his updated results. Note that although Norway and Sweden appear in his "ethnicity" estimate he does not have any documented ancestry from either country in the last 400 years or so. I fully expect Norway and Sweden to disappear from his estimate the next time Ancestry update their reference populations.


My mum was previously in two communities: (1) Southern England with South East England as a sub-region; (2) Wales and the West Midlands. She is now in the Central Southern England community and has Dorset and Somerset has a sub-region. See below for a screenshot of my mum's updated results.


Previously it was possible to access the confidence score for each community/region. I can no longer find a way to do this. I hope this feature will eventually be restored. We also used to have the ability to filter matches by region. This option has now disappeared but I understand that there are plans to restore it.

For my family the results haven't changed too drastically but the new communities do provide a marginal improvement on the previous results and are a good reflection of some of our predominant ancestries. As more people test and more people are added to the genetic networks that form the basis of the communities we can expect the results to change over time. I imagine that it will eventually possible to break the results down into more individual counties.

Have you had some updated communities? What do you think of your results?

Further reading
Related blog posts