Monday, February 19, 2018

LivingDNA Review

LivingDNA are a British DNA company providing an ethnicity report (autosomal DNA) and a Y-DNA haplogroup (if you're male), and mtDNA haplogroup, for $159 (sales as low as $89 are periodic though). It does not include matching with other testers, although the company says this will be coming in the future, for autosomal DNA (I suspect they're trying to build up their database of testers first). They do offer a way to upload your raw data from other companies for free, however, it's well hidden and hard to find on their site (you can access it here), you won't get your results until August 2018, and it's unclear what the results will include.

As a British company, they have focused greatly on British DNA and offer the most breakdown available for this region than any other company at the moment. They also offer the most breakdown for Europe, the Middle East, Native America, and parts of Asia, but they are oddly lacking in any Jewish populations, and their breakdown for Africa and Oceania is fairly average. You can compare their breakdown of populations to other companies here.

But just how accurate are these more specific breakdowns? It's important to remember all DNA ethnicity reports are only an estimate, and in my experience, the more specific the regions are, the more speculative it is. It's difficult to say just how accurate the specifics at LivingDNA are. Of the known locations my British branches have come from, they include: Lancashire, Kent, Scotland, Hertfordshire, Essex, and Suffolk. However, there's probably other locations I don't know about, plus, DNA can go back further than my tree. My LivingDNA results within Great Britain include the
following (also shown on map below):
My regions of Britain and Ireland from LivingDNA
  • South England 8%
  • East Anglia 6.6%
  • Northumbria 6.2%
  • Southeast England 3.8%
  • Central England 3.6%
  • South Central England 2.7%
  • Lincolnshire 2.7%
  • North Yorkshire 2.7%
  • Devon 1.5%
  • Northwest Scotland 1.5%
  • South Wales 1.5%

This is not representative of Lancashire, but it does cover my other known regions, and then some. Unfortunately, Lancashire is my most recent English branch (immigrated in the mid 1800s), so you'd think I'd have more of that than anything, whereas the other areas are from colonial times. Again, it's difficult to say how accurate this may be given that DNA can be more representative of about 1000 years ago, while my tree has only been researched as far back as about a few hundred years. Additionally, given the small percentages, it's entirely possible some of these are just attributed to noise (like a false positive).

What is very consistent with my family tree is that the only result in Ireland I get is actually a part of Northwest Scotland (Scots-Irish). Despite having a couple "Mc's" in my tree, they are all Scots-Irish, not Irish. Also, the total amount of 40.6% in Great Britain & Ireland is very consistent with my known ancestry. I estimate from what I can that my tree is approximately 35% British. Other reviews have been saying that LivingDNA tends to overestimate their total British results, so I was pleasantly surprised to see mine were fairly accurate.

What about the rest of Europe? Here's the results:
  • Europe (South) 30.2%
    • North Italy 17.3%
    • Tuscany 10.4%
    • Aegean 2.5%
  • Europe (North and West) 27.8%
    • Germanic 17.1%
    • Scandinavia 10.6%
  • Europe (East) 1.4% (on "Standard" setting, this is unassigned)
    • East Balkans 1.4%
My Europe South regions from LivingDNA

A total of 30.2% in Southern Europe is somewhat consistent with my tree (I had one Italian grandparent, so 25% on paper), but interestingly it's in almost exact agreement with most other companies. AncestryDNA says 31%, FamilyTreeDNA says 33%, and 23andMe says 29.5%. MyHeritage are the only outliers with 41.6% (which is one of the reasons I feel MyHeritage are the worst for ethnicity). However, looking at LivingDNA's breakdown for it, this is not really consistent with my tree. Most of my Italian branches have been researched back to the 1700s, and they are all from Southern Italy or Sicily, primarily three towns: Monteroduni, Sulmona, and Polizzi Generosa. LivingDNA has my results mainly in upper and mid Italy. You could possibly argue that Monteroduni and Sulmona are right on the boarder of the region they are calling "Tuscany" (the middle portion in pink on the map above/right), but certainly, Polizzi Generosa (Sicily) is not highlighted at all. Granted, the southern tip of Italy is highlighted as a part of the "Aegean" region, but I only get 2.5% in this category. Populations charts (example below) frequently show how North Italy and South Italy are genetically very different, so for my largest results in Italy to be in North Italy when my Italian ancestry is from Southern Italy just doesn't seem right. The entire Italian side of my family are dark haired, dark eyed, with olive toned skin. We are definitely Southern, and that is disappointingly not shown in LivingDNA's results.

Population chart from AncestryDNA - the closer the dots,
the more genetically similar (note the dots for Italy
show two groups, the larger one is northern Italy,
the smaller one is southern Italy,  showing
how genetically different they are)
Next we have a total of 27.8% in North & West Europe, with 17.1% Germanic and 10.6% Scandinavia. This could just be a coincidence, but if not, then a big congratulations is in order to LivingDNA, because they are pretty much the first company to accurately tell my British, Germanic, and Scandinavian DNA apart from one another. Every other company jumps from one extreme to another, or plays it safe by lumping a large portion of my DNA into a "broadly" Northwest European category, unable to break it down further (23andMe). According to my tree, I should be about 25% Germanic (Western Europe) and 12.5% Norwegian (Scandinavian). At other companies, Western Europe ranges from 0% to 17.9%, and Scandinavia ranges from 0% to 12.3%. While the upper ends of these ranges seem on par with LivingDNA, it is always at the expense of the other group (i.e., 12.3% in Scandinavia means 0% in Western Europe). If you're interested, you can see my complete results from all different companies here (although I did not include the sub-regions of Britain, there were too many). It's a shame Germany and Scandinavia can't be broken down further like Great Britain or even Italy are, but hopefully that will change in the future. I'll look forward to seeing how accurate it may be. I also note that LivingDNA was able to accurately tell Germany apart from France, something no other company has even attempted to do.

Lastly, we have the tiny 1.4% East Europe, which they're putting in more specifically in East Balkans (although the map coverage is the same for both). I have no known Eastern European or Balkans ancestry, but it's worth noting that in "Standard" mode, this 1.4% becomes "unassigned". So they are obviously unsure about this, and therefore it's likely just noise.

Similar to 23andMe, LivingDNA provides several levels of speculation or specification for your ethnicity results. There are three modes: Complete, Standard, and Cautious. Complete attempts to identify any "unassigned" DNA found in Standard mode. There was very little difference for me, which is why I used Complete mode here. As I mentioned, there was the 1.4% unassigned which got put in Europe East, and then there was 3% unassigned under Great Britain and Ireland which got put into the 1.5% Devon and 1.5% Northwest Scotland. Cautious mode groups regions more broadly (see below). Within each mode, there is an option to view results on a Global scale, Regional, or Sub-Regional. At Global, I'm 100% European on every mode. This is a little bit contrary to other companies, which often give me at least trace amounts of Middle East, North Africa, or South Asia. 

My results in Cautious mode
In Cautious mode, these are my Regional/Sub-regional results (also shown on map to the right):
  • Great Britain and Ireland 40.6%
    • Southeast England-related ancestry 18.2%
    • North Yorkshire-related ancestry 11.7%
    • East Anglia 6.6%
    • South Wales-related ancestry 1.2%
    • Great Britain and Ireland (unassigned) 3%
  • Northwestern Europe-related ancestry 27.8%
  • Pannonian Cluster-related ancestry 19.8%
  • South Italy-related ancestry 10.4%
  • Europe (unassigned) 1.4%

It's interesting to note that in Cautious mode, there is a 10.4% in "South Italy-related ancestry". It's not a very high amount, but it's interesting that it swapped from North Italy to South Italy for some reason. Meanwhile, my Scandinavian results have strangely disappeared completely. The map above is showing how some areas are found in more than one category. So the grayish blob over Germany is gray because it's in both "Northwestern Europe" and "Pannonian Cluster". Likewise, the brown parts of Britain are brown because they are in both "Great Britain & Ireland" and "Northwestern Europe". These results are more comparable with how other companies group their categories. That doesn't necessarily make it more accurate, just more broad.

My mtDNA haplogroup migration map from LivingDNA
As for the Y and mtDNA haplogroups, I am female so I have no Y haplogroup, and my mtDNA haplogroup is consistent with 23andMe and FTDNA's Full Sequence test: T2b. No revelations there. It includes a written history of the haplogroup, a coverage map, showing countries where your haplogroup is most commonly found, a migration map showing the route your haplogroup took out of Africa, and finally a Phylogenetic tree showing how your haplogroup descends from Mitochondrial Eve (or Y Chromosomal Adam). In comparison, 23andMe only offers the written history, the migration map, and the Phylogenetic tree, no coverage/frequency map. Also noteworthy, while 23andMe and LivingDNA include roughly the same amount of mtDNA raw data (23andMe includes 4,318 mtDNA SNPs, while LivingDNA includes more than 4,000), LivingDNA includes significantly more Y-DNA SNPs (roughly 20,000 to 23andMe's 3,733). Of course, neither of them include mtDNA or Y-DNA matches, so if that's what you're looking for, you'd have to take FTDNA's dedicated tests.

LivingDNA also provides a very detailed, interactive display of your results to share with others. Here's mine. While other companies often provide a similar way of sharing your results, none that I've seen have been quite this detailed or interactive. Does it share too much? LivingDNA also allows you to control what you share by giving you the option to remove elements or widgets.

I was hesitant to test with LivingDNA, given their lack of DNA matching, and the higher price tag, I felt like what you got wasn't worth that much money. Then it was on super sale over Christmas so I decided to take the plunge. I am pleased with the ethnicity report - at regional level, it's been the most accurate for me so far, but the sub-regional results need some work. Particularly if you already know your haplogroups, I wouldn't pay full price for this test, but I do think it's worth exploring, especially if they add DNA matches in the future. 

Wednesday, January 17, 2018

Gencove Review

Some of the apps Gencove offer
Gencove sells DNA tests for $59.99, but they also offer a free upload of your raw DNA data if you tested elsewhere. With the free upload, you get all the same options you do if you tested with them, namely an ethnicity report and matching with DNA relatives.

They also offer "apps", some from third parties. There is even a Promethease app for $10, though it would be cheaper and probably easier to just upload directly to Promethease (see a full review of Promethease here). There's also an app for GenePlaza, which was also previously reviewed here. Though the app is free, GenePlaza's reports each cost a small fee. Clicking on the GenePlaza app in Gencove merely takes you to GenePlaza's website. The other apps are free too, but they aren't particularly useful. They include:
  • Discover your microbiome - Bacteria and viruses that live in your mouth
  • My Genome - Info about your genomic data
  • Sleep - Are you a morning or evening person?
  • iobio.io - Compare your genome to ClinVar
  • YouGenomics India - Help improve genomics for South Asia
  • Gencove Mobile App - Compare results with friends on iOS or Android
  • Open Humans - Contribute to research and citizen science

When I tried Microbiome it simply said "Microbiome not available" with no explanation as to why, so that was totally useless.

My Genome is just that - it's where you find your raw DNA data. You can download your raw data, you can view which apps on Gencove you've given permission to access your data, and you can view and manage your consent to participate in research.

The Sleep app is interesting but the results claimed I'm a morning person, which I have never been. The app asks you a few questions about your sleep habits before showing your results and it did note "It seems that the genetic score and questionnaire results don’t match - an interesting outlier! That's probably because the genetics of sleep is not very well understood yet."

iobio
The iobio app loads your DNA to gene.iobio.io which is a little bit of a technical app that will tell you if you have any variants of certain medically related genes. For example, it includes a report on BRCA1 and BRCA2, which are genes associated with breast and ovarian cancer. Despite the technical looking nature of the site, it will tell you, in plain English, if you carry any variants of the genes included in the report or not. Hovering over each gene will pop up a brief summary of what it is associated it. Most of them are likely somewhat rare, since I had no variants for any of them. There are 40 in total: PTEN, BRCA1, BRCA2, TP53, STK11, MLH1, MSH2, MSH6, PMS2, APC, MUTYH, VHL, MEN1, RET, RB1, SDHD, SDHAF2, SDHC, SDHB, TSC1, TSC2, WT1, NF2, COL3A1, FBN1, TGFBR1, TGFBR2, SMAD3, ACTA2, MYH11, MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL3, ACTC1, PRKAG2, GLA, MYL2, LMNA, RYR2, PKP2, DSP, DSC2, TMEM43, DSG2, KCNQ1, KCNH2, SCN5A, LDLR, APOB, PCSK9, RYR1, CACNA1S, ATP7B, BMPR1A, SMAD4, OTC. If you have reason to check on any of these and want a quick, free way to do this, this is a good option, but it can also be easily accessed independently of Gencove, just go to http://iobio.io, however, it's not very user friendly and I couldn't find a way to upload my data, so going through Gencove may actually be the better option.

YouGenomics India, recently renamed "Genavli Biotech", is a research project for South Asia, attempting to improve ethnicity reports for people with South Asian ancestry. Naturally, it wouldn't be useful for anyone who is not South Asian but if you are, you should look into this. As far as I can tell, Gencove's app simply links to the YouGenomics India website.

The Gencove Mobile App doesn't really offer anything that the website doesn't apart from some surveys which I presume are for research purposes. It allows your to see your ethnicity report and the unavailable microbiome report, and connect with or invite your friends. That's about it. 

The Open Humans app merely takes you to openhumans.org, which is an open research project. Gencove does not load your data there, so there's really no need to go through Gencove if you wish to participate in this project.

Gencove's populations for their ethnicity report
Most people will likely be most interested in the ethnicity report. There are 26 populations available, some of them are broad, large regions, while others only cover a small region. They include: Northern and Central Europe, Northern Italy, Northern British Isles, Southwestern Europe, Middle East, Eastern Mediterranean, Bengal, Central Africa, Eastern Africa, Northern Africa, Central Indian subcontinent, Southern Indian subcontinent, Oceania, Southeast Asia, Northeast Asia, Anatolia-Caucasus-Iranian Plateau, Central Asia, East Asia, North-central Asia, Northeast Europe, Scandinavia, Finland, Southern Africa, Western Africa, Ashkenazi Jewish, Americas. A map showing what these populations cover is shown left/above.

My personal results were not particular accurate, although I did note that if I added together all my results in populations probably associated with my Italian ancestry versus those from my Northwest European ancestry, the numbers were consistent with what most other companies say. Here are my Gencove results:

My Gencove ethnicity report
48% Northern and Central Europe
21% Northern Italy
15% Northern British Isles
7% Southwestern Europe
6% Middle East
3% Eastern Mediterranean

My Italian ancestry is southern, not northern, but if you add up the results for Northern Italy, Southwestern Europe, Middle East, and Eastern Mediterranean, you get 37%, which is very similar to the 36% from AncestryDNA and 38% from FTDNA. While my results in more specific regions may be all over the place across different companies, the divide between northern Europe and southern seems very distinct with me so when an ethnicity report is consistent with that, I know there's at least some reliability to it. 

Lastly, Gencove offer the "Relative Radar" which finds people you share DNA with. Unfortunately, there must not be very many testers/uploaders in their database because it found none for me so all I can say about it is that it seems to use a visual display, plotting relatives who share more DNA with you closer to your profile icon.

Conclusion: Since it's free, there's really no harm in checking out Gencove (unless you have concerns about research participation). Because some of their "apps" simply link to other sites, it looks like they offer more than they really do. The ethnicity report, sleep app, and iobio data were the only really interesting or useful options, but even with those, don't expect too much. I definitely wouldn't pay $59.99 to test with them, although the low price point in comparison with other testing companies may be appealing, you would get more out of your money by testing with AncestryDNA or 23andMe and then uploading to Gencove for free.

Monday, January 15, 2018

GPS Origins Upload Review

There are several different DNA tests available from HomeDNA, but this is a review of their "GPS Origins Algorithm" test which allows you to upload your raw DNA data from another company for an ethnic origins analysis. It costs $39 and as far as I can tell, it's pretty much the same results you'd get if you'd bought their "GPS Origins Ancestry Test" for $199. It does not include DNA matching with other testers or any kind of  health report.

Migration routes seem a little misleading, and generic
I found the results to be not very accurate, and even a little bit misleading. The information talks a lot about prehistoric and ancient origins, even though an autosomal SNP test doesn't generally go back that far. Other info says the test results "begin over 1,000 years ago" which is consistent with other autosomal ethnicity tests, which usually state the results represent about 500-1000 years ago. There's also a lot of information about Y and mtDNA which makes it sound like these include Y and mtDNA, even though it doesn't. It even has a map showing "migration routes", one in red and one in blue, which makes it look maternal and paternal. Not only is that impossible since I am female and don't have Y-DNA, but there is also a note: "Although both Migration Patterns represent your Maternal and Paternal DNA routes, we do not differentiate which route is maternal and which is paternal." So why make them blue and red? And why are there only two "routes"? I have several European origins, not only according to my tree, but also according to this ethnicity report. While GPS Origins do offer a Y test and an mtDNA test, they are not included in the autosomal DNA test.

Info on my Sardinian migration route when clicking on
one of the map markers (above)
The migration routes are suspicious because they don't offer much explanation as to how they determined these routes. From what I can tell, it seems like the "routes" are just generic info tossed up for people who get results in one part of Europe or another. For example, I got 11.7% in Sardinia, and my "blue" route shows it starting in Sardinia and moving north through Italy. Basically, the routes just seem to be providing generic info on the common migration pattern of Sardinians. The other "red" route appears to be from either my Fennoscandia results or Western Siberia. Again, I'm not very clear on how they chose these two routes, or why there's only two of them, apart from the fact that they seem to be trying to make them look like paternal and maternal results when they're not.

GPS Origins claims the migration route include "precision targeting—sometimes down to the village or town" which is a gross exaggeration. The map markers may look precise, but when you read the info attached to it, you can see it's not that specific.

The results in Sardinia, Fennoscandia, and Western Siberia are a little off to begin with. I'm getting 21.5% in Fennscandia, 11.7% in Sardinia, and 11.6% in Western Siberia. I do have Scandinavian roots in Norway, but it should only about 12.5%. The Sardinia results are probably coming from my Italian ancestry, but peaking in Sardinia doesn't seem right. As for Western Siberia, I have no ancestry there at all.

My ethnicity percentages
My full results are:

#1 Fennoscandia 21.5%
Origin: Peaks in the Iceland and Norway and declines in Finland, England, and France

#2 Sardinia 11.7%
Origin: Peaks in Sardinia and declines in weaker in Italy, Greece, Albania, and The Balkans

#3 Western Siberia 11.6%
Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

#4 Orkney Islands 11.5%
Origin: Peaks in the Orkney islands and declines in England, France, Germany, Belarus, and Poland

#5 Southern France 9.9%
Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

Why are they talking about Y and mtDNA in my autosomal
DNA results?
#6 Basque Country 9.3%
Origin: Peaks in France and Spain Basque regions and declines in Spain, France, and Germany

#7 Tuva 8.1%
Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

#8 Southeastern India 5.4%
Origin: Endemic to south eastern india with residues in Pakistan

#9 Northern India 5%
Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

#10 The Southern Levant 3%
Origin: This gene pool is localized to Israel with residues in Syria

#11 Arabia 1.6%
Origin: Peaks in Saudi Arabia and Yemen and declines in Israel, Jordan, Iraq, and Egypt

#12 Northwestern Africa 1.1%
Origin: Peaks in Algeria and declines in Morocco and Tunisia

#13 Western South America 0.3%
Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

You can compare this with my results from other companies here.

The Legal Genealogists says GPS Origins is one not to bother with, and based on this I would agree. I definitely would discourage anyone from buying a test with them, considering it costs $199 compared to the more popular DNA companies charging $99 or less. You're basically paying twice the amount to get inferior ethnicity reports and no DNA matching with other testers. As for the $39 upload, it may be worth it for curiosity sake, but don't expect much from it. I found it very disappointing.

Here's another thorough review from another blogger.

Wednesday, January 3, 2018

The Importance of Primary Sources

This death certificate is only a primary source for the death
info. His parents names are actually wrong, and his birth year
is in conflict with records from when he was alive, suggesting
the informant, his son, may have gotten it wrong.
I often see people asking about which source is better for a certain fact or event and this is a good time to address the differences between a primary source and a secondary source. A primary source is a document which is recorded at the time of the event it's detailing. A secondary source is one that is detailing an event that occurred in the past, and therefore may be more likely to be incorrect. A primary or secondary source can also be a person, regarding whether or not that person was alive/witness to the event in question. So to understand the reliability of a record, we have to understand what it's a primary source for, and what it's not. Here's a quick rundown:
  • Birth records are the only primary source for a birth. This may include a birth announcement in the newspaper, but the further back you go, the less likely this becomes. Equally, the further back you go, the less likely that civil vital records were kept. Delayed birth certificates aren't a primary source, but may be the only record of a birth in existence. Also keep in mind that some places would fine individuals for reporting a birth too late, which means they may have lied about the birth date to avoid being fined.
  • Baptism records are only a primary source for the baptism, not the birth. However, if the baptism occurred only a few days after the birth, that's pretty much as good as a primary source for the birth too (if it recorded the birth date - do not assume the baptism and birth date are the same if both aren't recorded). Especially if there's no birth record in existence, a baptism record is likely as good as it's going to get. However, if the baptism took place years after the birth, maybe even months, that is not a primary source for the birth because enough time has passed for the actual birth details to have been remembered incorrectly.
  • Marriage records are only a primary source for the marriage. Particularly if the parents of the bride or groom were deceased, you can't be sure their names are correct. Be careful not to mistake a marriage bann, engagement announcement, or marriage license for the actual marriage.
  • Death records are only a primary source for the death. If it includes an address where the deceased was living at the time of death, then it's also a primary source for that. But it's a secondary source for the birth date and location, both because the document is normally recorded many years after the birth (unless it's an infant death), and because the informant for the death record is often someone who wasn't even alive or present at the time of the deceased's birth. It's also not a primary source for the parent's names or birth locations; it's very common for those details to be incorrect. Death records are usually a good source for the burial location, even though they are recorded before the burial takes place, and therefore that info theoretically could change before it happens.
  • Obituaries are generally considered a type of death record and therefore can be considered a primary source for the death if they are published within a few days of the death, as is typical. Excepting potential printing errors, of course (i.e. the informant may have provided the correct death information, but the typist misprinted it).
  • Gravestones aren't really a primary source for anything! At the most, they may be a primary source for the location of the burial, but I have seen gravestones erected for people before their death, who then actually wind up buried elsewhere. However, when this happens, there's usually a lack of at least a death date on the gravestone. It's also not a primary source for the date of the burial, since gravestones don't normally have the burial date listed on them. You might think it's a primary source for the death date, but gravestones often aren't created for weeks or even months after the death, plenty of time for people to remember the exact date incorrectly. 
  • Cemetery/burial records are only a primary source for the burial information. Unlike gravestones, these usually include the interment date and wouldn't exist unless the deceased was actually buried there.
  • Census records are only a primary source for data that was current at the time the census was taken, such as: residence, occupation, citizenship, literacy, etc. All other data that occurred prior to the census - birth/age, marriage, immigration, etc is secondary. Additionally, even things like the occupational data may be subject to the knowledge of the informant and could be incorrect. Also don't forget that in the US, pre-1880 censuses did not record relationships to the head of the household. While you can often surmise relationships based on the order in which people are listed, ages, and names, you can't be sure about them without other supporting documents to confirm. 
  • Family bibles may or may not be a primary source for any or all of the data within, depending on when each item of information was recorded and who recorded it. Unfortunately, there's generally no way to know for sure when the data was recorded, or who by. You can sometimes get an idea based on the handwriting and/or different types of pens used at different times. For example, you might note the birth info was recorded at a different time from the death info. But this still doesn't assure they were recorded at the time of those events. They could have each been recorded years after the fact, whenever the author (and we may not even know who the author was) got around to it.
  • Wills and Probates can contain a lot of valuable and reliable information, like the names of someone's children, the details of their estate/property, etc. But even though they are related to the death fact, they typically don't contain a date or location of the death, let alone a cause of death. Don't mistake the will or probate dates for the death date, but you can usually get a time frame for the death date - sometime after the will date, and before it was probated.
  • Lineage books are a secondary source for everything in them, since they are written after all the events took place. However, many lineage books use primary sources for at least some of their information. That doesn't necessarily mean the entire book is reliable, but the particular data coming from primary sources should be. Not all authors note their sources, but many do.
A gravestone with no dates - this person was
actually buried in a different cemetery (I
believe his parents erected gravestones for
their children in the family plot, but some of
them wound up choosing other cemeteries. This
is not typical in my experience.
Naturally, we do not always manage to find a primary source for each bit of information and that doesn't mean we can't use secondary sources. Even primary sources can be wrong sometimes, they are just much less likely to be so. We just have to work with what we have, and what exists, and understand what is more or less likely to be accurate. Having data from a secondary source doesn't mean we can't put that data or that source in our tree, it just means we should keep looking for better or additional resources to help confirm or deny it. Family trees are forever a work in progress and no one should assume that once a piece of information is put into a tree, it means you're confident it's accurate. The sources you cite in your tree should speak for themselves as to their reliability.

Judging which secondary source is more reliable for what type of conflicting data can be difficult, and we have to weigh when, how, and by who the data was recorded/provided. You may think it makes the most sense to go with a birth year that you find on most of the records for an individual, but what if all those records are from later in his life, or even after his death? A record from his childhood, closer to when he was born, and when his parents, who were there for the birth, were still alive and one of them may have been the informant may actually prove to be the more reliable source. Of course you can never know for sure, so it's also best to put all recorded facts in your tree as alternate data, but you still have to pick a default/preferred one. Hopefully, this has given you some things to consider when choosing a default/preferred fact to go with, and given you a good understanding of primary and secondary documents.

Monday, November 27, 2017

Genome Link Review

Genome Link - Knowledge Base
Genome Link, powered by Awakens, Inc., is a third party website that accepts raw DNA data from 23andMe and AncestryDNA to provide some health reports for free, and even more for a $89 fee (currently on sale for only $39). It does not include an ethnicity report.

The health report includes your risk of some diseases, as well as things like physical traits, personality (mental health), intelligence, nutrition, and fitness. Unfortunately, the way it presents your results is very technical and confusing. It does not explain your results in plain English so that most people can understand it easily. What's more, is that the section which is easier to understand does not even include your personal results.

Floating bubbles in Knowledge Base
There's two sections: Explore Genome (shown below), and Knowledge Base (shown above and right). The names suggest Explore Genome is where you'll find your own results, and Knowledge Base is general information, but newcomers to the field may not understand this. So at first glance, Knowledge Base looks like where you would find your health reports, but these are actually just reports on the general population's tendency towards these conditions and traits. Clicking on them will show you a chart with floating bubbles (shown right) - the bigger and more bubbles, the higher or lower a population's tendency on the scale. Different colored bubbles indicate populations from different parts of the world. Europe is blue, Asia is pink, etc. So you can see whether Asians, Africans, etc are more or less prone to certain things. It's interesting, but it really doesn't tell you anything about yourself. What's worse is that it's poorly explained and at first makes it look like these are your personal results - but as you can see in the screenshot, why would I have pink (East Asian) bubbles when I have no East Asian ancestry? These are not my results.

Exploring my genome
Where you find your personal reports is instead under "Explore Genome", but this section is highly technical and not easy to use. On the far right are your chromosomes you can click through and on the far left it lists a ton of conditions and traits in seemingly no particular order (though there is a search field above) and clicking on them will show you in the large middle space where in your genome they appear with a letter underneath indicating your genotype (shown left). This visual display is totally unnecessary, you can see all the empty space used just to tell me my genotype is "A." Most people just want to know whether they are at a higher or lower risk for a condition, but the report won't tell you this, not in plain English. All it will say is if you have a certain genotype, you should click on the link for more information. The link will take you to the publication of a medical study, which is highly technical and probably not going to be understood by most people. And you can't assume that having the certain genotype means you're at a higher risk for that condition. For example, it may sound like I am a carrier for Cystic Fibrosis because it says "If you have A then check the evidence below" - and according to them, I do have "A" (genotype). But according to every other health report I've run on my DNA, I am not a carrier for Cystic Fibrosis. So this could be very misleading. Sure enough, opening up their link to the medical publication isn't useful for a laywoman like myself, as it's full of highly technical data I can't even begin to understand.

There is a "Help" button in the lower right, but it's just a short FAQ which really doesn't tell you much more than what I've just explained.

Conclusion: While you do get a good amount of health reports for free, they are fairly useless for the average individual as they do not explain, in plain English, what they mean. And while you can also get many more reports for the $89 fee, it would still be useless unless you're an genetic academic and can understand the medical publications. If they were to add better interpretations of the results so most people could understand them, this could be a very comprehensive health report, especially given what you get for free. As for the $89 fee, you can get just as many reports (which are much easier to understand) from Promethease.com for a mere $5, so the Genome Link's fee seems extremely high, even if, as I write this, it's on sale for only $39.

Saturday, November 25, 2017

Promethease Review

A screenshot from Promethease's health report
Promethease.com is a third party website for providing a comprehensive health report from your raw DNA data. It's not free, but it is extremely affordable at only $5 per report. They accept DNA from 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage, LivingDNA, Genos, and possibly others. Promethease recommends trying to upload regardless of what company you tested with as "many formats" should work. If it doesn't work, they encourage you to email them.

There are two options when you purchase a health report: you can create a free account, or you can get your report without an account. With an account, your raw DNA data which you upload is saved on the site (until/unless you ever decide to delete it). The report generated from it is deleted from the website after 45 days, however, you can regenerate the report from your saved raw data for free at any time. If you manage more than one kit, you can include them all on one account (but each report still costs $5). If you don't create an account, after 24 hours, everything (including your raw DNA data) will be deleted from their site and if you ever need to regenerate the report, you would have to pay again. Either way, the report is downloadable to save on your computer for future use, and so you can give a copy to your doctor. So creating an account is beneficial for regenerating the report at any time for free, especially if there are updates to the report. But for those who are concerned with privacy and don't want to store their DNA on the site, they have that option. For more information on Promethease's privacy policy, see here.

Promethease's tutorial
The first thing you'll see in your health report is a tutorial that pops up when you open it. I would suggest going through it and opening the links it contains for further information. The data Promethease throws at you can be a little technical and a lot overwhelming, but the tutorial definitely helps.

Although it explains, in plain English, what different genes are associated with and what it means, whether it's good or bad for you, etc, the most confusing thing about it is that you can have one gene that says you have a decreased risk of something, and another gene that says you have an increased risk of the exact same thing. How that plays out in reality is really something you'd have to ask your doctor. Essentially, all Promethease is doing is pulling data from SNPedia, which is like Wikipedia for genetics (they source their info from peer-reviewed scientific publications), so you don't have to go looking up each one of your genes and what they might be associated with.

The amount of information the report includes makes it impossible to view everything at once, which is why they've included various ways to search, filter, and sort the results. If you want to see everything on cancer, for example, you can either use the search bar at the top for "cancer", or select cancer from the "medical conditions" drop down bar on the right. It will then list all genes you have which are associated with cancer, good or bad, or "not set" (see image above right). I normally untick the option for "not set" because this basically means there's not enough information to say whether the association is good or bad and that means it doesn't really tell you anything.

Read through all the info and click "more info" to get
complete data on what a gene is associated with.
Sometimes when you select conditions from the drop down menu, a report may not readily sound like it's associated with that condition. For example, when I select cancer, one of the reports is for "Possibly impaired folate metabolism" (shown left) and the information included doesn't mention cancer. However, reading the whole summary, tells me the gene is "linked to slightly increased risk for several types of brain cancer." This is good to know, considering my grandfather died of brain cancer. Additionally, when I click on "more info" at the bottom of the details, it takes me to this page, which includes a huge long list of others conditions it's associated with, not mentioned in the summary. So make sure you read everything thoroughly and when there is an option to click for "more info", click it. Keep in mind that a single gene may be associated with more than one condition and that may be why, at first glance, it doesn't seem associated with the condition you selected even though it is.

Magnitude chart
Also note the "Magnitude" number. This is a measure of the interest factor. SNPedia recommends magnitudes under 2 aren't worth paying much attention to. Above 3 should be particularly noteworthy. That means you may have a "bad" gene for a certain condition, but if the magnitude is low, it's probably not worth concerning yourself over. So if you have one gene that says you have a higher risk of something, and another gene that says you have a lower risk of the same thing, take a look at the magnitude for each. You may even want to filter out any reports under a magnitude of 2 or 3, as the ones above those magnitudes are the ones you're going to want to pay the most attention to.

Conclusion: Although a little technical and can be confusing if you have genes that seemingly conflict with one another, the amount of information you get for a mere $5 is absolutely worth it, particularly because they do explain, in plain English, what the results mean. This is easily the most comprehensive health report available, especially for the price. The ability to download the report in its entirety is extremely beneficial as well, not only for future reference, but also so you can give it to your doctor (an option that is surprisingly lacking on many other health reports I've used), and I would strongly recommend taking it to your doctor as well, for a better understanding.

Sunday, November 19, 2017

GenePlaza Review

GenePlaza is a third party website that allows you to upload your raw DNA data from testing companies including 23andMe and AncestryDNA, and provides you with different DNA reports, for small fees.

It offers some ethnicity reports, and some traits, and nutritional reports. To the left you can see a screenshot of all the "apps" or reports they offer and how much they each cost. The upload of your DNA is free, and they even provide you with $3 credit for uploading, which will buy you at least one app/report - so you get at least one for free. Not a bad deal, and the other apps aren't very expensive either, ranging from $1-5.

However, it doesn't provide a true health report with disease risks, only "traits" like Intelligence, Sleep, Taste. etc. The apps for Neuroticism and Weight are probably the closest to health reports and may be of use to some people, but there are other sites that will provide a much more comprehensive health report. On GenePlaza, they tell you whether you're likely to be predisposed to each condition or not, including a chart on how your results compare with other GenePlaza users.

GenePlaza's example of the Ethnicity Calculator plot chart
Of the three ethnicity options, the "Ancestry" app is likely the one most people are looking for. The K12 Ancient Admixture Calculator only reports on prehistoric populations like Hunter-Gatherer or Farmer. While it can be interesting, most people are looking for their more recent admixture report. There's two of those: "Ethnicity Calculator" and "Ancestry". The Ethnicity Calculator is simply a plot chart. It works by providing a chart showing the different populations included and how closely or distantly they relate to each other (the closer the dots on the chart, the more closely they are to one another) and then showing you where on the plot chart your DNA fits in the best. It does not provide any percentages for each population you match, which is what most people are looking for.

That brings us to the "Ancestry" app, shown below. It costs $1.89, meaning you can get it for free with the $3 credit they give you for uploading. This will provide a report much like you received with the company you tested with, percentages and all. However, the regions included are broad, for example, I got 55.7% Northwest European, 27.6% Southwest European, 15.2% Ambiguous West Eurasian, and 1.5% Ambiguous. According to GenePlaza, Ambiguous "indicates a percentage of your DNA file that did not match with any of the sources in our reference panel." So it means 1.5% of my DNA didn't match any of their samples, and 15.2% of my DNA couldn't be narrowed down further than "West Eurasian".

For me, this is fairly accurate, if not very specific. My tree is 25% Southern European (Southern Italian/Sicilian), and 75% Northern European (British, German, and Norwegian). If you add the Ambiguous results to Northwest European, that's almost exactly consistent with my tree. However, it conflicts with most other DNA ethnicity reports. 23andMe, AncestryDNA, and FamilyTreeDNA, all seem to agree I'm more like 62-64% Northern European and 36-38% Southern. Take from that what you may, keeping in mind all ethnicity reports are an estimate.

You'll note there is an option to expand my results for Northwest and Southwest European. This provides details on the more specific populations I matched from those regions, but it does not provide a percentage for these groups. For Northwest European, it says I most closely match populations from Argyll Bute (an area of Scotland), England, Norway, and Orkney Islands (off the Northern coast of Scotland). This is fairly consistent with my tree - my British roots are indeed Scottish and English, though I don't know where in Scotland so I can't confirm Argyll Bute and Orkney Islands, but the interesting this about this is I often get Orkney results in Oracle too (see here for details on what Oracle is). The only thing this break down is missing is my German roots.

My break down for Southwestern European is a little farther off the mark. They seem to think I most closely match Basque, South France, and Spain but obviously this is actually my Italian DNA.

NOTE: There has since been added a four ethnicity calculator called K25 Admixture Calculator, which means it includes 25 categories, some of which are very specific regions. I have not tested it yet for accuracy but it looks very interesting. It costs $5. Worth noting is that it has 3 categories for Native American, but none for Jewish.

GenePlaza's example of the Intelligence report (I'm probably
not that intelligent, lol)
Conclusion: Easy to use and explains everything in plain English, doesn't include much of the technical data in the background. Report options are few, but you can at least get your ethnicity break down for free and the other apps aren't expensive. Each app has an example preview showing you what you'll get if you purchase it, so you can decide whether it's worth it or not. For the free ethnicity report, it's worth checking it out, but the purchase of the other apps may not be worth the cost. Although they are inexpensive, there are other options that will provide more reports for a similar cost or even for free. See a list of upload options for your DNA here.

Friday, November 17, 2017

LiveWello Review

LiveWello report explains how I have a decreased likelihood
of gluten sensitivity and celiac disease
LiveWello is a site where you can upload your raw DNA data from several testing companies including 23andMe, AncestryDNA, and FamilyTreeDNA and get reports on a number of health related issues. It costs $19.95 to upload your raw DNA data, but they also offer an additional subscription for $5.95 monthly or $60 yearly. But what all do you get with those different options?

With the $19.95 one time upload fee, you gain access to some reports from LiveWello which explain, in plain English, whether you have an increased, normal, or decreased risk of whatever the report is about. In addition, you have access to the "Gene Library" which is a huge library of different health reports created by third parties. It's very extensive, but the drawbacks are that it doesn't explain in plain English what your risks are, and it doesn't allow you to search for a certain type of report. All you can do is scroll through the list of available reports (listed in order that they are added, with no other way to sort them) and hope to find what you're looking for. The reports only provide the raw DNA and leaves the interpretation up to you, and that means you need some understanding of DNA and how genetic variance works. Many of the Gene Library reports don't even tell you what conditions are associated with the gene(s) it's reporting on, suggesting it's only really beneficial for academics or health care professionals.

Disappointing? A bit. For $19.95, you don't get much, and then they want you to pay even more. Compared to options like Promethease, which provides hundreds of reports for only $5 (one time fee), it seems like you're paying a lot more to get a lot less with LiveWello. In addition, note that although you can upload multiple kits to one account, the fees for LiveWello (both the one time upload fee and subscription) apply to each kit you want to upload. So, let's say you manage your kit, and both your parents kits - full access to LiveWello for all of you would cost about $60 in upload fees, and about $18 monthly. That starts to really add up.

Gene Variance report from "Gene Library" template doesn't
include any explanation of what the data means (increased,
decreased, or average risk)
With the subscription, you gain access to all reports provided by LiveWello, and they also claim you gain access to "all the features included in your gene variance report" (these are for the Gene Library), but I am unclear what this includes since my gene variance reports look exactly the same before and during the subscription. So although the Gene Library is extensive, for most people, it won't be of much use unless you are knowledgeable about gene variance and how they work.

It may look like the color coding explains a tendency towards something good or bad, but it doesn't appear to be consistent and doesn't explain how having both green and red results makes you more or less prone to something.

With the one time fee, you get the following 28 reports (not including Gene Library):

1. COMT Gene and Sensitivity to Pain
2. Nexium, acid reflux disease and CYP2C19 drugs
3. Warfarin and CYP2C9 drugs
4. Plavix, blood thinners and CYP2C19 drugs
5. Response to diabetes medication - Sulfonylureas
6. Hepatitis C Treatment
7. Preference for sweet foods
8. Tramadol and CYP2D6 drugs
9. VDR Taq Gene and Osteoporosis
10. Lupus
11. Vitamin B12
12. MTHFR and Risk of Depression
13. COMT Gene and Personality Traits
14. Vitamin B6
15. Alcohol tolerance
16. Anti-depressant Response: Paxil, Celexa, Effexor or Elavil
17. Folate and the MTHFR gene
18. Caffeine and Anxiety
19. Kidney disease risk and MTHFS gene
20. Oxycodone and CYP2D6 drugs
21. Vitamin A
22. Hormone Replacement Therapy
23. Response to cholesterol lowering medication
24. Sexual Dysfunction due to Celexa, Lexapro, Prozac, Paxil or Zoloft
25. Alcohol abuse and risk of esophageal cancer
26. Zofran and CYP2D6 drugs
27. MAOA - The Warrior gene
28. Metformin

With the additional subscription, you get 93 more reports (not including Gene Library):

1. Aspirin Allergy - Asthma Risk   (Subscription only)
2. Risk of Duodenal Ulcer   (Subscription only)
3. CYP Gene and Irregular Heart Rhythm   (Subscription only)
4. Genes Related to Manic Symptoms in Bipolar Disorder   (Subscription only)
5. COMT Gene and Irritable Bowel Syndrome   (Subscription only)
6. Histamine Gene and Sensitivity to NSAIDS (Aspirin, Alleve, Advil, Motrin)   (Subscription only)
7. Floxacillin Associated Liver Toxicity   (Subscription only)
8. Narcolepsy   (Subscription only)
9. Susceptibility to Both Crohn's Disease and Ulcerative Colitis   (Subscription only)
10. FUT2 Gene and the Gut Microbiome   (Subscription only)
11. Hot flashes in post menopausal women   (Subscription only)
12. Response to bupropion treatment for smoking cessation   (Subscription only)
13. Susceptibility to food poisoning caused by Norovirus   (Subscription only)
14. COMT Gene and Antipsychotics   (Subscription only)
15. G6PD Gene and Risk of Hemolysis with Bactrim   (Subscription only)
16. Methamphetamine and Risk of Psychosis   (Subscription only)
17. Painful Menstrual Period and BDNF Gene   (Subscription only)
18. COMT Gene and Response to Effexor   (Subscription only)
19. MTHFR Gene and Pravastatin Efficacy   (Subscription only)
20. Risk of Deep Vein Thrombosis   (Subscription only)
21. Levofloxacin and Risk Of Seizures   (Subscription only)
22. Response to Treatment of Blood Pressure with Benazepril   (Subscription only)
23. Response to steroid treatment of Crohn's disease   (Subscription only)
24. COMT Gene and Tobacco Use Disorder   (Subscription only)
25. MTHFR Gene and risk of Stroke   (Subscription only)
26. Medication Overuse Headaches   (Subscription only)
27. Risk of Acute Psychosis with Cannabis   (Subscription only)
28. Processed Meat and Risk of Colorectal Cancer   (Subscription only)
29. Response to Vitamin E Supplementation   (Subscription only)
30. Fat and Obesity (FTO) Gene and Risk of Alzheimer's Disease   (Subscription only)
31. Cold Sores   (Subscription only)
32. APOE gene and Alzheimer disease risk   (Subscription only)
33. Risk of liver damage with Depakote (valproic acid)   (Subscription only)
34. Aspirin Allergy - Hives   (Subscription only)
35. Risk of Developing Multiple Sclerosis   (Subscription only)
36. Efficacy of Blood Pressure Medication, Norvasc   (Subscription only)
37. NOS Gene and Response to Viagra   (Subscription only)
38. APOE Gene, Cholesterol level and Diets   (Subscription only)
39. Vitamin D   (Subscription only)
40. Response to Carisoprodol (SOMA)   (Subscription only)
41. Heart Failure Treatment with Bidil   (Subscription only)
42. Breast Cancer Treatment   (Subscription only)
43. MTHFR, Homocysteine and Nitrous Oxide Anesthesia   (Subscription only)
44. Hormone Replacement Therapy, SULT1A Gene and Risk of Endometrial Cancer   (Subscription only)
45. Abacavir   (Subscription only)
46. Migraine response to vitamin supplementation   (Subscription only)
47. NTRK2 Gene and Lithium Efficacy   (Subscription only)
48. Smoking cessation with nicotine replacement therapy   (Subscription only)
49. GNB3 Gene and Antidepressant Toxicity   (Subscription only)
50. Response to Narcolepsy Drug - Modafinil   (Subscription only)
51. BDNF Gene and Depression - Response to Paxil   (Subscription only)
52. Tegretol Efficacy in Treatment of Seizures   (Subscription only)
53. NOS3 Gene and Response to Blood Pressure Medications   (Subscription only)
54. Phenytoin and CYP2C9 drugs   (Subscription only)
55. Heroin Addiction   (Subscription only)
56. SLC2A3 Gene and Dyslexia in Children   (Subscription only)
57. Sensitivity to Muscle Relaxants Used in General Anesthesia   (Subscription only)
58. APOE Gene and Exercise Response   (Subscription only)
59. General Anesthesia - postoperative nausea and vomiting   (Subscription only)
60. G6PD deficiency, risk of malaria and drug-induced hemolysis   (Subscription only)
61. STXBP5L Gene and Facial Aging   (Subscription only)
62. Multiple Chemical Sensitivity   (Subscription only)
63. MTHFR Gene and Smoking Behavior   (Subscription only)
64. Response to Ibuprofen (PTGS gene)   (Subscription only)
65. Fibromyalgia and Chronic Widespread Pain   (Subscription only)
66. MTHFR Gene and Migraine with Aura   (Subscription only)
67. MTHFR, Metformin and risk of blood clots   (Subscription only)
68. Tylenol and Risk Of Liver Failure   (Subscription only)
69. 5-fluorouracil   (Subscription only)
70. MTHFR Gene and Risk of Male Infertility   (Subscription only)
71. OPRM1 Gene and Opioid Antagonists   (Subscription only)
72. COMT, LRP2 Genes and Risk for Gout   (Subscription only)
73. Obesity risk   (Subscription only)
74. NSAIDS and Acute Coronary Syndrome risk   (Subscription only)
75. SSRI Antidepressants and CYP2C19 Gene   (Subscription only)
76. Susceptibility to Hypertension   (Subscription only)
77. Hypersensitivity to Mercury   (Subscription only)
78. Gluten intolerance genes   (Subscription only)
79. Choline - dietary requirement in premenopausal women   (Subscription only)
80. COMT Gene and Skeletal Muscle Decline in Older Women   (Subscription only)
81. Elite physical power and sprint performance   (Subscription only)
82. Omega-3 Fatty Acids   (Subscription only)
83. Susceptibility to Pregnancy-induced hypertension   (Subscription only)
84. Polycystic Ovary Syndrome (PCOS)   (Subscription only)
85. Naltrexone and Treatment of Alcoholism   (Subscription only)
86. Earwax and Body Odor   (Subscription only)
87. MTHFR gene and Diabetic Neuropathy   (Subscription only)
88. Risk of Cough with Blood Pressure Medication   (Subscription only)
89. Cluster Headaches and Response to Treatment   (Subscription only)
90. COMT Gene and Response to Opiods   (Subscription only)
91. Salt sensitivity   (Subscription only)
92. Risk of Severe Hypersensitivity to Tegretol   (Subscription only)
93. Genes Associated with Empathy   (Subscription only)

Not all reports are available depending on which company
you tested with
Another thing to factor in is the fact that if you uploaded your raw DNA data from AncestryDNA, FamilyTreeDNA, and possibly other companies, some of the reports may not be possible due to the necessary SNPs not being included. Not all testing companies include the same SNPs or the same amount of SNPs. FamilyTreeDNA in particular removes about 3,000 medically relevant SNPs. So you could wind up not even having access to all these reports even when you subscribe. With AncestryDNA, I noticed a number of reports were "incomplete because none of the SNPs in it were found in your raw data." And even if you have some of the SNPs necessary, if you don't have all of them, it still may not be able to generate the report and say you have "insufficient genotypes to determine response for" that report. These included but may not be limited to (and may vary depending on the company you tested with):

1. SLC2A3 Gene and Dyslexia in Children
2. Floxacillin Associated Liver Toxicity
3. Response to diabetes medication - Sulfonylureas
4. G6PD Gene and Risk of Hemolysis with Bactrim
5. Methamphetamine and Risk of Psychosis
6. Tramadol and CYP2D6 drugs
7. Response to steroid treatment of Crohn's disease
8. Oxycodone and CYP2D6 drugs
9. Abacavir
10. NTRK2 Gene and Lithium Efficacy
11. Tegretol Efficacy in Treatment of Seizures
12. NOS3 Gene and Response to Blood Pressure Medications
13. Phenytoin and CYP2C9 drugs
14. Hormone Replacement Therapy
15. G6PD deficiency, risk of malaria and drug-induced hemolysis
16. Response to Ibuprofen (PTGS gene)
17. Sexual Dysfunction due to Celexa, Lexapro, Prozac, Paxil or Zoloft
18. Zofran and CYP2D6 drugs
19. Risk of Cough with Blood Pressure Medication
20. Choline - dietary requirement in premenopausal women
21. General Anesthesia - postoperative nausea and vomiting
22. Vitamin B6
23. Risk of Deep Vein Thrombosis
24. Hot flashes in post menopausal women
25. APOE Gene, Cholesterol level and Diets
26. Nexium, acid reflux disease and CYP2C19 drugs
27. Warfarin and CYP2C9 drugs
28. Plavix, blood thinners and CYP2C19 drugs
29. Narcolepsy
30. Susceptibility to Both Crohn's Disease and Ulcerative Colitis
31. FUT2 Gene and the Gut Microbiome
32. Susceptibility to food poisoning caused by Norovirus
33. Risk of Acute Psychosis with Cannabis
34. Alcohol tolerance
35. Cold Sores
36. APOE gene and Alzheimer disease risk
37. NOS Gene and Response to Viagra
38. Vitamin D
39. Response to Carisoprodol (SOMA)
40. Hormone Replacement Therapy, SULT1A Gene and Risk of Endometrial Cancer
41. APOE Gene and Exercise Response
42. SSRI Antidepressants and CYP2C19 Gene
43. Risk of Severe Hypersensitivity to Tegretol

That's more than a third of all the reports LiveWello provides (not including Gene Library).

Conclusion: The 28 reports you get for $19.95 are probably not worth the money, and can probably be obtained from other venues for less. However, if you're going to spend the $19.95 to upload, you might as well subscribe because it's only another $5.95 and you get a good deal more for that - you can cancel after the first month and you won't be missing anything. If they wind up adding a report you need or want later, you can always renew your subscription for another month. You may want to try cheaper venues like Promethease first though, you might find it is more comprehensive for much less money. For decent free options, I would try Codegen, GeneKnot, or Impute.

See a list of more places you can upload your DNA to here.

Friday, November 10, 2017

AncestryDNA's New Arrangement of Ethnicity and Genetic Communities

An ethnicity report showing new arrangement of
Genetic Communities
You may have recently noticed your AncestryDNA Ethnicity Report and Genetic Communities look a little different and I've been seeing a lot of people who are confused about them so let me clear some things up. Ancestry posted on their blog about the changes, but didn't really address some of the confusion about it.

First, your ethnicity report hasn't changed. A couple of the category titles have change - for example, "Ireland" is now called "Ireland/Scotland/Wales" but in case you never noticed, that category always primarily included those countries. It has not changed to include more countries that it didn't before, only the title has changed to better reflect the areas it has always covered. Below you'll see a screenshot I took before the changes were made. You'll see the details for the category "Ireland" were always "Primarily located in: Ireland, Wales, Scotland" and "Also found in: France, England". If you look at the details for the newly named "Ireland/Scotland/Wales" you'll see it says the very same thing.

This is why it's so important to read all the details of each category, which they keep making harder and harder to find. Currently, you have to click on the category and at the bottom of "Overview" (you may have to scroll down and click "continue reading") there's a button that says "Read More". Make an effort to check this information for every category you have results in. If you haven't looked over it before, you may be surprised to see just how many countries or areas are included in that category, both primarily and "also found in", and just how much overlap that means it has with neighboring categories too.

"Ireland" always primarily included Scotland and Wales, too. The category
name has merely changed to better reflect these areas.

Additionally, your percentages haven't changed. You may now notice that some Genetic Communities are found as sub-groups of your ethnicity categories (see screenshot at top). Nothing about your results in either features has changed, they have just rearranged things so the layout and display is different. Some Genetic Communities are still found listed separately and these are now being called "Migrations" (see screenshot at top).

These numbers are merely how many sub-groups
(Genetic Communities) are found under that category.
Most importantly, I've seen people confusing the numbers found when clicking on "see all 150+ regions" with their results or percentages. I can't make this clear enough: these are not percentages and they have nothing to do with your personal results. They are merely the number of all sub-groups (Genetic Communities) which are available so they're the same for everyone. You will note that if you expand each category/sub-group, the numbers correlate to how many sub-groups there are, and once you can no longer expand to show more, the numbers disappear. Also note the screenshot I've provided (right) - compare it with your own and you'll see the numbers are the same. They are not a further break down of your results. When you click on "see all 150+ regions", the only indication of your personal results is that the categories and sub-groups (Genetic Communities) you have results in will have a colored dot to the left of them (and these are the very same categories and groups you've already seen on your personal results before you clicked on "all see 150+ regions" - there's nothing different here). Categories or sub-groups you have no results in will have a grey dot next to them instead. The only thing you get out of clicking on "see all 150+ regions" is seeing what other categories and Genetic Communities are available which you didn't get results in.

Tuesday, October 17, 2017

An Oracle Analysis

I'm going to illustrate how I interpret my Oracle results, because I still see a lot of people asking "what do my Oracle results mean?" If you haven't already, you may want to read my intro guide to Gedmatch's Admixture and Oracle, but I'd like to elaborate on that a little bit.

Firstly, it's important to remember that the results can be very speculative and it's best not to take them very literally. People in neighboring regions simply share too much DNA to always be able to tell them apart with accuracy. That means the more narrowed down the areas are in the result, the more speculative it is. You could be German, for example, and get French results because they are neighboring countries who share a lot of DNA. It doesn't mean you're French, it just means this particular calculator put that French/German shared DNA into French instead of German.

Eurogenes K13 Oracle 4, using 4 populations approximation
Secondly, your results are going to be different for each calculator you use so don't just stick to one, explore all those which apply to your background (ie, don't go using Ethiohelix when you're 100% European). Certain calculators may give you more or less accuracy than others. In my personal experience, Eurogenes K13 Oracle 4 (right) isn't very accurate. It really wants me to be Jewish and I'm really not - I have no known Jewish ancestry and don't get any Jewish results from any of the big 4 companies, or in any of Gedmatch's Admixtures. It crops up in the odd Oracle result, but none so much as Eurogenes K13 Oracle 4 populations. I personally have found K15 and EUtest Oracle's to be more accurate, and since K15 is a more recent version of EUtest, that's what I'm going to use to demonstrate how to read Oracle results in some more depth than before.

I find the best thing to do is rather than look at your Oracle results and try to pick one combination that fits you best, or shows the closest distance, look at the results on the whole. Which populations are you seeing the most? Which ones the least? Although I like to look at 4 populations the most because I am primarily from 4 different regions in Europe, you can also look at the 1, 2, and 3 populations modes.

These are my Eurogenes EUtest V2 K15 Oracle 4 results:

1 Orcadian + South_Italian + West_German + West_German @ 4.425306
2 French + South_Italian + West_German + West_Norwegian @ 4.689746
3 South_Italian + Southwest_English + West_German + West_German @ 4.689806
4 East_Sicilian + Orcadian + West_German + West_German @ 4.747531
5 Italian_Jewish + Orcadian + West_German + West_German @ 4.835878
6 East_Sicilian + Southwest_English + West_German + West_German @ 4.850750
7 Italian_Abruzzo + West_German + West_German + West_German @ 4.853912
8 North_Dutch + South_Italian + West_German + West_German @ 4.863277
9 French + Orcadian + South_Italian + West_German @ 4.911067
10 South_Italian + Southeast_English + West_German + West_German @ 4.914701
11 Tuscan + West_German + West_German + West_German @ 4.922722
12 Central_Greek + Orcadian + West_German + West_German @ 4.922800
13 South_Italian + West_German + West_German + West_Norwegian @ 4.927629
14 Irish + South_Italian + West_German + West_German @ 4.941526
15 South_Italian + West_German + West_German + West_Scottish @ 4.958009
16 East_Sicilian + French + West_German + West_Norwegian @ 4.978409
17 East_Sicilian + French + Orcadian + West_German @ 4.982550
18 South_Italian + West_German + West_German + West_German @ 5.005996
19 South_Italian + Spanish_Galicia + West_Norwegian + West_Norwegian @ 5.010231
20 Central_Greek + Southwest_English + West_German + West_German @ 5.011045

So rather than saying the top results must be the most accurate because it's the closest distance, and determining it to be only somewhat accurate because it did identify my German, Italian, and Scottish ancestry, but not my English or Norwegian, let's look at the entire results as a whole.

Map showing my known ancestor's birth
places in Europe
What am I seeing the most? Probably West German. This is very accurate, I have a lot of West German ancestry on both sides of my tree, and I estimate it makes up about 25% of my tree. I also have a couple Swiss-German branches, which is still fairly consistent with West German. There's one ancestor who was from Bavaria, which is a region of Germany more to the east, but I have no idea what part of Bavaria - could have been the western most part for all I know. What I do know is that I rarely ever get admixture/ethnicity results in Eastern Europe and when I do, it's normally in such small portions, it's likely noise. So this is all very consistent with my tree.

I'm also seeing South Italian and some other Italian regions like East Sicilian and Abruzzo. This is incredibly accurate. I do indeed have Sicilian, Abruzzo, and other Southern Italian ancestry. My paternal grandmother was of entirely Italian descent so that makes up another 25% of my tree. My Sicilian branch is a bit more Northern Sicily than Eastern, but that's fairly negligible. There's one count of Tuscan and as far as I know I have no Tuscan ancestry, but that too is probably not very significant since it only shows up once.

There's a few West Norwegians thrown in there, which is also accurate, I have one great grandparent who was Norwegian, making up 12.5% of my tree. Several branches were indeed from Western Norway, although one branch did come from the more Eastern towns of Bamble and Skien.

Map showing my population results for
Eurogenes K15 Oracle 4, compare with above map
You may also notice a few Orcadian and West Scottish populations. This is somewhat accurate, I do have several Scottish or Scots-Irish branches dating back to colonial times, but where exactly in Scotland they were from isn't really known. Orcadian (people from the Orkney Islands) seems a little unlikely as my understanding is most Orcadian immigrants went to Canada through the Hudson Bay Company rather than the US. But if we consider Orcadian as a representation of my Scottish or even British heritage, it makes sense. The Orcadians were also influenced by the Vikings, so there's also a potential connection to my Norwegian side. My overall British branches make up about 34% of my tree, and in addition to Scottish, includes English, so it's not surprising to find a few instances of Southeast or Southwest English. As you can see from the map above, I do indeed have ancestry in Southwest and Southeast England, although I have more recent roots in Northern England, near Manchester so it's a shame it didn't pick this up. It's possible Oracle is underestimating my British ancestry, since there's only a few English populations included, but when you consider how genetically similar the British and Germans are, and knowing how many instances of West German are listed, it makes some sense.

I lastly have a smidgen of colonial Dutch and French Huguenot in my tree but I don't know how realistic it is to expect that to show up in admixture results, as it may have been from too long ago. They make up about 1-2% each of my tree. So when I see a few results for North Dutch and French, I'm taking it with a grain of salt. I'd like to think it could be from colonial ancestry but the way Oracle works by identifying the populations you match most closely, it doesn't seem likely I would closely match a population from so far back in my tree. It seems more likely that it's just being picked up from neighboring regions where I have ancestry.

Likewise, I wouldn't put much thought into the remaining few instances of Italian Jewish, Central Greek, Irish, and Spanish Galicia. Irish is probably just representing my British background, as those two groups are closely related, and likewise, Italian Jewish, Central Greek, and Spanish Galicia may be related to my Italian heritage since they're all from that Mediterranean area. In any case, since there's only one or two counts of them, it's easy to ignore them.

So overall, despite the fact that it doesn't always identify my British/English ancestry as much as it maybe should, it's actually remarkably accurate when you look at it on the whole. Compare the two maps above, one showing the origins of my ancestors and the other showing my Oracle results, and they really aren't far off each other (keeping mind some of the locations for the Oracle map cover a larger area than what the pinpoints represent). Mapping it out is another good, fun way to analyze your admixture or Oracle results, if you'd like to try it, just go to My Google Maps.

I don't normally worry too much about the distance unless it starts getting really high. For example, K13's Oracle has closer distances than K15, but the populations in K15 are far more accurate for me than K13. I am NOT saying K15 is the best option for everyone. When I look at my dad's K15 Oracle results, they are mostly inaccurate, constantly insisting he is Lebanese Druze, which seems very off base. I can't even promise that there will be an Oracle calculator that is as accurate for you as Eurogenes K15 is for me, since I haven't really found one for my dad that is this accurate (he does get a lot of Abruzzo results in various calculators, which is accurate, but there's also a lot of populations that are kind of out there for him).

Also keep in mind some of the calculators contain a lot of ancient (prehistoric) populations. If you see some weird names like "Battle Axe" or "Bell Beaker", these are probably ancient populations (Battle Axe is Neolithic, Bell Beaker is western Europe in late Neolithic-early Bronze Age).

I hope this gives some more detailed insight in how you might interpret your own Oracle results. If you are adopted and don't know your ancestral background, it's difficult to know which calculators will be more accurate than others. You should definitely still take all this with a grain of salt, but it is fun to examine and compare with what we do know.