Tag Archives: DTC testing


Friday SNPpets

This week was big on #CRISPR stuff. That drama about the off-target alterations, and the pushback, consumed much oxygen. But there’s plenty of the usual stuff too–new software, personalized medicine marches on, DTC genetic testing issues, new samples from ancient sources. Best thing: the script to convert fastq to emojis.

Oh–I’m off next week because I’ll be on the road without much chance to capture the tweets with my butterfly net.

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


Video Tip of the Week: Direct to Consumer Genetic Testing and Genetic Counselling

At OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, I know, it still varies). But outreach really is getting better. There are journals now that are also enforcing more reader-friendly ways to describe the research, with non-jargon summaries and some terrific visual aids.

Increasingly, there are also videos associated with papers. I just came across this one, and thought it was a nice example of an important issue for non-scientists to access.

So this looks at direct-to-consumer (DTC) services available in Europe, but some of the same ones are available in the US. Of course, in the US, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Sigh.

Hat tip:


Middleton, A., Mendes, Á., Benjamin, C. M., & Howard, H. C. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. Personalized Medicine, (14:3) , Pages 249-257 , DOI 10.2217/pme-2017-0001.



Friday SNPpets

This week’s SNPpets include several new tools that I want to examine, including functional annotations in a couple of different ways. But other stuff includes designing DTC consumer products,  NLM’s future directions, a new Genomics subreddit, and stunning phylogenetics representations among other interesting reads.

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Of Mormons and Mozambique: a cursory look @ 23andMe ancestry data

So, as a lot of people, I received my family’s 23andme results yesterday. Well, 3 of 4. Our youngest daughter’s spit apparently has little DNA, she had to spit again. Her results are to come later. As I mentioned in earlier posts, I wasn’t planning to be surprised of my own or my husband’s results. And even if I was on the ancestry front, I didn’t expect it to have too much meaning. Of course, since our daughter is an adopted African-American, I expected to find interesting information there, information we have little knowledge of. So, today I will look at our ancestry, later I’ll take a look at health.

I’ve only had a chance to look at 23andme’s analysis reports for ancestry. To go deeper later,  I’ve downloaded the raw data, installed SNPTips and am starting to preparing for some other analysis. But for now, here is what we found, surprises and confirmations.

The Haplogroups find… nothing surprising for me.

My paternal lineage is haplogroup I1*. A haplogroup predominantly found inScandinavian populations. No surprises there, and possibly a confirmation of anecdotal evidence. The Lathe/Leathe/Leeth name (all variations of my last name through 500 years of history) is English, but our research suggested that it originated from the Norse invaders/settlers of Danelaw. Well, that seems to confirm that.

My maternal lineage is haplogroup I1a1, a European, possibly Celtic, group. Makes sense, my maternal lineage is Irish/Scottish. No surprises.

Who really is Indian?

I found something interesting with Ancestry painting (where the determine the geographic location of chromosomal inheritance). I was 99% European, 1% African. See that little box on chromosome 8, it’s African. What does this mean? Where is the Asian?

My great-grandmother is of Native American descent. Her ancestry is Mattaponi. That much is documented. Why does it not show up here? 23andme says that ancestry painting won’t pick up Native American ancestry (it uses Asian populations in the HapMap data for it’s analysis) if there isn’t a “full-blooded” native American in the last 5 generations. My great-grandmother is 4 generations back. In her photos she looks at least partially native, her birthplace was a Mattaponi town and family documents and stores are pretty conclusive. But that’s why I said “descent.” Though we assume from oral history and documents her mother was full-blooded, we don’t know that for sure and we don’t know her father’s heritage completely. More importantly, the Virginia native groups such as the Mattaponi (and Chickahominy, Pumunkey and others) have lived among and intermingled with Americans descended from Europeans and Africans for nearly 400 years. So, as I suspected, my great-grandmother wasn’t full-blooded, but rather mixed-race individual of Indian culture. But as I said in my previous post, what was most important to her life and who she was, her genetic heritage with possibly African and European admixture, or her cultural heritage with it’s large native American foundation? The latter I suspect, though the former was obviously an influence.

Of course, this all goes to the argument of ‘who is an Indian’ which I won’t delve into too deeply. Early in the 20th century, obsessed with racial purity, some Virginia officials tried to prove Virginia’s native population wasn’t native because of the admixture. Today the discussion continues among the tribes themselves. I would fall on the side of culture and heritage over genetics, but it’s not a simple thing.

The African descent I see? Perhaps it’s carried over from her, or from my maternal lineage with it’s origin in plantation and slave-holding families. I believe it’s from my Mattaponi great-grandmother because of a story my grandmother once told me.

To get more data about the Native American lineage, I’d probably have to get my father’s maternal lineage and haplogroup and his ancestry painting. It might tell us more. For example, my husband’s ancestry painting showed 100% European, but his father had 3% Asian (from a Mediterranean lineage). Ancestry markers disappear eventually.

If there is anything that DTC genomic testing does, I hope it does change our view of who we are. I hope that it reinforces my belief that our culture is less ‘genetic’ than we seem to think today and that our culture is a vibrant mix of influences. That only time and a million tests will tell. I am quite sure it will have some impact.

Mormons and Africans:
An interesting side note to this is that our family story, as related to me by my grandmother, suggested we indeed had an African American ancestor from our Native American lineage. When I was 17, I joined the Mormon church. The church at the time did not allow people of African descent to hold the priesthood (all lay males held the priesthood in this lay church). They insisted it wasn’t the color of one’s skin, but rather their ancestry. When I mentioned the possibility of our ancestry (and some documentation that suggested it), I was barred from the priesthood. I finally was ordained almost a year later, right before the ‘revelation’ (long story).

So, 30 years later, it’s confirmed with data. I have a drop of African ancestry. I think it would be highly interesting to do genomic scans on white Mormons today who held the priesthood before 1978. Did they have African ancestry and hold the priesthood? I dare say a good number did. Perhaps another reason the policy was changed.

Speaking of Africa, Mozambique:

Our oldest daughter’s scan was also completed. Out of privacy concerns (which I’ll talk about in another post) I will only post some basic ancestry and no healthinformation.

Her maternal haplogroup is L3e1e, a lineage that most likely starts in Mozambique. Some preliminary data suggested that much of our daughter’s African ancestry was Nigerian region and possibly from what is now Angola, and it probably still is, but this was a surprise.

But for the maternal lineage, interestingly, very few slaves came from Mozambique directly to the United States. Mozambique was a Portuguese colony and they sold and transported slaves mainly to South America and the coasts of the Indian ocean. Where and when did this maternal lineage arrive to the Southern parts of the United States?

Tantalizingly, I found one voyage of the slave trade that goes carries Africans sold into slavery in Mozambique and transports them to the Caribbean from the Voyages database. What do I find that tantalizing? Because we do know that one of our daughters genetic grandmothers was ‘creole’ as reported by her birth mother. We weren’t sure what that meant in this context, but perhaps it’s Caribbean? Perhaps these are frayed ends of a lineage we could connect someday.

Looking at her ‘ancestry painting’, she is typical for African Americans, a strong admixture of African (76%), European (21%) and Asian (3%, possibly Native American) background. I haven’t figured out completely how to interpret this, but I suspect one parent was more “European” than the other.

What have I learned from the ancestry part of the 23andme test? It has confirmed, as I suspected most of my ancestry as I know it from my genealogy. It has clarified and added a slight question to my Native/African ancestry I would like to delve into more (and the genealogy since that is the least-researched line frankly).

For our adopted daughter we learned a bit more and possibly able to transport her genetic heritage back several centuries.

Has it affected how I see who I am or my daughter is? No, not really. It confirms our genetic heritage and strengthens our understanding of our cultural heritage.

But I’m intellectually fascinated by it…so now comes more analysis, Admixture, Haploview, UCSC Genome Browser, SNPTips, here I come.

PS. Also have a bit of Neandertal in my genetic heritage, but I have a bit more research to do to confirm that  :D.

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…