Tag Archives: haploview

What’s the Answer? Haploview and LD plots?

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is….

 Is Haploview the best method for defining LD blocks?

The answer to this question is, not necessarily, but it’s good.

The answer given goes into some detail as to what methods one might want to consider:

I would look at the methods used by Gil McVean and others in determining recombination hotspots across the human genome. I would also read papers by DW Bowden on MYH9 as I know that they narrowed the susceptibility region (end-stage renal disease) with LD and recombination hotspots.

It may be that all three methods are more or less equally informative for your region, thereby giving “fuzzy” boundaries. Recall that LD boundaries are not as precise as a single SNP coordinate – although results from Haploview, HelixTree and others often give that impression.

Mentioned here:

Haploview (a publicly available analysis tool)
HelixTree (for fee analysis tool)
Might also want to check analysis tools listed here or here.

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.

News bits: WikiGenes opportunity; HapMap data issue

Ok, I’m back from Thanksgiving and catching up on some emails and found a couple of news items I wanted to pass along.

WikiGenes invitation to edit a Nature Genetics paper

Here’s an interesting “experiment” I got notified about. You could potentially get authorship on this paper if you contribute to the development of this article.  Here’s the email I got from the WikiGenes mailing list–but click over for more details and you can see the article over there. I haven’t had time to check it all out yet, but as there is a deadline I wanted to mention it now.

Dear Mary,
The editor of Nature Genetics has commissioned a collaborative standards paper on Genome Wide Association Studies. An editable draft of this paper is now online at WikiGenes, http://www.wikigenes.org/GWAS.html?wpc=12

I hope this is an interesting opportunity for you, because significant contributions to this draft might get you a co-authorship on the final paper in Nature Genetics.

I would also like to use this occasion to ask you a favor.

If you like WikiGenes, please tell your friends about it. We do not have the budget of big publishers, so we depend fully on word-of-mouth publicity.

Or you could also help us by linking to WikiGenes from your website. Thank you!

Best of science,
Robert

Robert Hoffmann, PhD
Branco Weiss Fellow
WikiGenes – Evolutionary Knowledge
http://www.wikigenes.org/

HapMap data in the HaploView tool

This came across from the HapMap mailing list. We tell people about using HapMap + HaploView all the time, so I wanted to mention this possible issue with some of the data:

Dear HapMap users,

Recently, there are several questions about Haploview data format errors when users tried to analyze HapMap release 28 data.  The current Haploview version (4.2) does not recognize the new individuals in release 28 and the software will generate an error similar to “Hapmap data format error: NA18876″ when trying to open the data.

Haploview is developed and maintained by an organization different from HapMap.  Please contact Haploview help desk (haploview@broadinstitute.org) for questions specific to this software.

Sincerely,

Hua Zhang, Ph.D.
dbSNP Group
NCBI/NLM/NIH

Tip of the Week: HapMap data in Haploview

HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. Haploview can be used with user data or data downloaded from the HapMap project. Though, version 4.1 did not work for phase III HapMap project data, so the user had to use phase I and II data if they wanted to use version 4.1. Haploview has now been updated to version 4.2, allowing the user to use HapMap phase III data.

That’s a lot of versions and phases :). The short of it is, if you use Haploview 4.2, you can view and analyze data from any phase of the HapMap project.

Today’s tip briefly shows you how to download data from the HapMap project and view it in Haploview.

Tip of the Week: Visualizing Genotypes

SeattleSNPs genotypeAnd maybe it will help you visualize peace too :). There are several sites and software programs (Haploview and GVS are two) that will help you do visual genotype, we are going to show you one here that is simple to use at SeattleSNPs. This tip will show you how to access SeattleSNPs VG2 software and quickly visualize SNP allele genotype data for a gene, either your own data or that from the SeattleSNPs project.

Autism: regional duplications and deletions?

I was reading my local newspaper just now and spotted this intriguing information:

Boston researchers find genetic trigger for 1 percent of autism

….The discovery, reported on-line in the New England Journal of Medicine this afternoon, stems from the most extensive genome scanning for autism done so far. The scans found that in just over 1 percent of people with autism, a chunk of about 25 genes had been either duplicated or deleted, mainly in spontaneous mutations not carried by their parents….

The team was led by Mark Daly. I saw him recently at MGH giving a talk to students on genome-wide association studies. He is also responsible for developing great software, including HaploView and other tools. We have used HaploView to examine the HapMap data–you can pull data from the HapMap browser and load it right in to HaploView for a more detailed look at it.

I want to check out that paper: Association between Microdeletion and Microduplication at 16p11.2 and Autism

Fascinating information.