National Geographic Photo Books

Sunday, September 24, 2006

Y-DNA Haplogroup Update

The Italy DNA Project now has fifty y-DNA members, so I thought this would be a good time to update the haplogroup frequency data for the project. Here's the current version:


Estimated Frequency of Haplogroups in Italian Population
Calculated Frequency of Haplogroups in Italy DNA Project

I have highlighted the haplogroups where we are still seeing what I consider to be a significant difference between our group and my best analysis of the overall Italian population. Our sample size is still small, though, so just a handful of participants can skew the numbers high or low.

Still, I suspect that our sample is biased towards southern Italy (due to the patterns of emigration to the U.S. from Italy in the late 1800's and early 1900's) which accounts for the dearth of R1b and the abundance of E3b and J2. But even then, the frequency of these haplogroups in our project is higher than some estimates for southern Italy itself.

Friday, September 15, 2006

Autosomal marker classification of Europeans

A recent article in PLoS Genetics, a peer-reviewed open-access journal, entitled "European Population Substructure: Clustering of Norther and Southern Populations" by Michael F. Seldin et al. found that it is possible to accuratedly segregate Europeans into northern and southern populations using a battery of autosomal single nucleatoid polymorphisms (SNPs).

Unlike the directly inherited y-chromosome and mtDNA tests that we use in the project, this project looked at autosomal DNA which is received from both the mother and father. Autosomal DNA is useful at assigning you to a population group (Asian, African, European, etc) but not to a particular family.

This paper is of note in part because Italian and Spanish samples essentially define the southern European genotype. 84 of the 86 Italian participants were classed as "southern", with participants from norther Italy generally more likely to have a greater "northern European" component than participants from southern Italy.

Click here to read the article. Here's the abstract:

Using a genome-wide single nucleotide polymorphism (SNP) panel, we observed population structure in a diverse group of Europeans and European Americans.
Under a variety of conditions and tests, there is a consistent and reproducible distinction between “northern” and “southern” European population groups: most individual participants with southern European ancestry (Italian, Spanish, Portuguese, and Greek) have >85% membership in the “southern” population; and most northern, western, eastern, and central Europeans have >90% in the “northern” population group. Ashkenazi Jewish as well as Sephardic Jewish origin also showed >85% membership in the “southern” population, consistent with a later Mediterranean origin of these ethnic groups. Based on this work, we have developed a core set of informative SNP markers that can control for this partition in European population structure in a variety of clinical and genetic studies.

Wednesday, September 13, 2006

GENOMA - Molecular Genetics Laboratory

It's been a little quiet the last few weeks. There have been few new results in the project, and no new relevant academic papers have caught my attention.

However, I have found a lab in Italy that can perform y-STR and mtDNA tests so I thought I'd mention it here.

Genoma is located in Rome, and offers a pretty wide array of genetic testing services. Many are medical or paternity-related, but they do offer a 17 loci y-chromosome STR test as well as HVR1 and HVR2 mtDNA testing. An Italian facility might be helpful if you intend to test Italian relatives: some Europeans are reluctant to send DNA to American labs.

The Y-STR test that Genoma offers is the Applied Biosystems AmpF/STR Yfiler kit, and Genoma charges 200 euros (about $254) per sample. The Yfiler kit is often used in academic studies and examines the following loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS 635 (aka Y GATA C4), and Y GATA H4. There are no commercial labs in the U.S. that offer all 17 loci, but the FamilyTree DNA 37-marker test and the Relative Genetics 43-marker test each overlap the Genoma test at 16 loci.

The Genoma 17 loci test offers what I would call moderate discriminatory capacity: somewhat better than a basic 12-marker tests but, because it omits some highly variable markers (e.g. DYS449 and DYS464a/b/c/d) it is notably less discriminatory than the 25-, 26, 37-, or 43-marker tests that are most popular in the U.S. I calculated the average mutation rate of the 17 loci Genoma panel to be about 0.0030.

For reference, I had eleven perfect 12-marker matches in ySearch and five perfect 17-marker matches. That's a notable improvement, but still a lot of false positives.

So, you get a $250 test with Genoma yields somewhat better discriminatory capacity than a $100 test with FTDNA or the Genographic Project BUT you have an Italian lab to work with. For some situations, that might not be a bad tradeoff.

I don't have all the details of the mtDNA tests yet, but I do know that the cost is the same (200 euros) and you'd get HVR1 and HVR2 results.

If you know of other Italian genetics labs that offer competitive services, please let me know via the comments link below or by emailing me (