April 04, 2012

Cryptic distant relatives are common in genetic samples

Table S1 has some statistics on different populations.

PLoS ONE 7(4): e34267. doi:10.1371/journal.pone.0034267

Cryptic Distant Relatives Are Common in Both Isolated and Cosmopolitan Genetic Samples

Brenna M. Henn et al.

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and ‘unrelated’ population samples. Using these bounds as a guide, we detected tens of thousands of 2nd to 9th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies.

Link

5 comments:

terryt said...

"The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies".

In animal breeding it produces what are usually known as 'throwbacks'. Characteristics of 'ancient' breeds pop up in single members of a herd of cattle or flock of poultry for example. The genes that pop up are, of course, usually recessive.

German Dziebel said...

My notes on this paper are at http://anthropogenesis.kinshipstudies.org/2012/04/the-effect-of-long-term-endogamy-and-cryptic-consanguinity-on-identity-by-descent/

dok101 said...

From Table S1: "Populations included from the 23andMe database were based on self-reporting by customers of 4 grandparents from the same country."

So they have the few dozen Assyrians split between Turkey, Iran, Iraq, the Levant, etc.

Anyway, more reason to believe projects such as Dodecad and Eurogenes > 23andMe. At least for our purposes.

For the record, I am an Assyrian from Iran. I am a predicted RF "cousin" to each and every one of the Assyrians of the "Nestorian" faith on 23andMe (~30 individuals at last count). Regardless of their country of origin. I had no idea these individuals even existed, before testing with 23andMe.

MOCKBA said...

So what does it mean for the recreational DNA genealogists? The magnitude of IBD seems to be too blunt a tool for historically endogamous populations, as it throws too many false positives? But aren't specific recombination boundaries still usable for IBD conclusions? Do we have enough informative marker density to figure out the boundaries with sufficient precision? Or higher density is required? Or perhaps even going for truly rare variation, like those few hundred to few thousand recent de novo point mutations and CNVs which would be highly specific for true recent IBD segments?

PS @ dok101 - aren't most Assyrians concentrated (and somewhat remixed) in Illinois these days? Or the Assyrians of former Russian empire are still residing in the Caucasus and Russia?

Andrew Oh-Willeke said...

Not too surprising. I have an exceptionally good knowledge of my geneology and as a result have some sort of family interactions with a number of my fourth cousins, but that is quite exceptional and I would have no idea who any of more distant relatives might be. Few people know for sure who anyone more distant than a first or second cousin is.