We have about 3.08 billion base pairs. Therefore, we have about 6.16 billion bases and over 30 generations before we have to make a choice between one ancestor and another, one allele and another, at a particular base pair.

No that’s not how it works. You don’t have 3.08bn independent base pairs, you have 22 independent autosomes, the bases within which have a correlation structure dependent on recombination.

About 30 generations at about 30 years per generation is about 900 years. 900 years ago our world population was between 310 million and 790 million. It is likely no more than 2/3rds of those have descendents to the present, given the effect of the plagues that happened between 900 years ago and now.

Without inbreeding, however, at 30 generations you have 1,073,741,824 ancestors. If the whole world were in your ancestry, then you would still have many cases of “inbreeding” with sixth cousins, seven times removed.

However, even if there were only 30 ethnic groups in relative reproductive isolation from each other, until the last 200 years there has been very little genetic sharing between groups. There was not much interbreeding, for instance, between native Americans and Mongolians 200 years ago. Genealogical ancestry does not extend much beyond 400 years ago.

Therefore, we can say that your genetic ancestors and your genealogical ancestors are in the same set and equivalent.

Data: Epistasis is ubiquitous and dominant in yeasts (On the classification of epistatic interactions. Genetics (2010), 184: 827–37).

Theory: Humans are unlikely to be much less complex than yeasts.

Data: No one ever saw pure additivity on a micro level (metabolic pathways and protein-protein interactions).

Theory: If it is not true on a micro level, it is unlikely to be true on a macro level. If anything, more non-linearity with rising level of complexity is likely.

BTW, did you see this recent paper in Science:
http://www.sciencemag.org/content/335/6064/82.abstract
These are worms, not humans, of course, but still, quite interesting .

It is known that recombination is not equal across the genome, and there are known recombination hotspots. It would be interesting to see how this analysis would look if you incorporated recombination rates across the genome. All of the data is accessible from HapMap’s website http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/latest/rates/

Also, it is strange to me that you see such a leveling off in number of ancestors at 125, it even looks like the number of ancestors drops a little at 15 generations. Does your code include a minimum threshold for being identified as a relative? Otherwise, I don’t think that is possible.

Nice work, I hope you could generate a simulation with the recombination rate data, because it is way out of my league to try something like that.

I am definitely a ‘liberal’ when it comes to sequencing, and the venues in which it should be applied. I think that the diagnostic benefits that can be obtained will revolutionize medicine.

I would also agree that current US medicine is not ready for routine clinical sequencing. However, I think that the rate of development of genomics and genetics provides the US healthcare industry an opportunity to evolve over the next decade. Open more Genetic Counseling programs in order to train more counselors. Improve on genetic training of doctors. And take the opportunity to educate the general public.

I see these challenges as opportunities, not insurmountable obstacles. There in lies hope for success.

Keep up the great blog.

Thanks for the updates – they’re much appreciated.

I have to admit, I’m somewhat shocked by Dr. Hayden’s point in rebuttal to Dr. Drmanac’s “hype”, which seems to be that the U.S. isn’t ready for it, so it shouldn’t happen. First, I hope the argument was more nuanced than that. (I know how hard it can be to encapsulate someone’s argument when blogging!) Second, I find that reason to be entirely obtuse… there are many other big markets outside of the U.S. that HAVE figured out how to deliver health care to their citizens, even if it is a fine balancing act.

RANT: Whether we like it or not, medicine moves forward when we find new diagnostic tools – and this one has the potential to provide good diagnostic tools. The fact that it also can provide more nuanced information that we have to learn to interpret is no reason to shy away from the technology as a whole. Doctors will learn how to use the information when it gives them a better tool for saving lives, and improving the quality of life for their patients. /RANT.

At any rate, I hope the conference is going well, and I appreciate the bits of information you’re able to share! Thanks again!