A Neanderthal - Further Confirmation And Much More On Personal DNA

I like the idea of getting my own DNA analyzed and studying the results.  In an earlier post, I described some results of an analysis through a National Geographic project, and the finding that 2.5% of my DNA was from Neanderthals.  The ability to sequence ancient DNA is a relatively new capability and in the few years that it has been done, it has yielded a number of significant findings.  The applicability to the field of psychiatry is limited at this time to 2 references (1,2).  An additional search on ancient DNA and psychiatry yields 4 additional references (4-6) looking at the early origins of mutation and how the associated disrupted regulatory mechanisms could lead to psychopathology.  One of the susceptibility markers for schizophrenia dates back to the last glacial maximum or 24,500 years BCE.  

After trying out the National Geographic site,  I decided to see if the 23andMe site had anything more to offer.  I pulled up their web site, paid the fee and they sent me a sampling kit.  Their sampling technology if different in that they use a tube of saliva as the sample rather than a scraping from the buccal mucosa.  They send you a number of e-mail updates and finally a notification that your DNA has been processed and the necessary reports have been generated.  There are 67 reports in all that focus on ancestry, carrier status, wellness, and traits.  Some reports are more useful than others.  For example it is interesting that a 4th digit on the hand longer than the second digit or a second toe longer than the great toe are inherited characteristics with certain probabilities.  Unless there are some additional health implications involved I don't really care about my longest toe or finger.  The data I am looking for is precisely the data that the FDA told 23andMe that it should not market in the first place.  That initial FDA warning looks at the testing that the company was offering.  In this document the abbreviation PGS is used for "Personal Genome Service":

"Some of the uses for which PGS is intended are particularly concerning, such as assessments for BRCA-related genetic risk and drug responses (e.g., warfarin sensitivity, clopidogrel response, and 5-fluorouracil toxicity) because of the potential health consequences that could result from false positive or false negative assessments for high-risk indications such as these. For instance, if the BRCA-related risk assessment for breast or ovarian cancer reports a false positive, it could lead a patient to undergo prophylactic surgery, chemoprevention, intensive screening, or other morbidity-inducing actions, while a false negative could result in a failure to recognize an actual risk that may exist......."

I am sure there are plenty of posts around the Internet on the regulatory aspects of DNA testing and what the FDA is doing to protect the American public.  23andMe does have consistent qualifying statements saying that none of the data is for medical purposes, only for research and education.  My interest is purely personal research and education.  What more can I learn about DNA, genetics, molecular biology and human diseases.  As noted in my original, what more can I learn about my ancestry and the fascinating subject of Paleogenetics and the associated big questions like why is Homo sapiens - the genus and species of all current human beings the only surviving Homo genus.  Why are all of the others extinct?  I also think that it is quite instructive to remind ourselves that as members of that species we all started out in East Africa and migrated all over the world.

Looking at the test results from the 23and Me analysis, there are four major categories and some are more useful than others.  Those categories include ancestry, traits,  carrier status, and wellness.  Since ancestry was the focus of the National Geographic experiment I took a look at that report first.  In terms of methodology the 23and Me technology looks at overlapping regions of DNA and homology with comparison regions of known ethnic groups.  I prepared the following table to look at the predictive value of the 23andMe approach compared with the National Geographic technique looking at the purported ancestries of my grandparents. (click on any graphic to enlarge)  

As noted in the above table, there is more coverage of ethnicities, using the 23andMe approach with  the best example being that it picks up Norwegian, Swedish, and Dutch markers that were not present in the NatGeo analysis.  There are a few problems that might not be obvious at first.  The test subject does complete information about ethnicities and populations of origin that may be incorporated into the algorithm that assigns probabilities of certain ancestry.  These questions reminded me of the clinical data required for quantitative electroencephalogram machines in the 1990s.  The algorithms were supposed to predict psychiatric diagnoses, but the clinical data that was required with every test, frequently interfered with what the machine was going to select.  I take a very dim view of what appear to be scientific decisions being made on the basis of added speculative data.   The ancestry interpretations also depend the level of confidence assigned to the analysis.  As an example, take a look at the following genealogy assessments - the top a conservative estimate and the bottom much more speculation.  Significant changes in the analysis occur just based on how speculative the analysis is.  All things considered, I am quite interested in the range of the analysis and all correlations at this point rather than precision, but is some cases precision is apparently available.         

All together there are 3 ancestry reports and the most interesting report for me was the Neanderthal analysis.  The test looks at 1,436 traits across the genome and generates a report based on a map of all 23 chromosomes and a table that takes a more detailed look several markers.

The traits report was significantly less interesting to me.  It answered the question about whether or not a genetic markers for a trait existed.  For example, the length of the second toe on the foot and the length of the fourth finger on the hand.  The testing predicts that I have a 96% chance of lighter skin and very little chance of freckling.  That is true.

Carrier status was similarly not very interesting.  There was a major focus on congenital illness rather than risk of chronic illness.  Some of the carrier states mentioned include: ARSACS, Agenesis of the Corpus Callosum With Peripheral neuropathy(ACCPN),  Autosomal Recessive Polycystic Kidney Disease (ARPKD) and 33 others.  My carrier status for these relatively rare conditions was negative.  That was really no surprise considering my age, family history, and the fact that most of these are illnesses of infancy or childhood.

The wellness section contained 6 reports and a few were moderately interesting.  Caffeine consumption is regulated by variants near the CYP1A2 and AHR genes and I have those variants.  The prevalence of these variants in various populations are also estimated and it seem that these variants are high.  I do tend to consume significant amounts of caffeine and it is hardly noticeable.  It seems like I am drinking decaffeinated beverages.  I have the rs73598374 variant in the ADA gene that is associated with deep sleep.  I do sleep for short periods of time, but my activity monitor suggests that my sleep may be deeper than people who sleep more hours.  I also have the rs3923809 variant in the BTBD9 gene that predicts more movement in sleep.  The R577X variant in the ACTN3 gene is present and that is associated with a greater portion of fast twitch muscle fibers or what the site refers to as sprinter/power muscle type.  The final two wellness traits were lactose intolerance and the alcohol flushing reaction.  I knew that I had neither trait prior to the genetic testing.

Apart from the Neanderthal testing, the most interesting aspect of the this service is that ability to search your genome looking for points of interest.  I think that this will eventually be the most interesting aspect of these services as long as the users keep in mind that having a genotype, especially of a complex polygenic illness is a probability statement rather than a guarantee.  I am testing out two ways to do these searches.  The first strategy is based on protein analysis and I used a recent paper on bipolar disorder (I have a strong family history) to see if I could find any of these markers.  The original paper suggests that there are higher plasma concentrations of 6 proteins in bipolar disorder including GDF-15, HPX, HPN, MMP-7, RBP-4, and TTR.  A direct search yields a significant number of hits for HPX (5), HPN (14), and TTR (89) genes with specific information on markers, genomic position, possible variants and genotype.  In this case the original paper was a protein analysis and as far as I can tell there is no genetic analysis of the subgroup with higher levels of the identified proteins.  I have sent an e-mail to the lead author to see if I missed any papers on that issue.  An example of the data available searching on these proteins for the HPX protein is shown below:

The second option would be to search for known genotypes.  It is no secret from previous posts that I have asthma that was quiescent for most of my life that was reactivated about 3 years ago by a upper respiratory infection.  Asthma is an interesting disorder because the genetics are very complex just like psychiatric disorders.  For the critics who suggest that there are no tests of any sort for psychiatric disorders, these two sentences are from the latest chapter on the genetics of asthma from UpToDate (9) are instructive:

"Exploration of the genetics of asthma has also been hampered by the fact that there is no "gold standard" diagnostic test for asthma, and the clinical diagnosis is inconsistently applied.  To circumvent these issues, investigators have studied the distribution of asthma-related traits, including bronchial hyperresponsiveness and measures of atopy (eg, total serum IgE levels, skin test reactivity) in addition to the presence of an asthma diagnosis."

This same author reviews the genetic research on asthma to date and points out that prior to the retirement of the Genetic Association Database in 2014 there were over 500 genetic association studies on asthma that identified hundreds of candidate genes for asthma.  From those candidate gene studies, she gives the most replicated genes as filaggrin (FLG) - an epithelial barrier gene also important in atopic dermatitis,  ORMDL3 - a transmembrane protein, Beta-2 adrenergic receptor gene, and Interleukin-4 receptor gene.  Genome-wide association studies (GWAS) have supplanted candidate gene studies and over 50 GWAS have been done in asthma.  These studies have identified other candidate genes and generally shown that GWAS done in populations with European ancestry seem to have little applicability in more ethnically diverse populations.  ORMDL3 was identified in both types of studies so I searched for that in my own DNA and came up with the following:

            
In order to look at specific markers and asthma risk, I searched on one of the genotyped markers (rs8076131) in PubMed and came up with 7 papers on asthma susceptibility.  Searching more broadly on ORMDL3 showed 132 references that were less specific.

This ends my preliminary review on the availability of personal genomics for education and research purposes by individuals.  I hope to come up with more effective strategies to look at several additional disease phenotypes that I either personally possess or that were present in my first degree relatives.  For me, the paleogenetics and personal genome browsing were the most interesting aspects of this data.  For educational purposes, it highlights the difficulties of correlating genetics with disease phenotypes due in part to the fact that multiple genes and polygenes can produce the same phenotype and that makes the activity of specific genes difficult to determine in a DNA sample.



George Dawson, MD, DLFAPA

      



References:

1:  Srinivasan S, Bettella F, Mattingsdal M, Wang Y, Witoelar A, Schork AJ, Thompson WK, Zuber V; Schizophrenia Working Group of the Psychiatric Genomics Consortium, The International Headache Genetics Consortium, Winsvold BS, Zwart JA, Collier DA, Desikan RS, Melle I, Werge T, Dale AM, Djurovic S, Andreassen OA. Genetic Markers of Human Evolution Are Enriched in Schizophrenia. Biol Psychiatry. 2015 Oct 21. pii: S0006-3223(15)00855-0. doi: 10.1016/j.biopsych.2015.10.009. [Epub ahead of print] PubMed PMID: 26681495.

2:  Mariotti M, Smith TF, Sudmant PH, Goldberger G. Pseudogenization of testis-specific Lfg5 predates human/Neanderthal divergence. J Hum Genet. 2014 May;59(5):288-91. doi: 10.1038/jhg.2014.6. Epub 2014 Mar 6. PubMed PMID: 24599118.

3:  Sipahi L, Uddin M, Hou ZC, Aiello AE, Koenen KC, Galea S, Wildman DE. Ancient evolutionary origins of epigenetic regulation associated with posttraumatic stress disorder. Front Hum Neurosci. 2014 May 13;8:284. doi: 10.3389/fnhum.2014.00284. eCollection 2014. PubMed PMID: 24860472; PubMed Central PMCID: PMC4026723.

 4:  Zhang W, Tang J, Zhang AM, Peng MS, Xie HB, Tan L, Xu L, Zhang YP, Chen X, Yao YG. A matrilineal genetic legacy from the last glacial maximum confers susceptibility to schizophrenia in Han Chinese. J Genet Genomics. 2014 Jul 20;41(7):397-407. doi: 10.1016/j.jgg.2014.05.004. Epub 2014 Jun 2. PubMed PMID: 25064678. 

 5:  Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun. 2015 Mar 10;6:6404. doi: 10.1038/ncomms7404. PubMed PMID: 25752243; PubMed Central PMCID: PMC4355952. 

 6:  Toyota T, Yoshitsugu K, Ebihara M, Yamada K, Ohba H, Fukasawa M, Minabe Y, Nakamura K, Sekine Y, Takei N, Suzuki K, Itokawa M, Meerabux JM, Iwayama-Shigeno Y, Tomaru Y, Shimizu H, Hattori E, Mori N, Yoshikawa T. Association between schizophrenia with ocular misalignment and polyalanine length variation in PMX2B. Hum Mol Genet. 2004 Mar 1;13(5):551-61. Epub 2004 Jan 6. PubMed PMID: 14709596.

7:  FDA Warning Letter to 23andMe

8:  Frye MA, Nassan M, Jenkins GD, Kung S, Veldic M, Palmer BA, Feeder SE, Tye SJ, Choi DS, Biernacka JM. Feasibility of investigating differential proteomic expression in depression: implications for biomarker development in mood disorders. Transl Psychiatry. 2015 Dec 8;5:e689. doi: 10.1038/tp.2015.185. PubMed PMID: 26645624.

9:  Barnes KC.  Genetics of Asthma. In: UpToDate, Barnes PJ, Raby BA, Hollingsworth H (Ed), UpToDate, Waltham, MA. (Accessed on April 8, 2016)


Attributions:

All of the above graphics and tables with the sole exception the the ancestry table were generated with on site software at 23andMe based on my personal DNA sample.

Neanderthals - Real Human Differences and Stereotypes

That's right - I am 2.1% Neanderthal.  There have been some fascinating developments in human paleogenetics in the past decade including the characterization of genomes other hominins including the Neanderthals and the Denisovans from old remains.  It casts a different light on some of the stories based on stereotypes from the past.  For example, the common view of Neanderthals were that they were strong, but not very intelligent or sophisticated beings.  As as result Homo sapiens could easily outcompete these brutes and as a result modern day man is the only surviving species.  It was quite a surprise to learn that after the Neanderthal genome had been characterized portions of it could be identified in the modern human genome and that ancient DNA may have a role in the HLA (human leukocyte antigen) genes that play a central role in immunity.  There is the related question about whether incorporating the DNA of a new species could lead to certain autoimmune problems.   That fact compounded my interest in this area that was originally piqued by the first NatGeo Genographics project.  That project gave confirmation and graphics to the fact that at some point or another about 60-70,000 years ago, our ancestors walked out of the Rift Valley in East Africa and began their migrations around the globe.  Some of those folks migrating north through Europe encountered Neanderthals and Denisovans along the way.  Contrary to the conventional story that humans "outcompeted" them, they mated and produced offspring.

A quick review on relevant taxonomy.  From zoology, the naming convention is Genus and species.  Modern humans are Homo sapiens.  Considering this convention there were about 16 different species of the genus Homo and apart from Homo sapiens all of the others are extinct.   That includes Neanderthals (Homo neanderthalensis) and Denisovans.  In historical terms, at one time or another there was more than one Homo genus walking the earth.  Looking at a graphic from the Smithsonian suggests that Homo sapiens, Homo floresiensis,  Neanderthals (Homo neanderthalensis), and Denisovans were all walking the Earth sometime in the time zone about 20-30,000 years ago.  Genetic technology has revolutionized this area of morphology based research.  There is a lot of speculation but no good conclusions about why Homo sapiens is the only surviving species.

I don't know if they still teach this in Medical School but in all of my major rotations I was taught to describe the patient in the first sentence by age, sex, and ethnicity based on outward appearance.  There were various rationales provided for that opening sentence but even in medical school (now a long time ago) they did not make a lot of sense to me.  Of course there were cultural and political influences on these descriptions.   The "38 year old black male..." became the "38 year old African-American male..." at some point and back again depending on the politically correct term of the time.  It was all very unscientific, but many physicians seemed to think that it was a more medically precise way to talk about the patient and condense relevant information about that patient.  I did not have to consider anything beyond "male-female" versus "man-woman" to decide that my notes would never start with these words.  The only facts that I capture in my opening lines is the actual age of the patient and whether they are a man or a woman.  Male and female are non-specific terms and don't reflect the fact that I am talking about a human being.  You could say that this is an old convention, but I still see it as present in most medical records that I review.  In fact, it has stretched so that in some cases the characterization of white people has progressed from White to Caucasian to European, even though the person in question and their family has not set foot in Europe in over three or four generations.  I guess I also missed the politically correct convention that white folks were now "European Americans" and yet I have seen that frequently in medical records.

I read a paper in Science about 20 years ago that there were no genetically significant differences based on race or skin color.  It what seemed like a surprisingly simple statement, the authors pointed out that all humans are much more genetically related to one another than to non-human primates.  Genetic differences based on skin color and facial features were trivial to non-existent.  If you look at it that way that opening line:  "24 year old Hispanic female..." becomes little more than an unscientific stereotype.  Why include it in the medical record?  Some might say that it provides the opportunity for the delivery of culturally appropriate health care.  If that is the case, I would suggest including a more accurate description of the patients culture (as described by them) rather than presuming their culture based on their physical appearance or a check off on a standard intake form.  Scientific rather than stereotyped descriptions of people should be the standard.

A related issue is how much people actually know about themselves and their family of origin.  On the average, most of the people I talk with about their family histories know the high points for about 3 generations.  Physicians are typically focused on heritable diseases but most third and fourth generation Americans in this country don't know much about how their families migrated to the US and where they were migrating before that.  The first humans migrated out of the Rift Valley in East Africa about 70,000 years ago.  That is 2800 generations ago, maybe more if we need to correct for the short longevity of prehistoric man.  The fact that we are all Africans to start with and that so-called racial differences were a byproduct of the migration is a huge fact that nobody talks about.  It has far reaching implications and it is why I like to talk about it.

The other issue is what happened to the Neanderthals?  The story used to be that the Neanderthals were typical cave men.  They were squat muscular, and not very bright.  Their fate was considered to be extinction because they were outclassed and outcompeted by Homo sapiens.  Paleogenetics has led to those assumptions being challenged.  An excellent Nova special called Decoding Neanderthals captures some of the surprise and excitement of some of the first scientists who discovered Neanderthal DNA in the human genome.  That program also looks at how inferences can be made about prehistoric beings based on both the archaeological evidence and the genetic evidence.  In the case of archeology, the complexity of Neanderthal flint tool technology was investigated.  They had a method of making flint tools with a broad sharp edge that could be resharpened.  It was termed Levallois technology and the complexity suggests a higher level of intelligence than is commonly assumed.  The second Neanderthal technology that was discovered was using a type of pitch on some of their implements.  To manufacture this early epoxy required mastery of a thermal process again suggesting advanced intelligence.  The final piece of evidence is the presence of the FOXP2 gene.  This gene is responsible for speech and language in humans.  There are FOXP2 variants, but when the Neanderthal DNA was decoded, it contained a copy of the FOXP2 gene identical to modern humans.  That technology and the fact that Neanderthals were also social beings makes it a little more difficult to explain how they were "outcompeted" by Homo sapiens.  I have not seen any theories about how that competition might have included direct incorporation of large numbers of Neanderthals directly into the Homo sapiens population.  What are the numbers of Neanderthals who could have been incorporated into the population given the current DNA percentages?  I suspect that it could have been large.   

 To use an example from my own ancestors, I constructed a table looking at the stated ethnicities of my grandparents.  My maternal grandparents had been in the US for a generation longer.  My paternal grandmother still spoke and read her native language.  My maternal grandfather knew just small bits of Swedish.  He taught me a prayer in Swedish but did not know the translation and neither do I.  Small customs usually having to do with celebrations and food persisted to a small degree but on the balance my family was Americanized.  Comparing the stated ethnicities of my grandparents to DNA markers results in a couple of matches, but as many question marks.

Will there come a time when genetics will allow for better probability statements about who might inherit what disease?  Given the fact that my haplotypes occur in less than 1% of the current NatGeo database of over 650,000 subject - maybe.  But that depends on a lot more study and a medical record descriptor about presumed ethnicity has very little to do with it.  There is a related issue about how the science of paleogenetics can be politicized like any other branch of science.  Chris Stringer wrote an excellent commentary about this in Nature.  He observed a trend speculating that some genomes were more "modern" than others based on their content of "ancient" DNA.  He summarizes this well in two sentences:

"Some of us have more DNA from archaic populations than others, but the great majority of our genes, morphology and behavior derives from our common African heritage.  And what unites us should take precedence over that which distinguishes us from each other."

The current evidence also seems to suggest that the migration out of Africa is only part of the story.  The identical FOXP2 gene found in both Neanderthals and modern humans, suggests a common ancestor long before the African migration.  There are currently 7 billion people on earth.  The processing power of the human brain means that there are 7 billion unique conscious states.  It should not be too difficult to imagine that isolated groups of humans in in recent times will result in different  appearances, customs and practices.  The all too human characteristic of promoting the interests of these groups even to the point of warfare against others seems to be a common element of human consciousness.

A more widespread appreciation that these distinctions are by convention only might moderate a tendency for groups to see themselves as different or "better" than other groups of modern humans.  That leap of consciousness will hopefully happen in future generations.


George Dawson, MD, DFAPA



Supplementary 1:  One of the most striking aspects of this project is the economics of it all.  Over 680,000 people willing to pay $200 apiece for this information.  Researchers take note.  This may be a new way to fund research and generate large amounts of data at the same time.  You probably need a willing department head,  IT department, and IRB.  There is also a question of collaboration.  Is there any correlate between mental illnesses and the genomes of the Neanderthals and Denisovans?  If I have a well characterized sample of research subjects with a specific problem does it make sense to look at that issue?

Supplementary 2:  There are currently only 19 references to the issues of ancient DNA in Medline at this time.  Seems like another good area for research.

Supplementary 3:   My old high school biology text was ahead of its time in another way.  I remember that it predicted that the human race would eventually appear to be uniform due to increased mobility and intermixing of different races.

Supplementary 4:  The infographic at the top of this post was generated by the National Geographic Genographic Project based on my DNA sample.

Supplementary 5:  The evidence of bias against Neanderthals in popular culture is significant.  My first thought was the Geico commercials based on the premise: " three pre-historic men who must battle prejudice as they attempt to live as normal thirty somethings in modern Atlanta".  Even the Wiki piece refers to them as "Neanderthal-like".  Wikipedia has interesting references on this page and also a separate page entitled "Neanderthals in popular culture."

Supplementary 6:  Updated NatGeo infographic accessed on April 9, 2016.  NatGeo knows how to make a world class infographic.  Note that the sample size has gone from 678,632 to 742,652.  The remaining details are about the same but there is more updated information on the web site.

References:

1:  Stringer C.   Evolution: What makes a modern human.  Nature. 2012  May 2;485(7396):33-5. doi: 10.1038/485033a. PubMed PMID: 22552077.