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In 2005 two well-known human geneticists, Francis Collins and Thomas Gelehrter, made a bet: Collins <a href="http://www.gnxp.com/blog/2006/08/collinss-wager.php" target="_blank" rel="noopener">wagered</a> that by the 2008 American Society for Human Genetics meeting, genomewide association studies would have led to the discovery of at least four “validated &#8211; not just guessed at” susceptibility variants for at least five common diseases.
Collins won his bet (and hopefully his beer) — by a margin of more than 200 variants.   According to the <a href="http://www.hugenavigator.net/HuGENavigator/startPageWatch.do" target="_blank" rel="noopener">Human Genome Epidemiology Network</a>, there have been 328 genomewide association studies published to date, and there is no sign of a slow down. This type of research has clearly been successful. But how useful are the variants they identify?
There are two directions from which to consider this question. One is to ask whether the common variants found in genomewide association studies add to science’s understanding of the biology of various common diseases, as well as medicine&#8217;s ability to treat them.   The other is to ask whether the results of genomewide association studies have made it possible to predict individual genetic risk for various diseases.   Three opinion pieces, each with a different perspective, address these questions in the New England Journal of Medicine this week.
<a href="http://content.nejm.org/cgi/content/full/NEJMp0806284" target="_blank" rel="noopener">David Goldstein</a>, director of the Center for Human Genome Variation at Duke’s Institute for Genome Sciences and Policy, doesn’t doubt the veracity of variants found in genomewide association studies.   But he does think that it’s time for geneticists to take a new approach.
“I believe attention should shift from genome scans of ever larger samples to studies of rarer variants of larger effect,” he writes in his NEJM commentary.
Goldstein says continued use of genomewide association approaches that look for common variants associated with common diseases and traits will ultimately lead to an unwieldy number of variants, each with vanishingly small effect sizes. For example, after making some assumptions he calculates that approximately 93,000 common variants could be needed to explain 80% of the population variation in height.
But variants with small effects can be biologically informative, argues <a href="http://content.nejm.org/cgi/content/full/NEJMp0808934" target="_blank" rel="noopener">Joel Hirschhorn</a>, a Harvard genetics professor, in the second NEJM Perspective.   For example, genomewide association studies have identified variants associated with type 2 diabetes, high cholesterol and low bone density that are located in genes targeted by drugs already approved by the FDA for the treatment of these conditions.
“Each of the associated variants at a drug-target locus explains less than 1% of phenotypic variation in the population, demonstrating that small effect sizes do not preclude biologic importance,” he writes.
The discovery of variants with small effect sizes can also point scientists in the direction of new avenues for drug research, says Hirschhorn.   Genomewide association studies of age-related macular degeneration and Crohn’s disease have both revealed new mechanisms of disease that are now being pursued as therapeutic targets.
In the final NEJM Perspective, <a href="http://content.nejm.org/cgi/content/full/NEJMp0810107" target="_blank" rel="noopener">Peter Kraft and David Hunter</a> from the Harvard School of Public Heath address genomewide association studies from the point of view of risk prediction.   They argue that while reliable risk predictions may be possible someday, testing for susceptibility based on common variants is currently premature for most conditions.   Like Goldstein, they note the small effect sizes associated with many of the common variants found so far.
“These factors suggest that many, rather than few, variant risk alleles are responsible for the majority of the inherited risk of each common disease….Estimates of risk based on established locus associations are therefore likely to change substantially in the next few years [as more variants are found],” Kraft and Hunter write.
Hirschhorn has a more optimistic view of the value of the variants identified through genomewide association studies.   He maintains throughout his article that the point of doing these studies is not risk prediction, but does say that it is likely that for some diseases, useful predictive information will emerge.   In fact, for some diseases the variants found to-date already give as much information to clinicians as other routinely used measures.
“For several diseases, associated variants already explain 10 to 20% or more of heritability, a magnitude that is similar to the proportion of risk explained by nongenetic tests in widespread clinical use (such as levels of low-density lipoprotein cholesterol or prostate-specific antigen),” Hirschhorn writes.
Hirschhorn goes on to argue that it is not how of much a disease’s genetics a variant or collection of variants explains, but how this information can shift the cost-benefit ratio of available clinical interventions.
“For diseases without potential therapies, even perfect prediction might not be clinically useful.   By contrast, for diseases with effective preventive measures that are too costly or for which the risk-benefit balance is nearly neutral, small increments in predictive power could help effectively target preventive efforts, with substantial clinical impact,” he writes.
Looking back at that 2005 bet between Collins and Gelehrter, it’s clear that not even the biggest names in the field could imagine just how far human genetics would come in such a short amount of time.   There’s no disputing that the study of common DNA variants has pushed science forward. And as new technologies and methods are developed, we&#8217;re sure to see even more progress.   We here at 23andMe hope to be a part of some of those new discoveries.

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328 Genomewide Association Studies and Counting … What Now?

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Researchers have identified a genetic variation that may raise the risk for stroke by affecting brain cells’ ability to respond to injury.
Stroke is the third leading cause of death in the United States, striking <a href="http://www.strokeassociation.org/STROKEORG/AboutStroke/Impact-of-Stroke_UCM_310728_Article.jsp" target="_blank" rel="noopener">almost 800,000</a> people each year. High blood pressure, high cholesterol, smoking, diabetes, obesity and a history of cardiovascular disease can all increase the risk of having a stroke, but studies of families and twins indicate that genes play a substantial role too.   So far, however, the genes underlying stroke risk in the general population remain undetermined.
Scientists combined data from several large studies comprising almost 29,000 people from the United States and the Netherlands to look for genetic variations associated with stroke risk. Their results, published online today in the <a href="http://content.nejm.org/cgi/content/full/NEJMoa0900094" target="_blank" rel="noopener">New England Journal of Medicine</a>, link a region of the genome not previously associated with stroke to increased risk in both black and white populations.
Strokes can be either hemorrhagic (caused by a broken blood vessel that bleeds into or around the brain) or ischemic (caused by a blood clot that blocks blood flow to the brain). Most strokes are the ischemic type.
Combined analysis of data from Caucasian study participants from the United States and the Netherlands revealed that the A version of this SNP is associated with a 1.29 times increased risk of ischemic stroke.   The SNP was also associated with an increased risk for ischemic stroke in a large African American study group — 1.42 times for each copy of an A.   Analysis of a smaller group of African Americans failed to yield a significant association between and stroke.
The risk of stroke is almost doubled for African Americans compared to white Americans, and African Americans are more likely to die from stroke or complications from stroke than any other ethnic group. This SNP is located near the NINJ2 gene, which encodes a protein that has been implicated in nerve cell injury response in animal studies.   Several other SNPs in and around the NINJ2 gene showed modest association with stroke. The authors of the study suggest that SNPs affecting how much protein is made from the NINJ2 gene might influence the brain&#8217;s response when deprived of oxygen by a blood clot.

Genetic Variation May Increase Risk Of Stroke

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Over the past decade, there has been no shortage of studies focused on the relationship between Neanderthals and our own species, Homo sapiens. Researchers have dug deep into the fossil record and our genomes to uncover how closely related we are to the Neanderthals, whether we interacted with them, and even whether our two species shared offspring.
But what about the Neanderthals themselves? We know that beginning around 400,000 years ago, they occupied over 3 million square miles of Europe and Western Asia, from Spain to Iraq. &nbsp; We know that they developed a unique tool technology and that they buried their dead. &nbsp; But what we really don&#8217;t know is how they compared to each other: &nbsp; were there in fact distinct Neanderthal sub-groups, shaped by the vastly different environments in which they lived? &nbsp; Or can they all be considered a single, genetically similar population? These questions are addressed in the most recent issue of <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005151" target="_blank" rel="noopener">PLoS One</a> by anthropologists from the UniversitÃ© de la MÃ©diterranÃ©e in France, using a method that is both unique and comprehensive. 
 
This study is of interest not only because it attempts to understand Neanderthal diversity, but also because it utilized data from a various sources. &nbsp; First, the researchers collected data from the mitochondrial DNA sequences of 12 separate Neanderthal skeletons. These skeletons ranged in age from 29,000 to 100,000 years and were uncovered in various parts of the Neanderthal homeland, from Siberia to Spain. &nbsp; The researchers then took physical measurements of the skeletons themselves. Finally, they developed and ran complex computer simulations based on the genetic and skeletal data, in an attempt to discover the most likely scenario for how Neanderthals evolved and spread across much of Eurasia.
The authors concluded that the most likely scenario for how the Neanderthals populated Europe and Western Asia involves three Neanderthal sub-groups: one centered in Western Europe, another in Southern Europe, and the final group in the Levant/Western Asia. &nbsp; They propose that the Neanderthals within each of these sub-groups were more genetically – and perhaps physically – similar to each other than they were to members of another sub-group. &nbsp; This is contrary to the idea that the Neanderthals were a single, uniform population.
This result begs the question of cultural distinctions between the sub-groups. &nbsp; After all, if they were genetically and physically different from one another, it is entirely plausible that cultural differences, such as tool technologies, between the sub-groups also existed. &nbsp; The authors hope to understand cultural differences between Neanderthal sub-groups in the same way as they&#8217;ve understood genetic and physical differences. &nbsp; And, as more fossils are found and more DNA extracted, we will hopefully develop – with even more confidence – a clear picture on the origins and movements of Neanderthals.

There’s More to Neanderthals than Meets the Eye

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Myopia, or nearsightedness, affects more than a <a href="http://www.nei.nih.gov/eyedata/pbd_tables.asp" target="_blank" rel="noopener noreferrer">quarter of the U.S. population</a>.
Doing a lot of “close-up work,” including reading, may bring on the condition or make it worse (as a society’s literacy rates rise, so does the rate of myopia), but there is a considerable genetic component too.
Myopia usually develops because the eyeball grows to be too long. In animal models of myopia, changes in eye tissue associated with reduced levels of a growth factor called TGF-Î²1 have been shown to be responsible for this elongation.
Two recent studies tried to connect TGF-Î²1 to myopia in humans by looking at genetic variations in the gene that encodes the protein, but the results were conflicting.
The authors of a new study, published online today in the <a href="http://archopht.ama-assn.org/cgi/content/short/127/4/541" target="_blank" rel="noopener noreferrer">Archives of Ophthalmology</a>, sought to clarify the role of the TGF-Î²1 gene in human myopia by analyzing several genetic variations in 300 nearsighted Chinese people and 300 with normal vision. The nearsighted people had a particularly severe form of myopia known as high myopia (usually defined as -6.00 diopters or worse, but this study used -8.00 diopters).
The researchers found that one SNP in the TGF-Î²1 gene in particular was associated with high myopia. Each A at decreased the odds of developing the condition by 0.67 times.
The authors say that their results solidify the TGF-Î²1 gene as a player in myopia, but the question of how affects the gene or the risk for the condition remains unanswered. Analysis of the TGF-Î²1 gene sequence showed that the different versions of might affect the amount of protein made from the gene, but further laboratory experiments will be needed to explore this possibility.
Alternatively, may be just a signpost pointing the way to a nearby genetic variant that truly affects the risk of myopia.

Focusing on a Genetic Link to Myopia

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We&#8217;ve set out to build the world&#8217;s largest online PD genetics community, and we&#8217;re thrilled to report that more than 2,000 people have enrolled &nbsp;since the initiative was launched last month. Owing to tremendous support from <a href="http://thepi.org" target="_blank" rel="noopener noreferrer">The Parkinson&#8217;s Institute</a> and Clinical Center and <a href="http://www.michaeljfox.org/" target="_blank" rel="noopener noreferrer">The Michael J. Fox Foundation</a>, their networks of patients have responded overwhelmingly. Assembling this many participants for traditional research studies usually takes months, if not years, to accomplish – by harnessing the power of the web and the enthusiasm of individuals, 23andMe can dramatically change the pace of research.

This puts us well on the way to our goal of enabling 10,000 individuals to help advance research into the genetics and other aspects of the condition. With this number of participants, we hope to be able to make discoveries about aspects of the causes, progression and treatment of Parkinson&#8217;s that smaller studies simply haven&#8217;t had the power to detect.
As members of the community, PD patients receive the the 23andMe Personal Genome Serviceâ„¢ &nbsp; for $25 instead of the usual $399. Along with all the <a href="https://www.23andme.com/howitworks/" target="_blank" rel="noopener noreferrer">benefits</a> of the service, the Parkinson&#8217;s community gives members:
<ul>
<li>research surveys aimed at gathering each patient&#8217;s experience with the disease, including age of onset, rate of progression and response to therapies.</li>
<li>the opportunity to ask questions and share stories with other members.</li>
<li>PD-specific reports relating to currently known genetic correlations.</li>
</ul>
Individuals who have been diagnosed with PD can sign up to participate via the website of the &nbsp;Michael J. Fox Foundation.
Even if you don&#8217;t have Parkinson&#8217;s, anyone can help with this research by setting up a free &nbsp;<a href="https://www.23andme.com/user/signup/" target="_self" rel="noopener noreferrer">23andMe demo account</a> and taking the Parkinson&#8217;s background survey. &nbsp;And, of course, 23andMe customers are encouraged to join the effort by filling out the survey, too. &nbsp;Together, we&#8217;re changing the pace of research!

On Our Way to 10,000: 23andMe Welcomes First Members of Parkinson’s Disease Community

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Ever since European explorers first came upon the African Pygmies in the mid-19th century, they have fascinated anthropologists and other researchers.   Their short stature (they rarely grow to over 5 feet), unique languages, and distinct genetic signatures have led to much speculation on how such groups of humans evolved.   Now, a new study published in the April 10 issue of <a id="fi4b" title="PLoS Genetics" href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000448" target="_blank" rel="noopener">PLoS Genetics</a> tackles this speculation head-on, using a novel and comprehensive approach in unraveling the origins of Pygmies.

When examining the origins of a particular group of people, many studies focus on a single part of the human genome; the Y-chromosome for example, or mitochondrial DNA.   However, the authors of this study wanted to get a complete picture of the genetic history of the Pygmies, so they looked at 24 separate regions of the human genome.   Altogether, the authors examined more than 33,000 letters of DNA for each of the 236 individuals they sampled.
After collecting and analyzing DNA samples from several different Pygmy groups, nearby Bantu-speaking farmers and other hunter-gatherer groups, the authors ran more than a million computer simulations on the data they had collected, allowing them to deduce the most likely scenario for how the Pygmies became so genetically distinct.
This is the second time in recent months that geneticists have offered an account of Pygmy population history. In February, a paper in <a id="zcpd" title="Current Biology" href="../2009/03/05/the-origins-of-the-forest-dwelling-african-pygmies/" target="_blank" rel="noopener">Current Biology</a> concluded that western Pygmies began interbreeding with their agricultural neighbors about 2,800 years ago.
The new PLoS paper concludes that Pygmies and their neighbors, non-Pygmy African farmers, had been separated for more than 50,000 years before that. They both shared a common genetic ancestor who lived nearly 56,000 years ago at a time when humans were spreading throughout the African continent, settling and thriving in the rainforests, savannahs, and coastal regions.   It is also around this time that the first human groups left Africa, journeying into Asia.
As these various groups of people began finding their own niches in the diverse African environment, they began to distinguish themselves culturally, physically and genetically.   The authors of this study believe that it is from this time onward that the unique physical form of African Pygmies began to evolve.
But the computer simulations also revealed much about the genetic diversity of the Pygmies themselves.   Pygmies today are generally divided into two ethnic groups:   eastern and western. Each has a somewhat different history, culture and genetic signature, though both are relatively similar in stature.
The authors believe that it was the environment that led to the separation of these two groups.   About 20,000 years ago, the Ice Age was at its peak.   As glaciers covered most of northern Europe, and sea levels dropped across the globe, the abundant rainforests of sub-Saharan Africa began to shrink.   A once lush and expansive tropical forest was now a series of smaller, drier forests, interspersed with savannah grassland.   The growing separation of the forests, the authors propose, led to the growing separation of peoples who had once lived side by side. Various Pygmy groups retreated to isolated pockets of the shrinking forests.   By the Ice Age&#8217;s peak, the once homogeneous Pygmies had split into two main groups.   The computer simulations confirmed the authors&#8217; hypotheses, putting the most likely split at around 21,000 years ago.
Today, the western &#8211; or Mbenga &#8211; Pygmies inhabit the West Congo Basin, while the eastern &#8211; or Mbuti &#8211; Pygmies, live in the forests of the Democratic Republic of the Congo.   And, while each group is short in stature, the past 20,000 years of biological and cultural evolution has made each group unique.   This study serves as a reminder of the wealth of history that is housed in our genes, if we only know where to look.

New Study Provides More Genetic Evidence for Origins of African Pygmies

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How can geneticists tell when a genetic difference between two human populations is an accident and when it’s the result of natural selection?
As our species moved out of Africa and spread out across the globe, there were a lot of chances for random DNA mutations to occur.   Many of these were neutral — they didn’t help or hurt a person’s chances for survival or reproduction — and whether they stuck around in a population’s gene pool was just a matter of luck. But some of these mutations actually helped people deal with the environmental changes and challenges they were facing.   These advantageous mutations tended to build up in frequency over the generations as they enhanced the reproductive success of the people who inherited them.
In some cases, there’s a satisfyingly simple story that demonstrates how a random mutation led to an advantage.   The version of the lactase gene that confers lactose tolerance, for example, is much more common in people of European ancestry than those with African or Asian ancestry.   This fits with the fact that about 8,000 years ago some of the world’s first dairy farmers emerged in — you guessed it — Europe.   For these people, the ability to digest milk would clearly have been a boon.
But some genetic differences between populations haven’t been so straightforward to explain. For example, one version of a variation in the p53 gene is found at higher levels in people with European ancestry than in those with African ancestry.   Is this just a matter of chance, or was there a reason this version of the gene increased in frequency as people moved north?
The best guess scientists have had so far is that the genetic difference has something to do with latitude and, by extension, exposure to UV radiation from the sun.   It’s certainly a plausible explanation.   The p53 gene helps protect cells from cancer, and UV radiation is known to be mutagenic.   But almost any difference between European and African populations would correlate with latitude, so that doesn’t prove anything.
In a study published online last week in the American Journal of Human Genetics, a group of researchers analyzed this p53 variation in Asian populations that are closely related genetically (at least compared to European vs. African populations), but nonetheless live at very different latitudes.   Their results were somewhat surprising.   The p53 variation does vary with latitude, but it’s not correlated with UV radiation level.   Instead, it’s how cold it gets in the winter that seems to matter.
Researchers analyzed rs1042522 in 4,029 people from 67 populations located throughout eastern Asia, from 11 ° south of the equator (Indonesia) to 65 ° north (northern China). They found that the C version of this SNP is more common at higher latitudes, as was expected based on the work in European and African populations.
The amount of UV radiation a locale receives, however, showed no correlation with the frequency of the C version of the SNP.   Instead, it was chillier winter temperatures that seemed to translate into more people in the population having the C version of rs1042522.
<img loading="lazy" decoding="async" class="size-full wp-image-3306 alignright" title="rs1042522" src="https://blog-api.23andme.com/wp-content/uploads/2009/04/rs1042522.jpg" alt="" width="355" height="253" srcset="https://blogcms.23andme.com/wp-content/uploads/2009/04/rs1042522.jpg 921w, https://blogcms.23andme.com/wp-content/uploads/2009/04/rs1042522-300x215.jpg 300w, https://blogcms.23andme.com/wp-content/uploads/2009/04/rs1042522-768x550.jpg 768w" sizes="auto, (max-width: 355px) 100vw, 355px" />
But why would the C version of rs1042522 be advantageous in colder climates?   Like so many genetic adaptations, it may all come down to making babies.
Using previous research about p53 as their guide, the authors of the study tested the ability of different forms of the p53 gene — containing either a C or a G at rs1042522 — to activate LIF, a gene important for embryo implantation in the womb, at different temperatures.
The results of these experiments indicate that the C version of the p53 gene is better at activating LIF in the cold.   This suggests that as populations moved into colder climates, those people with the C version of rs1042522 might have had an easier time conceiving (and therefore would have left behind more offspring, who in turn would pass the C version of the SNP on to their children).
But can a colder climate really bring down conception rates?   The parents of “<a href="http://www.cnn.com/2007/LIVING/wayoflife/09/27/blizzard.babies/index.html" target="_blank" rel="noopener noreferrer">blizzard babies</a>” might disagree, but the authors point out that in cattle at least, cold temperatures have been shown to have an effect.
Bonus: 
The researchers also looked at rs2279744, a variation in the MDM2 gene that (like rs1042522 in p53) is found at different frequencies in different populations.   The MDM2 variation did not vary with latitude or temperature, but did correlate with UV radiation levels.   Populations with higher UV radiation exposures had higher frequencies of the G version of rs2279744.
The MDM2 gene encodes a protein that reduces cellular levels of the p53 tumor suppressor protein. The G version of rs2279744 leads to higher levels of MDM2 protein, and thus lowers levels of p53.   The researchers speculate that as people moved out of Africa and into Asia, the lower levels of DNA-damaging UV light meant they could afford to have less p53 in their cells.   Because lower p53 levels are better for embryonic development, the scientists think nature would have favored the G version of rs2279744.
Bonus Bonus: 
Do p53 and MDM2 sound familiar?   Last week the Blog covered recent reports linking rs1042522 to <a href="https://blog.23andme.com/articles/snpwatch-genetic-variation-in-tumor-suppressor-may-predict-worse-outcome-for-african-american-colorectal-cancer-patients/" target="_blank" rel="noopener noreferrer">colorectal cancer survival in African Americans</a> and rs2279744 in <a href="https://blog.23andme.com/articles/snpwatch-genetic-variation-may-explain-why-young-women-are-at-greater-risk-for-melanoma-compared-to-young-men/" target="_blank" rel="noopener noreferrer">MDM2 to melanoma risk in young women</a>.
Map of rs1042522 frequencies is from the <a href="http://hgdp.uchicago.edu/" target="_blank" rel="noopener noreferrer">HGDP Selection Browser</a>.

Researchers Tie Variation in Cancer Gene to Winter Temperatures

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Although the itchy, red rashes that plague people with atopic dermatitis are usually set off by environmental irritants and allergens, the root of the condition (a type of eczema) is thought to be genetic.
A new report, published online this week in the journal <a href="https://dx.doi.org/10.1038/ng.347" target="_blank" rel="noopener noreferrer">Nature Genetics</a>, shows that a DNA variation previously associated with Crohn’s disease may be one of the genetic risk factors for atopic dermatitis.
Researchers analyzed the genetic data of more than 3,500 people with atopic dermatitis and more than 4,900 controls from Germany, Poland and the Czech Republic.   Their results showed that compared   people with two Cs at a specific SNP, to those with one T have 1.16 times higher odds of having atopic dermatitis, while those with two Ts have 1.47 times increased odds.
The researchers estimate that 13% of the population with European ancestry has two Ts at this SNP. 
A <a href="https://dx.doi.org/10.1038/ng.175" target="_blank" rel="noopener noreferrer">recent report</a> associated the SNP with Crohn’s disease.   In that study, each T increased the odds of Crohn’s by 1.16 times.   The authors of the current atopic dermatitis study note that Crohn’s and atopic dermatitis share several features — recurrent bouts of inflammation, cells that fail to form proper barriers (in the intestine and skin, respectively) and deficient immune responses against bacterial infections.   They suggest that the association of with both conditions may explain why there is a high incidence of eczema in people with Crohn’s disease.

Genetic Variation May Increase Risk For Atopic Dermatitis

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Researchers may have identified a genetic reason for why some people are more susceptible to chronic infection with the hepatitis B virus than others.
Whenever a person contracts a virus, the immune system is usually able to clear the infection from the body completely.   But more than 400 million people worldwide have a chronic form of hepatitis B that remains in their livers and puts them at risk for cirrhosis and liver cancer.
Age at infection is one of the most important factors in determining whether hepatitis B will become chronic.   Most people infected with hepatitis B after the age of five are able to fight it off, but the majority of those who are infected as infants or very young children never get rid of the virus. In a new report, scientists show that variations in an immune system protein may also contribute to whether a person will end up with chronic case of hepatitis B. These results, published online today in the journal <a href="https://dx.doi.org/10.1038/ng.348" target="_blank" rel="noopener noreferrer">Nature Genetics</a>, may help scientists understand more about the how hepatitis B causes disease and could someday facilitate the development of new treatments.
Researchers analyzed the DNA of more than 2,000 people with chronic hepatitis B and more than 4,000 controls from Japan and Thailand. Two genetic variations   showed significant associations with the condition.   For both, each copy of an A reduced the odds of chronic hepatitis B infection by about 40%.
The researchers note that the protective A versions of the SNPs tend to be found at lower frequencies in areas with high rates of chronic hepatitis B.   While the scientists don’t contend that genetic factors are the sole determinants of disease prevalence, they do suggest that these factors might exert a substantial influence.
The genes in closest proximity to the two identified SNPs, HLA-DPA1 and HLA-DPB1, encode subunits of an immune system protein called HLA-DP.   Upon further analysis, the researchers found that variations in the HLA-DPA1 and HLA-DPB1 genes also affect the odds of chronic hepatitis B infection.
HLA-DP is one of several proteins that help alert the immune system to the presence of infections. The authors of the study suggest that changes in this protein might affect its ability to signal the immune system and could therefore result in a weak, or even completely absent, immune response to hepatitis B infection.   This, in turn, could lead to persistent infection with the virus.   In support of this idea, previous research has shown that some versions of the HLA-DPA1 and HLA-DPB1 genes affect the immune system’s response to the hepatitis B vaccine.
Map Image: <a href="https://commons.wikimedia.org/wiki/File:HBV_prevalence_2005.png" target="_blank" rel="noopener noreferrer">PhillipN</a>
Notes:
<ul>
<li>Box size is relative to chronic hepatitis infection rate.   Rates were determined by taking the average of the rates given by the authors of this study for each population.   These are only estimates.</li>
<li>Color indicates the frequency of the A version of or .   Lighter colors indicate lower frequencies.</li>
<li>Populations are broad categories: Asian, African, European, Central American</li>
<li>Subpopulations are <a href="http://www.sanger.ac.uk/humgen/hapmap3/" target="_blank" rel="noopener noreferrer">HapMap3 populations</a></li>
<li>Information can be recategorized by changing order of the population and subpopulation icons at the top of the graphic.</li>
</ul>

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