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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.

23andMe Blog

23andMe Blog Team

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>

Immune System Variations May Determine Susceptibility To Chronic Hepatitis B Infection

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The 23andMe Personal Genome Service offers information about customers&#8217; maternal and paternal ancestry by examining their mitochondrial DNA (which we all inherit from our mothers) and the Y chromosome (passed by fathers to their sons).
Over our species&#8217; history, new genetic variations have arisen spontaneously in those pieces of DNA and passed down through the generations. So researchers know that every person alive today with a particular variation – say a T instead of a G at a specific spot on the mtDNA – is descended from a single common ancestor. By sampling people from around the world, scientists have assembled &#8220;family trees&#8221; that trace back to the dawn of the human species in eastern Africa more than 100,000 years ago. Those trees are the basis of the haplogroup assignments we give our customers. Each haplogroup represents a particular branch – and, therefore, a unique sequence of SNPs.
Now, using a feature we&#8217;ve developed called the Haplogroup Tree Mutation Mapper, you can see exactly which SNPs we use to generate the 23andMe mitochondrial and Y chromosome haplogroup trees. This isn&#8217;t the kind of information everyone would necessarily want, but several customers who are especially interested in genetic genealogy have requested it. It can be used to compare our haplogroup assignments to those obtained elsewhere, for example.

The Haplogroup Tree Mutation Mapper is the first arrival in 23andMe Labs, our new technology sandbox, where we will showcase experimental features not currently available in our Personal Genome Service.   These features may still be in development, require specialized knowledge, or be of interest only to a subset of our customers. Each lab will have its own community so customers can compare notes, ask questions, and share ideas.
Some labs will be requested by customers—in fact, we welcome your suggestions—and others will be dreamed up by our scientists.
Finally, labs will be somewhat less refined and fluid than those available within the Personal Genome Service. A feature could be discontinued at any time or elevated to full integration with our Personal Genome Service.
We&#8217;re really excited about this new outlet for our ingenuity, and we hope it will also engage some of you!

23andMe Labs Kicks Off With Haplogroup Tree Mutation Mapper

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Colorectal cancer is the third most commonly diagnosed cancer in the U.S., and the third leading cause of cancer death.   In 2008 close to 50,000 people succumbed to the disease.
But not all groups are affected equally.   An American Cancer Society study found that colorectal cancer incidence rates are more than 20% higher for African Americans than Caucasians. Death rates from the disease are 45% higher.
Lifestyle factors, access to healthcare and cultural differences have all been proposed as reasons to explain the racial disparities in colorectal cancer survival. But new research from the University of Alabama, published today in the journal <a href="http://clincancerres.aacrjournals.org/cgi/content/abstract/15/7/2406" target="_blank" rel="noopener noreferrer">Clinical Cancer Research</a>, shows that for some African Americans, genetics may play a part too.
Researchers analyzed 373 colorectal tumors — 137 taken from African Americans and 236 taken from non-Hispanic Caucasians.   They found that African American patients with two Gs at in the p53 gene were 2.15 times more likely to die of colorectal cancer than those with one or no copies of a G at this SNP.   In Caucasians there was no association between survival and .
Seventeen percent of African American patients had two Gs at this SNP, while only 7% of Caucasian patients did.
The p53 gene encodes a tumor suppressor protein that protects against cancer, in part, by telling damaged cells to self-destruct instead of turning into tumors.   Mutations in the p53 gene that disrupt its function are a common feature of many cancers. (These mutations are distinct from the variation.)
Although the findings will need to be replicated in larger studies, the study’s authors suggest that might be a race-specific prognostic marker for African American patients with colorectal cancers and that someday analysis of this SNP might aid in designing optimal treatment regimens.

Genetic Variation In Tumor Suppressor May Predict Worse Outcome for African American Colorectal Cancer Patients

<img loading="lazy" decoding="async" class="alignright size-full wp-image-3220" title="skincancer" src="https://blog-api.23andme.com/wp-content/uploads/2009/03/skincancer.jpg" alt="" width="320" height="211" srcset="https://blogcms.23andme.com/wp-content/uploads/2009/03/skincancer.jpg 320w, https://blogcms.23andme.com/wp-content/uploads/2009/03/skincancer-300x198.jpg 300w" sizes="auto, (max-width: 320px) 100vw, 320px" />
Melanoma, a rare but potentially deadly form of skin cancer, is more common in women under 40 than in men in the same age group.   After age 45, the tables are turned: men are more likely to be diagnosed with melanoma.
Between the ages of 40 and 50 happens to be when many women enter menopause or perimenopause, a time of declining estrogen levels.   This has prompted some researchers to suggest that estrogen exposure may play a part in melanoma risk.
In a report published last week in Clinical Cancer Research, researchers show that a genetic variation previously associated with several other cancers may be the link between estrogen and melanoma in younger women.   The riskier version of the variation increases the odds a woman will be diagnosed with melanoma before age 40 more than fourfold.
“Potentially, we have a genetic test that might identify pre-menopausal women who are at higher risk for melanoma.   And if that’s the case, then we might want to have increased surveillance of those patients including more frequent visits to the doctor, more rigorous teaching of skin self-examination, and other preventive steps,” said Dr. David Polsky, the study’s lead author, in a statement.
In a sample of 227 people with melanoma — 93 women and 134 men — researchers found that women with two Gs at a specific SNP in the MDM2 gene were diagnosed with the disease 13 years earlier than those with GT or TT at this SNP.   In men, there was no effect of on age at diagnosis.
About 52% of women with GG at this SNP were diagnosed with melanoma before age 50 — and 38% between ages 30 and 39.   Only about 22% of women with GT or TT were diagnosed before age 50. Although those figures are dramatic, it is important to remember that the SNP was not shown to affect melanoma risk generally, but the age at which people who do develop it are diagnosed.
Laboratory experiments have shown that the G version of this SNP causes the MDM2 gene to be turned on at higher levels in response to estrogen than the T version.
Higher levels of MDM2 protein may be relevant to melanoma, as well as other cancers, because its role in cells is to regulate a tumor suppressor protein called p53.   More MDM2 means less p53, which in turn can reduce a cell’s protection against turning into a cancer cell.
More research will be needed to confirm that there is an interaction between estrogen and the G version of SNP that affects melanoma risk.   The authors caution that their study was small, lacked information about the menopausal status of the women they studied and did not include a group of people without melanoma for comparison.
More work will also be needed to understand how the MDM2 gene and the protein it encodes affect cancer risk in general.   The G version of SNP has been associated with earlier onset for some cancers, including soft tissue sarcoma, diffuse large B-cell lymphoma, colorectal cancer, ovarian cancer and non-small cell lung cancer in women, and decreased survival in people with stomach and kidney cancer.   But there is evidence for improved survival in women with ovarian cancer who have the G version of this SNP.   Paradoxically, higher levels of the MDM2 protein (as would be expected with the G version of SNP shown to lead to earlier melanoma onset in the current study) have been associated with improved survival for melanoma.

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