Latino Genomes Point Way to Hidden DNA: 20 Million Missing Base Pairs Mapped

Jake Miller, Medical Xpress, August 8, 2013

Hidden in the tangled, repetitious folds of DNA structures called centromeres, researchers from Harvard Medical School and the Broad Institute have discovered the hiding place of 20 million base pairs of genetic sequence, finding a home for 10 percent of the DNA that is thought to be missing from the standard reference map of the human genome.

Mathematician Giulio Genovese, a computational biologist in genetics at HMS and at the Broad Institute, working in the lab of geneticist Steven McCarroll, HMS assistant professor of genetics and director of genetics for the Stanley Center for Psychiatric Research at the Broad Institute, found a way to use the genomes of Latinos to interpolate the locations of these missing pieces. Their findings will be published in The American Journal of Human Genetics on August 8.

“In nature, polymerase, the  that copies DNA within living cells, can sequence hundreds of millions of base pairs of DNA. The techniques we’ve developed to sequence DNA in the lab can only do relatively short segments, and we need to stitch those pieces together after the fact,” Genovese said. “So while we wait for sequencing technology to catch up with nature, we wanted to see if we could use mathematical patterns to find a place for some of the missing pieces.”

By using the genomes of admixed populations—populations, such as Latinos and African Americans that derive ancestry from more than one continent—the team developed a sophisticated  to help fill in the uncharted regions on the  map. The map is a key tool that geneticists rely on to find  and identify the functional genetic variations at the core of human diversity. The unmapped DNA also sometimes resembles known, mapped genes, which can interfere in attempts to study similar sequences.

{snip}

Surprisingly, the study also found that the genomes of Latino individuals are a uniquely powerful resource for assembling maps of the human genome. The study searched 242 Latino genomes from the 1000 Genomes Project Phase 1 for DNA sequences that have not yet been located on the reference human genome map.

“Throughout the history of genomic research, different populations have given unique gifts to genetic inquiry because of the history or structure of that population,” said McCarroll.

The power of the Latino genome for Genovese’s approach came from the contribution of the African ancestors that many Latino individuals have. Because of the long history of human evolution on the continent, the African genome is rich in genetic diversity. Other human populations evolved from subsets of that diverse population, as small groups migrated around the globe just a few tens of thousands of years ago. {snip}

“Latino populations have a relatively distinctive gift to give. Having some recent African ancestry, but just a little, can yield especially powerful information about what the structure of the human genome is in all populations,” McCarroll said.

When chromosomes recombine with each other in each generation, they do so in relatively large segments or chunks. In the genomes of Latinos— many of whom trace ancestry to European, Native American and African populations—the mixed European, Native American and African sequences form a mosaic of large segments.

Imagined as separate colors, an admixed genome would look like a mosaic with large red, green and blue tiles, rather than a video screen with tiny, mixed-color pixels.

Genovese developed an algorithm that could use a missing sequence’s proximity to known genetic markers to pinpoint where on the chromosome the missing pieces fit—a technique first reported in a related paper in February, which localized a smaller sample of genes.

The technique works best when individuals have some African DNA because the diversity among African genomes provides a high number of genetic markers. But Genovese discovered that his technique is most powerful when individuals have only a little African ancestry—because this genetic “signal” is then most localized to a small number of regions in their genomes. Because the sampled Latino genomes had low levels of African ancestry (on average, just a few percent, compared to around 80 percent in African Americans), it was more powerful for pinpointing where on the map the marker was.

The blank spots on the map that the researchers identified were the centromeres, the only places where the missing DNA could be hidden.

{snip}

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  • Romulus

    So who the hell gives a crap. What the heck kinda of study is this. A cheerleading rally for effing black miscegenation at the genetic level. The only thing blacks contribute to south America is cheap labor,rape,violence,crime and other assorted misadventures.

    • Spartacus

      Now now… In all fairness, they ARE the backbone of both the chicken and watermelon industries .

      • Sick of it

        So are white southerners, truth be told.

        • IstvanIN

          But without the violent crime.

          • Sick of it

            Well, we enjoy the fried chicken so much, there’s no need for violence…unless you try to take it away. Then things might get violent.

          • me

            Nah. Watermelon and fried chicken are delicious. Violence happens when Bantus overdose on ‘skittles and grape drank’…

          • Flossie

            Speaking of which . . . I read on a bulletin board somewhere that Trayvon’s postmortem revealed significant liver damage (significant for an otherwise-health 18-year-old) due to his having been a regular user of “lean” over the previous two years. Is there any truth to this? And while we’re dredging up the recent past, is it true his father left his boy’s corpse at the morgue for two or three days before claiming it? Thanks.

      • ShermanTMcCoy

        As in, “Why did the Bantu cross the road?”

        Obviously to follow the chicken.

  • Tim_in_Indiana

    They continue to make progress in discovering just how different genetic populations are.

    Now, hopefully, this information won’t be suppressed…

    • JohnEngelman

      As more is learned about the human genome it will be increasingly difficult to maintain the fiction that “race is only a social construct.”

    • Romulus

      With respect to your post, that’s the only thing that should be the focal point. It’s all in the wording.

  • Extropico

    There is no real question of the inferiority of Blacks intellectually. There is no debate on this; there is only suppression and dishonesty in the MSM. But I caution my friends here; just one genetic discovery that enhances intelligence for all mankind can change the dynamics. There is a great deal of government money researching this matter and not just in China. If the Blacks get the benefit of YT’s research, they can then have a lever to leapfrog us. Take a look at The Bourne Legacy. It is a really important movie for the “genetics are destiny” thought process.

    • Romulus

      Some would say that that kind of science is progressive. Science was the hallmark of the industrial revolution, no doubt. However, we are now seeing the diminishing returns of all the magic that’s been created. Every positive has an accompanying negative. Screwing around with natures systems has led to some very obvious negative returns, as evidenced by the collapse or extinction of many species, resource depletion,toxic air and water. You get the idea. Just because one can invent something ,doesn’t mean we should. It is the cost/benefit relationship. Looking back in hindsight, it was definitely a bad idea to unleash the power of the sun on planet earth(nuclear fission and fusion) even if it provided a means to the end of the war in the Pacific and electrical power generation. Einheeb even apologized for his efforts before he died. All that is to say,is that sometimes, it’s not nice to foul with mother nature.

      • Extropico

        Agree with an appropriate concern about mother nature. We must also avoid being too much like Luddites and we must eschew unilateral genetic disarmament.

      • BonusGift

        Good point. Its is interesting to note the fact that there are more ‘engineers’ and ‘scientists’ alive today (i.e., compared to the sum total of all of human history up to this point combined) yet the pace of invention and especially great leaps has probably never been slower (see, e.g., Peter Thiel’s thesis about the “technology deficit”; i.e., at least since the industrial revolution). In short, for us on AmRen it should come as no surprise that such technology leaps require one human element that seems to be lacking these days and it likely won’t happen without that special hated someone doing it. I say good luck with that and don’t forget there are no truly ‘free lunches’ in economics or science. Darn it if that most basic of YT wisdom seems lost on most these days.

        Also, I think it’s called “neomania” that many humans fall prey to ever so easily. Neomania is the worship of the new for the sake of being new (or at least being perceived new). For example, people who have no basic understanding of cell structure assume that some day soon human aging will be a think of the past (call it the “fountain of youth”). We want to believe we will not die and we want to believe in magic, combine the two and you can convince even a supposedly smart person to part with their wealth. Well, we are still looking for that fountain of youth, and we are still “waiting for superman”, and we are still waiting for pigs to fly. My point is that humans, and especially since YT’s magic industrialization, have a strong need to feel as if technology will save us, but seem to not consider if it will not save us, or as you point out, possibly make things worse. Food for thought anyway; and aint nature a bitch?

        • Sick of it

          Academia despises new ideas. Scientists come from academia. What we really see today is a new iteration of old ideas.

        • Tim_in_Indiana

          I’m going to look into Peter Thiel’s thesis. Very interesting. I had heard that technological advance is actually speeding up, but I’m open to alternative opinions.

        • FourFooted_Messiah

          We may have reached a sort of technoplateau, of the sort the optimistic sort of science-fiction writers would have none of. We’ve advanced so far, well, the XP bar just got a hell of a lot bigger in order to advance to the next level. Will we survive that long?

        • Tim_in_Indiana

          I’ve looked into what Peter Thiel says and so far, I’m not impressed. For example:

          “The housing bubble blew up so catastrophically because science and technology let us down. It blew up because our technocratic elite told us to expect an ever-wealthier future, and science hasn’t delivered.”

          He totally overlooks the real reason for the housing bubble, that the government gave out too many loans for unqualified minorities who couldn’t afford to pay them back.

          He also says that the great exception is information technology, whose rapid advance is no fluke: “So far computers and the Internet have been the one sector immune from excessive regulation.”

          But exponential advances in computers alone are enough to usher in huge progress. Add to that biotechnology and nanotech, which are also information technologies, and you’ve got the makings of a technological revolution.

          Thiel’s are interesting claims, anyway, coming from a guy who has invested quite a bit of money into cryonics research

          • “Information technology.”

            Which could mean quantum computing to solve protein folding, or it could mean blacks organizing mahogany mobs on Facebook.

          • FourFooted_Messiah

            Bleah. Computeres have nothing to do with crap. We cannot expect a wealthier future when increasing population demands that resources be spread thinner and thinner.

            Canada cannot fuel China, the US, and itself in perpetuity, so two of you have to go. 😛

          • BonusGift

            Of course he doesn’t get the housing bubble (i.e., if he told the truth on that one he wouldn’t be allowed a platform to speak); but the important point is the non-PC stuff about actual technology not what I would call fashion technology (e.g., ‘flash mobs’ and the next shape of the fancy walkie talkie we call a cell phone) which isn’t technology in the true sense of the term. For example, given the number of people calling themselves engineers and scientists we should be seeing unprecedented advances, yet we do not. I can still remember the hushed tones of the future of bioengineering and how it would be a game changer, virtually nada, still waiting … In fact, for example, I was talking with a engineer about cell phones who specializes in what I consider to be the most important aspect of cell phones (i.e., the quality of the phone call itself and/or signal strength) and he explained that over the last ten or so years it has gone down. I was initially floored at the realization of this and then I explained to him the Theil thesis and we both just grinned at the gullibility of humans to want to believe technology will solve all and always improve in a linear fashion. It’s kind of like wanting to believe we are all equal in a literal sense and if we are not then technology or allah will make some magical adjustment and then all will be well. Heck, they don’t call it “waiting for Superman” for nothing. Anyway, the dream of things like the ‘fountain of youth’ have always been around but today those things seem to be more likely to justify funding for a team of bureaucrats that call themselves engineers and scientists than actually slowing or reversing the aging process. Think of all the resources wasted on AGW (Anthropomorphic Global Warming – i.e., man caused global warming working through CO2). No most so called research these days seems to have a political bent or is just plain silly; and that which isn’t tends to be led by PC fools who wouldn’t know how to even frame the scientific question let alone invent a pet rock.

        • Romulus

          Thanks! I would also like to add that, as an individual, im not going to run out and be a birkenstock, granola eating tree hugger. If science is the course that humans believed would deliver heaven on earth, then our species must accept the good with the bad. So many lefties love to denounce the very systems that they helped create and lived so well by. Much of our science over the last 70 yrs. Can be directly attributed to refinements in electronics, which of course don’t work so well without a power source. Even very smart folks I talk to confuse Energy and technology. They go hand in hand, but are not the same thing. One is the hardware (tech), one is the software (fuel, Energy, power). Much of our existing technology will not work without the existing platforms and systems we’ve built to sustain them, especially without the Energy to match for scale.Someday ,the illuminati (pun intended) may harness the power of gamma rays or dark Energy, until then , I won’t hold my breath.

          • BonusGift

            Good point. I too find it laughable to just plain hypocritical that your average tree hugger eschews technology yet is reliant on it for their lifestyle (i.e., albeit possibly indirectly through general economic and technological advances). Furthermore, what I also find fascinating is how people that either can’t understand (e.g.,because they lack the cognitive ability to understand) or refuse to understand (e.g., because they lack the will to understand) the world around them and what drives it have a child like belief that that which they do not understand will save them and/or bring to life their misbegotten PC fantasies, for example. Even when their livelihood and/or life depend on it the vast swath of humanity truly seem to lack the ability for basic critical thinking.

      • Sick of it

        Clean fusion power would be great…it’s that filthy fission that’s causing problems. I’m not retarded enough to believe something is safe because some d-bag in a lab coat says it is…

        • me

          Mad scientists are still around. Instead of working in a castle in Transylvania, they’re working in government and corporate labs all across this great country of ours, funded by our tax dollars. Yay.

          • FourFooted_Messiah

            Torturing rats for years, and sucking in money because it’s “for cancer research” .. or shooting kittens in the head because it’s “for studying what happens when soldiers get shot”.

      • FourFooted_Messiah

        Humans made species go extinct before gunpowder was ever a wet dream of the Chinese. I guess the scientific advancements of the spear and the bow were a bad idea too.

        A better common name for “human” would be “killer ape”, it’s in our nature to be jerks to other life-forms.

    • Bossman

      You could be right about this. I believe our brains are really at the service of our reproductive organs.

  • APaige

    ‘Gift’ would never be the term to describe African ancestry.
    This that 20 million pairs of ‘socially constructed’ base pairs of genetic sequence?

    • me

      The ‘gift’ that keeps on giving….kind of like herpes.

  • Randall Ward

    This article is about how little we know, using math to predict what we can’t really know through observation. Our knowledge of how God built mankind is very very limited, but the religion of evolution marches on, never mind the constant defeats. “We know it is true.”

    • Bossman

      What is true?

      • Randall Ward

        The truth is we don’t know and we will never know, as long as we are on this earth. We aren’t intellegent enough to know the answers to ultimate questions. Just be satisfied that we can ask the questions.

        • Bossman

          Well what is not true is the allegorical tale of a supreme being called God planting a garden called paradise in the east of a place called Eden and then fashioning a nice white boy out of mud and then putting him in this garden and you know the rest of the story.

    • David Ashton

      There are problems with evolutionary theories. But there are known facts about the existing human subspecies, even if their relationship to the fossil record and genetically to one another have yet to be better clarified.

      What creationists of all types need to answer is whether the present human races were so designed by God and if so whether it is his will that they should be biologically amalgamated.

      I can hardly believe I am writing this, but trying to be fair: If all humans descend from a single pair (e.g. Adam and Eve) or from a single small group (e.g. Noah and his family) or from a single larger group (e.g. the community around Babel), and the biblical timeline is also accepted, then there must have been an accelerated evolution of humans along with a worldwide mass-disperson within some six thousand years. Is this more genetically or archaeologically credible than hominid evolution and dispersal over millions of years?

      The only alternative is that God deliberately created the different races, and so we are back to the moral issue: are we entitled to join what the creator put asunder? God is obviously a “sexist”. Isn’t God also a “racist”?

      • FourFooted_Messiah

        The question really is – no matter our religious/scientific beliefs, how strongly do we believe in “diversity”? I believe in diversity, but I also believe that the best way to preserve it is by keeping cultures/races apart to thrive on their own, and to keep their own unique paths. Who is anyone to say that human races shouldn’t be kept apart so that there might be several human species again one day? That can’t happen in a massive, all-breeding genetic pan-species morass. Evolution – species creation – only really works on smaller, GENETICALLY ISOLATED populations.

        I think the multi-culti race-mixing advocates are really anti-diversity, and anti-evolution.

        • David Ashton

          The permanent amalgamation of all existing populations in a global morass would bring the previous long evolutionary process of selection, development and variation to an end; and the first victim would most likely be our “white” race and its “western” culture. The latter specific possibility is much less remotely “hypothetical” than the former.

          • FourFooted_Messiah

            Of course, white race and culture are extrememly fragile – let the rest of them say we fear them. We should. We fear them bringing us back to some blasted Dark Age.

          • Bossman

            Evolution never stops. After all the races are “amalgamated,” something new and better could emerge.

          • David Ashton

            Will this possible “something” emerge from the pre-existent amalgam? If so, should it not be reabsorbed into the amalgam by miscegenation?

  • Bossman

    Hispanics are helping science to discover genes that may cure some diseases. Well then some you in this forum should have more respect for these mixed-breeds from south of the border.

    • sbuffalonative

      Hispanics are only providing genetic samples. It’s the white man who developed the science to do this genetic research. If anything comes from this research, it will be because of the work of the white man and not the lab rats.

  • FourFooted_Messiah

    No, I don’t think it’s advocating anything, it’s only taking advantage of genes that otherwise aren’t distinguished except with mixed-breed individuals. And separate, distinct, biological populations can be constructed from hybrids – witness the so-called Red Wolf, _Canis rufus_, which is a self-perpetuating bunch of WolfXCoyote halfbreeds. Latinos and Canadian Metis would seem to be about the same, and I’ve always suspected South Asians to be self-perpetuating half-breeds (yeah, yeah, start throwing the brickbats.)

    Frankly, I think modern biology has put itself in a quandary, because it is handcuffed by old-fashioned pigeonholing. Any “evolutionist” worth his salt should know that life is gradual, and full of gradation, and some of those gradations cannot be pigeonholed (blatant example – is Archaeopteryx a bird or a dinosaur? Probably proper answer – it’s a bit of both, and yet is neither.)

    Now, I’ve been through a lot of crap lately trying to explain my view, but everyone still seems to be stuck on pigeonholing. My favourite example (because it’s most familiar to me) is the Canids, particularly the North American group including coyotes, wolves, and domestic dogs (foxes are Vulpines, and are a separate, more catlike line of the dog family,and probably more primitive thus so than canids.) Now, while the dog has recently been reclassifed as a subspecies (RACE) of wolf, both dogs and wolves can also freely mate with coyotes, and create viable, fertile offspring that can mate with any other canid. Really, the three should be considered one species, with many races (wolf, coyote, German Shepherd, Shih-Tzu, Poodle, Rottwieler, etc).

    With me so far? Angry yet?

    Now. While I understand that whites, blacks, browns, yellows, whatever are all the same species, I can’t buy that we don’t have races in our species. And my next question is (brace yerselves) – how do we know we can’t breed with chimps? Yes, the chromosome count is messed, but it doesn’t stop horses and donkeys from making viable but sterile mules. And what if such offspring between man and chimp were not only viable, but fertile? OMG, such a can of theological and ethical worms. I notice Man was very careful to place himself and his closest relatives in SEPARATE GENERA. But is there really any validation for doing so? Shouldn’t the African Great Apes all be in the same genus, inclufing Man? We might still be separate species (I doubt we could cross with gorillas, and it’s possible we can’t, after all, cross with chimps in any which way shape or form), but why different _genera_?

  • David Ashton

    Dr David Rife, a leading international authority on cross-breeding among plants, animals and humans, long ago explained how the mixture of two populations, such as “black” and “white”, alters the distribution of genes but not the amount of variability (see e.g. “Race and Heredity”, in R. E. Kuttner (ed) “The Race Question in Modern Science” [NY 1967]). Thus hair form, skeletal dimensions, facial features, tooth formation and other traits will exhibit a tremendous range, mostly “independently of each other” (p.161).

    He adds that “hybrid vigor” cannot be expected among humans except in rare isolated cases. Wide crosses are haphazard, with little thought of improving mankind. Selection is not practiced before or afterwards (unlike domestic animal breeding). Some of the most talented human populations have abstained from crossing with other groups. Each of them (except Icelanders) have been subject to persecution at times. Selection may partially explain their outstanding qualities. Biologically there seem to be “no advantages to be gained from miscegenation” (p.167).

    • Bossman

      What you’re saying is neither here nor there. If there’s the phenomenon of “hybrid vigor” in plants and animals, then it sure exists in humans. All of nature is a continuum. When a person chooses a mate, they are making a selection based on personal taste. It may not always be a wise choice but it is still a selection.

      • David Ashton

        This selection is not the same as deliberate selection for animal breeding.
        Nor is it the same as selection by disease or environment.
        Rife and others have explained precisely why hybrid vigor as found in plants and animals has not been found in humans.

        • Bossman

          What exactly would a researcher be looking for to qualify as hybrid vigor in humans? Being bigger? Taller? Smarter? Sexier? Healthier? Mulattoes are generally better off than Blacks. If it doesn’t work for humans, then maybe as some has suggested it is because humans are already much too similar to each other than plant and animal species.

          • David Ashton

            Use a search engine.

      • Puggg

        But there is another concept, that’s the opposite of hybrid vigor, (I can’t remember its name), that presents more often.

        • Bossman

          It’s called retardation due to too much inbreeding.

        • David Ashton

          Outbreeding depression.

  • Stiv44

    I always heard that the black admixture in Latin America was “neglible”. At least in Mexico. I guess this proves that a little bit can go a long way .

  • Bossman

    Most of them are still more Indian than Spanish. Those that are 50% Spanish are generally very good-looking and look white. Watching the Spanish language TV channels of Univision and Telemundo will give you a good idea of what real Mexican Mestizos look like.

    • Jefferson

      You think all it takes is 50 percent Caucasian admixture to look White phenotype wise ?

      • Bossman

        Movie actor Anthony Quinn was the offspring of a short Mexican Indian woman and an Irish father. He grew up to be a tall handsome macho actor who could play the part of Greeks, Italians, Arabs and other ethnic roles. What more evidence do you want?

  • Rex

    Based on what we already know about these Ibero-Indians, that’s who they
    are, this assessment by Giulio Genovese is a total fabrication and to
    pay court to this fast growing invading group of Anti-American, Welfare
    people..