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Google Has Released an AI Tool That Makes Sense of Your Genome

Image result for genomeAlmost 15 years after scientists first sequenced the human genome, making sense of the enormous amount of data that encodes human life remains a formidable challenge. But it is also precisely the sort of problem that machine learning excels at. On Monday, Google released a tool called DeepVariant that uses the latest AI techniques to build a more accurate picture of a person’s genome from sequencing data. DeepVariant helps turn high-throughput sequencing readouts into a picture of a full genome. It automatically identifies small insertion and deletion mutations and single-base-pair mutations in sequencing data.

A number of tools exist for interpreting these readouts, including GATK, VarDict, and FreeBayes. However, these software programs typically use simpler statistical and machine-learning approaches to identifying mutations by attempting to rule out read errors. “One of the challenges is in difficult parts of the genome, where each of the [tools] has strengths and weaknesses,” says Brad Chapman, a research scientist at Harvard’s School of Public Health who helped develop DeepVariant. “These difficult regions are increasingly important for clinical sequencing, and it’s important to have multiple methods.”

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Everything Your Biology Teacher Told You About Earlobes Is Wrong

Image result for earlobeMost of us learned in high school biology that genetics can sometimes be incredibly simple. Some physical traits are the result of an easy equation containing a pair of parents’ genes. One trait—blue eyes, for example—results from recessive genes, but only if no dominant gene—the one to thank for brown eyes—shows up to take a stand. Parents each pass on two genes for eye color, or so your teacher probably told you. Depending on the combination, dominant genes can override any recessive genes to create their signature color. Sorry to break it to you, but very few traits actually work this way. Not even the classic example of eye color is actually so simple. With more genetic information available, it’s becoming clear that a number of different genes determine each feature. In a paper out this week in The American Journal of Human Genetics, scientists show that earlobes are no exception.

The researchers studied two different groups to identify those genes. They first recruited 10,000 people, sequenced their DNA, and examined their ears. From that initial set, the researchers spotted just six genes that played a role. But when they added their second group, which included 65,000 people who use the genetic testing company 23andMe (and have agreed to allow their samples to be used for research purposes) that number increased to 49. While the main point of this study is that seemingly simple genetic traits are far more complicated than previously thought, the fact that it took more than 10,000 people to identify those genes is also key. Geneticists often don’t like to perform population studies at such scale, because they are too large to zoom in on any specific details. But that means that we might not be getting the full picture, notes lead author John Shaffer, a geneticist at the University of Pittsburgh. Doing studies that combine small and large data sets could provide the best of both worlds, Shaffer says.

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Chimp Females Who Leave Home Postpone Parenthood

Image result for chimpanzeeWild chimpanzee females in western Tanzania who leave home or are orphaned take roughly three years longer to start a family. The researchers analyzed more than 50 years’ worth of daily records for 36 female chimps born in Gombe National Park. Stored in the Jane Goodall Institute Research Center at Duke University, the records are part of a larger database containing close observations of hundreds of wild chimpanzees, going all the way back to Goodall’s first field notes from the early 1960s. Several factors may contribute to the delay, the researchers said. Having left their family and friends behind, they must jostle for position in the pecking order of a new and unfamiliar group. In contrast, stay-at-home females benefit from better support. Females also started reproducing earlier if their own mothers were around while they were growing up, particularly if their moms were high-ranking — in part because females with high-ranking moms get better access to food.

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CRISPR-Carrying Nanoparticles Edit the Genome

In a new study, MIT researchers have developed nanoparticles that can deliver the CRISPR genome-editing system and specifically modify genes in mice. The team used nanoparticles to carry the CRISPR components, eliminating the need to use viruses for delivery. “What’s really exciting here is that we’ve shown you can make a nanoparticle that can be used to permanently and specifically edit the DNA in the liver of an adult animal,” says Daniel Anderson, an associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science (IMES).

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Twin Study Finds Genetics Affects Where Children Look, Shaping Mental Development

The image caption followsA new study co-led by Indiana University that tracked the eye movement of twins finds that genetics plays a strong role in how people attend to their environment. Conducted in collaboration with researchers from the Karolinska Institute in Sweden, the study offers a new angle on the emergence of differences between individuals and the integration of genetic and environmental factors in social, emotional and cognitive development. This is significant because visual exploration is also one of the first ways infants interact with the environment, before they can reach or crawl. “The majority of work on eye movement has asked ‘What are the common features that drive our attention?'” said Daniel P. Kennedy, an assistant professor in the IU Bloomington College of Arts and Sciences’ Department of Psychological and Brain Sciences. “This study is different. We wanted to understand differences among individuals and whether they are influenced by genetics.”

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New Model Reveals Possibility of Pumping Antibiotics Into Bacteria

Researchers in the University of Wisconsin–Madison Department of Biochemistry have discovered that a cellular pump known to move drugs like antibiotics out of E. coli bacteria has the potential to bring them in as well, opening new lines of research into combating the bacteria. The discovery could rewrite almost 50 years of thinking about how these types of transporters function in the cell. “Having to rework the model and essentially rewrite the textbook on what we knew about the transporters will really change the way we think,” she says. “I’m actually going to teach this paper in our intro graduate course because it’s such a good story of how having a model in your head can limit your thinking and experiments and you really miss important things.”

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Bonobos Help Strangers Without Being Asked

A passer-by drops something and you spring to pick it up. Or maybe you hold the door for someone behind you. Such acts of kindness to strangers were long thought to be unique to humans, but recent research on bonobos suggests our species is not as exceptional in this regard as we like to think. Famously friendly apes from Africa’s Congo Basin, bonobos will go out of their way to help strangers too, said Jingzhi Tan, a postdoctoral associate in evolutionary anthropology at Duke University. The impulse to be nice to strangers is likely to evolve in species where the benefits of bonding with outsiders outweigh the costs, said Tan, now a postdoctoral scholar at the University of California, San Diego. “All relationships start between two strangers,” Tan said. “You meet a stranger, but you may meet them again, and this individual could become your future friend or ally. You want to be nice to someone who’s going to be important for you.”

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Patrick Allard, Hannah Landecker and Amander Clark Awarded a John Templeton Foundation Grant

A UCLA research team led by Patrick Allard, assistant professor of society and genetics, has been awarded a $1.1 million grant from the John Templeton Foundation as part of the foundation’s funding efforts for research into genetics. The project’s co-leaders are Amander Clark, associate professor of molecular, cell and developmental biology, and Hannah Landecker, director of the UCLA Institute for Society and Genetics, and professor of sociology, who uses the tools of history and social science to study contemporary developments in the life sciences, including epigenetics.

The big questions Allard and his UCLA colleagues will address concerns whether we all have the same chance to live healthy lives and how much power individuals have over their own health. To what extent is our health pre-determined not only by our parents’ health, but going back several generations? “We hope that our findings will help us better understand how environmental exposure information is transferred across generations,” Allard said.

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