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takyon writes:

Scientists have used a new technique called 3D genome assembly to sequence the genome of a mosquito that can carry the Zika virus:

A team spanning Baylor College of Medicine, Rice University, Texas Children's Hospital and the Broad Institute of MIT and Harvard has developed a new way to sequence genomes, which can assemble the genome of an organism, entirely from scratch, dramatically cheaper and faster. While there is much excitement about the so-called "$1000 genome" in medicine, when a doctor orders the DNA sequence of a patient, the test merely compares fragments of DNA from the patient to a reference genome. The task of generating a reference genome from scratch is an entirely different matter; for instance, the original human genome project took 10 years and cost $4 billion. The ability to quickly and easily generate a reference genome from scratch would open the door to creating reference genomes for everything from patients to tumors to all species on earth. Today in Science, the multi-institutional team reports a method -- called 3D genome assembly -- that can create a human reference genome, entirely from scratch, for less than $10,000.

To illustrate the power of 3D genome assembly, the researchers have assembled the 1.2 billion letter genome of the Aedes aegypti mosquito, which carries the Zika virus, producing the first end-to-end assembly of each of its three chromosomes. The new genome will enable scientists to better combat the Zika outbreak by identifying vulnerabilities in the mosquito that the virus uses to spread.

[...] "Our method is quite different from traditional genome assembly," said Olga Dudchenko, a postdoctoral fellow at the Center for Genome Architecture at Baylor College of Medicine, who led the research. "Several years ago, our team developed an experimental approach that allows us to determine how the 2-meter-long human genome folds up to fit inside the nucleus of a human cell. In this new study, we show that, just as these folding maps trace the contour of the genome as it folds inside the nucleus, they can also guide us through the sequence itself."

By carefully tracing the genome as it folds, the team found that they could stitch together hundreds of millions of short DNA reads into the sequences of entire chromosomes. Since the method only uses short reads, it dramatically reduces the cost of de novo genome assembly, which is likely to accelerate the use of de novo genomes in the clinic. "Sequencing a patient's genome from scratch using 3D assembly is so inexpensive that it's comparable in cost to an MRI," said Dudchenko, who also is a fellow at Rice University's Center for Theoretical Biological Physics. "Generating a de novo genome for a sick patient has become realistic."

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (DOI: 10.1126/science.aal3327) (DX)

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