Human Genome's Breaking Points: Genetic Sequence of Large-Scale Differences Between Human Genomes

Human Genome's Breaking Points: Genetic Sequence of Large-Scale Differences Between Human Genomes

  10:04:00 AM    Science Lover

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A detailed analysis of data from 185 human genomes sequenced in the course of the 1000 Genomes Project, by scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, in collaboration with researchers at the Wellcome Trust Sanger Institute in Cambridge, UK, as well as the University of Washington and Harvard Medical School, both in the USA, has identified the genetic sequence of an unprecedented 28 000 structural variants (SVs) -- large portions of the human genome which differ from one person to another.

The work, published in Nature, could help find the genetic causes of some diseases and also begins to explain why certain parts of the human genome change more than others.

Scientists have identified the genetic sequence of an unprecedented 28,000 structural variants -- large portions of the human genome which differ from one person to another. (Credit: iStockphoto/Andrey Prokhorov)

The international team of scientists identified over a thousand SVs that disrupt the sequence of one or more genes. These gene-altering mutations may be linked to diseases, so knowing the exact genetic sequence of these variations will help clinical geneticists to narrow down their searches for disease-causing mutations.

"Knowing the exact genetic sequence of SVs and their context in the genome could help find the genetic causes for as-yet unexplained diseases," says Jan Korbel, who led the research at EMBL: "this may help us understand why some people remain healthy until old age whereas others develop diseases early in their lives."

This unprecedented catalogue of large-scale genetic variants also sheds light on why some parts of the genome mutate more frequently than others. The scientists found that deletions, where genetic material is lost, and insertions, where it is gained, tend to happen in different places in the genome and through different molecular processes. For instance, large-scale deletions are more likely to occur in regions where DNA often breaks and has to be put back together, as 'chunks' of genetic material can be lost in the process.

"We found 51 hotspots where certain SVs, such as large deletions, appear to occur particularly often" Korbel says: "Six of those hotspots are in regions known to be related to genetic conditions such as Miller-Dieker syndrome, a congenital brain disease that can lead to infant death."

Previous research had already linked SVs -- also called copy-number variants -- to many genetic conditions, such as colour-blindness, schizophrenia, and certain forms of cancer. However, because of their large size and complex DNA sequence, SVs were difficult to identify. In this study, the researchers overcame these difficulties, developing novel computational approaches that allowed them to pinpoint the exact locations of these large-scale variations in the genome, broadening the potential scope of future disease studies.

"There are many structural variants in everyone's genomes and they are increasingly being associated with various aspects of human health" says Charles Lee, a clinical cytogeneticist and associate professor at Harvard Medical School and Brigham and Women's Hospital, and joint leader of the study: "It is important to be able to identify and comprehensively characterize these genetic variants using state-of-the-art DNA sequencing technologies."

Data from this study is being made publicly available to the scientific community through the 1000 Genomes Project, an international public-private consortium to build the most detailed map of human genetic variation to date. The 1000 Genomes Project aims to sequence 2500 whole genomes by the end of 2012, resulting, by far, in the largest collection of human genomes to date.

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Nanoscale DNA Sequencing Could Spur Revolution in Personal Health Care

Nanoscale DNA Sequencing Could Spur Revolution in Personal Health Care

  2:22:00 PM    Science Lover

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In experiments with potentially broad health care implications, a research team led by a University of Washington physicist has devised a method that works at a very small scale to sequence DNA quickly and relatively inexpensively.

This illustration depicts a single strand of DNA moving through a nanopore that is being used to sequence the DNA. (Credit: Image courtesy of University of Washington)

That could open the door for more effective individualized medicine, for example providing blueprints of genetic predispositions for specific conditions and diseases such as cancer, diabetes or addiction.

"The hope is that in 10 years people will have all their DNA sequenced, and this will lead to personalized, predictive medicine," said Jens Gundlach, a UW physics professor and lead author of a paper describing the new technique published the week of Aug. 16 in the Proceedings of the National Academy of Sciences.

The technique creates a DNA reader that combines biology and nanotechnology using a nanopore taken from Mycobacterium smegmatis porin A. The nanopore has an opening 1 billionth of a meter in size, just large enough to measure a single strand of DNA as it passes through.

The scientists placed the pore in a membrane surrounded by potassium-chloride solution. A small voltage was applied to create an ion current flowing through the nanopore, and the current's electrical signature changed depending on the nucleotides traveling through the nanopore. Each of the nucleotides that are the essence of DNA -- cytosine, guanine, adenine and thymine -- produced a distinctive signature.

The team had to solve two major problems. One was to create a short and narrow opening just large enough to allow a single strand of DNA to pass through the nanopore and for only a single DNA molecule to be in the opening at any time. Michael Niederweis at the University of Alabama at Birmingham modified the M. smegmatis bacterium to produce a suitable pore.

The second problem, Gundlach said, was that the nucleotides flowed through the nanopore at a rate of one every millionth of a second, far too fast to sort out the signal from each DNA molecule. To compensate, the researchers attached a section of double-stranded DNA between each nucleotide they wanted to measure. The second strand would briefly catch on the edge of the nanopore, halting the flow of DNA long enough for the single nucleotide to be held within the nanopore DNA reader. After a few milliseconds, the double-stranded section would separate and the DNA flow continued until another double strand was encountered, allowing the next nucleotide to be read.

The delay, though measured in thousandths of a second, is long enough to read the electrical signals from the target nucleotides, Gundlach said.

"We can practically read the DNA sequence from an oscilloscope trace," he said.

Besides Gundlach and Niederweiss, other authors are Ian Derrington, Tom Butler, Elizabeth Manrao and Marcus Collins of the UW; and Mikhail Pavlenok at Alabama-Birmingham.

The work was funded by the National Institutes of Health and its National Human Genome Research Institute as part of a program to create technology to sequence a human genome for $1,000 or less. That program began in 2004, when it cost on the order of $10 million to sequence a human-sized genome.

The new research is a major step toward achieving DNA sequencing at a cost of $1,000 or less.

"Our experiments outline a novel and fundamentally very simple sequencing technology that we hope can now be expanded into a mechanized process," Gundlach said.

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Nanotechnology: Artificial Pore Created

Nanotechnology: Artificial Pore Created

  12:35:00 AM    Science Lover

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Using an RNA-powered nanomotor, University of Cincinnati (UC) biomedical engineering researchers have successfully developed an artificial pore able to transmit nanoscale material through a membrane.

Scientists inserted the modified core of a nanomotor, a microscopic biological machine, into a lipid membrane. The resulting channel enabled them to move both single- and double-stranded DNA through the membrane. (Credit: Image courtesy of University of Cincinnati)

In a study led by UC biomedical engineering professor Peixuan Guo, PhD, members of the UC team inserted the modified core of a nanomotor, a microscopic biological machine, into a lipid membrane. The resulting channel enabled them to move both single- and double-stranded DNA through the membrane.

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