Category Archives: Human Genetics

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In a study that will provide the foundation for scientists to better replicate natural stem cell development in an artificial environment, UCLA researchers at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research led by Dr. Guoping Fan, professor of human genetics, have established a benchmarking standard to assess how culture conditions used to procure stem cells in the lab compare to those found in the human embryo.

The study was published online ahead of print in the journal Cell Stem Cell.

Pluripotent stem cells (PSCs) are cells that can transform into almost any cell in the human body. Scientists have long cultured PSCs in the laboratory (in vitro) using many different methods and under a variety of conditions. Though it has been known that culture techniques can affect what kind of cells PSCs eventually become, no "gold standard" has yet been established to help scientists determine how the artificial environment can better replicate that found in a natural state (in vivo).

Dr. Kevin Huang, postdoctoral fellow in the lab of Dr. Fan and a lead author of the study, analyzed data from multiple existing research studies conducted over the past year. These previously published studies used different culture methods newly developed in vitro in the hopes of coaxing human stem cells into a type of pluripotency that is in a primitive or ground-zero state.

Utilizing recently-published gene expression profiles of human preimplantation embryos as the benchmark to analyze the data, Dr. Huang and colleagues found that culture conditions do affect how genes are expressed in PSCs, and that the newer generation culture methods appear to better resemble those found in the natural environment of developing embryos. This work lays the foundation on the adoption of standardized protocol amongst the scientific community.

"By making an objective assessment of these different laboratory techniques, we found that some may have more of an edge over others in better replicating a natural state," said Dr. Huang. "When you have culture conditions that more consistently match a non-artificial environment, you have the potential for a much better reflection of what is going on in actual human development."

With these findings, Dr. Fan's lab hopes to encourage further investigation into other cell characteristics and molecular markers that determine the effectiveness of culture conditions on the proliferation and self-renewal of PSCs.

"We hope this work will help the research community to reach a consensus to quality-control human pluripotent stem cells," said Dr. Fan.

Explore further: Technique to make human embryonic stem cells more closely resemble true epiblast cells

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Team proposes benchmark to better replicate natural stem cell development in the laboratory environment

By Shane Huntington

Neuroscientist Prof Seth Grant explains how genetics gave rise to the modern human brain, and how the very complexity that characterises our brains makes them vulnerable to neurological diseases that reveal themselves in mental illness.

SHANE HUNTINGTON

I'm Dr Shane Huntington. Thanks for joining us. Our ability to comprehend the environment around us, to adapt rapidly the changing conditions and to imaginatively express ourselves through art are all outstanding outcomes of an evolutionary process that has generated human brains of stunning complexity. But what is it that enables our grey matter to achieve such feats? Are these features solely the territory of human beings or do we share similar traits with other life forms? As with any mechanism, be it electrochemical or mechanical, added complexity leads to potential problems that are correspondingly complex to resolve. Diseases that affect the way we think and use our bodies are many and stem from a variety of causes but almost always situated in the brain. Today on Up Close we're joined by neuroscientist Professor Seth Grant to explore how the evolution of synapses has given vertebrates like us the ability to think and learn whilst also making us susceptible to mental illness and diseases of the brain. Seth Grant is Professor Molecular Neuroscience in the Centre for Neuroregeneration at the University of Edinburgh. He is in Melbourne to speak at the 2014 Melbourne Brain Symposium, an event jointly organised by the Melbourne Neuroscience Institute and the Florey Institute of Neuroscience and Mental Health. He is also delivering the annual Kenneth Myer Public Lecture as a guest of the Florey Institute. Welcome to Up Close, Seth.

SETH GRANT

Yes, thank you, Shane.

SHANE HUNTINGTON

I think we'll start with just the role that synapses actually play in the brain. Can you give us a description of where they fit in?

SETH GRANT

Well most people will realise of course that all organs in the body are made from cells and there's very large numbers of them but the nerve cells in the brain are very unusual compared to other cells in other parts of the body because they have specialised junctions between them which are called synapses. Now not only do they have junctions between them but the nerve cells in the brain have very long extensions or fibres which have names like axons and dendrites. Those long axons and dendrites have on them about 10,000 synapses per cell which means then that every nerve cell in the brain can contact as many as 10,000 other nerve cells. Just contrast that with a liver cell for example. A liver cell may only touch another 10 or 20 cells so nerve cells and the synapses are what make the brain different to all other organs.

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The cost of cognition: The blessing and curse of human brain complexity

Rare Mutation Detection w/ Digital PCR - ASHG 2014
Learn more at http://www.lifetechnologies.com/us/en/home/life-science/pcr/digital-pcr/rare-mutation-analysis.html.html Among several technologies on display at the American Society for Human...

By: Life Technologies

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Rare Mutation Detection w/ Digital PCR - ASHG 2014 - Video

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Newswise In a study that will provide the foundation for scientists to better replicate natural stem cell development in an artificial environment, UCLA researchers at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research led by Dr. Guoping Fan, professor of human genetics, have established a benchmarking standard to assess how culture conditions used to procure stem cells in the lab compare to those found in the human embryo.

The study was published online ahead of print in the journal Cell Stem Cell.

Pluripotent stem cells (PSCs) are cells that can transform into almost any cell in the human body. Scientists have long cultured PSCs in the laboratory (in vitro) using many different methods and under a variety of conditions. Though it has been known that culture techniques can affect what kind of cells PSCs eventually become, no "gold standard" has yet been established to help scientists determine how the artificial environment can better replicate that found in a natural state (in vivo).

Dr. Kevin Huang, postdoctoral fellow in the lab of Dr. Fan and a lead author of the study, analyzed data from multiple existing research studies conducted over the past year. These previously published studies used different culture methods newly developed in vitro in the hopes of coaxing human stem cells into a type of pluripotency that is in a primitive or ground-zero state.

Utilizing recently-published gene expression profiles of human preimplantation embryos as the benchmark to analyze the data, Dr. Huang and colleagues found that culture conditions do affect how genes are expressed in PSCs, and that the newer generation culture methods appear to better resemble those found in the natural environment of developing embryos. This work lays the foundation on the adoption of standardized protocol amongst the scientific community.

"By making an objective assessment of these different laboratory techniques, we found that some may have more of an edge over others in better replicating a natural state," said Dr. Huang. "When you have culture conditions that more consistently match a non-artificial environment, you have the potential for a much better reflection of what is going on in actual human development."

With these findings, Dr. Fan's lab hopes to encourage further investigation into other cell characteristics and molecular markers that determine the effectiveness of culture conditions on the proliferation and self-renewal of PSCs.

"We hope this work will help the research community to reach a consensus to quality-control human pluripotent stem cells," said Dr. Fan.

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UCLA Scientists Propose Benchmark to Better Replicate Natural Stem Cell Development in the Laboratory Environment

Welcome to ASHG 2014: Inside the Life Technologies Booth
Thousands packed the San Diego Convention Center this week to attend the 2014 American Society of Human Genetics annual meeting. But alas, countless others were not able to make the trip out...

By: Life Technologies

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Welcome to ASHG 2014: Inside the Life Technologies Booth - Video

Chuck Bednar for redOrbit.com Your Universe Online

Genetic analysis of DNA obtained from a 45,000-year-old modern human thigh bone has allowed researchers to narrow down the time frame in which mating first introduced Neanderthal genes into the human gene pool.

An international team of experts including scientists from the Max Planck Institute for Evolutionary Anthropology, the Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences and Harvard Medical School in Boston report in the latest edition of the journal Nature that interspecies mating first took place between 50,000 and 60,000 years ago.

The thigh bone studied by the genetics team was discovered in Siberia, and Dan Vergano of National Geographic noted that it is the oldest modern human bone discovered that far outside of Africa and the Middle East nearly twice the age of the next oldest, a 24,000-year-old fossil belonging to a boy that died elsewhere in the northern Asian region and whose genome was sequenced in 2013.

Study author and genetics expert Janet Kelso of the Max Planck Institute told Vergano that it was really exciting to have a really high-quality genome sequence of an early modern human that is this old, and that by using DNA from the bone to analyze the mans genetic map, they were able to find that he had roughly 2.3 percent Neanderthal genes. By comparison, modern men and women typically have about 2.1 percent Neanderthal DNA.

After its discovery, the bone reportedly changed hands multiple times before reaching the Max Planck Institute. Once there, the samples remarkably well preserved DNA enabled researchers to extract a genome sequence that Harvard University said was significantly higher in quality than most genome sequences of present-day people generated for analysis of disease risk.

Carbon dating and molecular analysis had revealed the sample belonged to an individual who lived 45,000 years ago and lived on a diet that included plants or plant eaters, as well as fish or other aquatic life forms. The genome sequence further revealed the individual, who has been identified as the Ust-Ishim man, was a modern human and, more specifically, a member of one of the most ancient non-African populations.

The morphology of the bone suggests that it is an early modern human; that is an individual related to populations that are the direct ancestors of people alive today anthropologist Bence Viola, who analyzed the bone, confirmed in a statement Wednesday. This individual is one of the oldest modern humans found outside the Middle East and Africa.

The sequenced genome was also compared to those of present-day humans of over 50 different populations, and it was found that the Ust-Ishim bone originated from a man who is more closely related to present-day non-Africans than to Africans. For that reason, the researchers conclude that he is among the first people to have left Africa and traveled to Eurasia. In addition, his genome was found to be somewhat equally related to both East Asians and to those that lived in Europe during the Stone Age.

The population to which the Ust-Ishim individual belonged may have split from the ancestors of present-day West Eurasian and East Eurasian populations before, or at about the same time, when these two first split from each other, explained Svante Pbo of the Max Planck Institute. It is very satisfying that we now have a good genome not only from Neandertals and Denisovans, but also from a very early modern human.

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Thigh Bone DNA Helps Narrow Down When Humans, Neanderthals First Intermingled

Up Close: PGM Dx at ASHG 2014
Learn more about the PGM Dx: https://www.lifetechnologies.com/us/en/home/clinical/molecular-diagnostics/diagnostic-instruments/ion-pgm-dx.html Since being previewed at the European Society...

By: Life Technologies

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Up Close: PGM Dx at ASHG 2014 - Video

The National Institutes of Health announced Wednesday that human testing has begun on a second experimental Ebola vaccine, VSV-ZEBOV.

The vaccine, which was developed by the Public Health Agency of Canada, uses a genetically altered version of vesicular stomatitis virus, which usually affects livestock and causes mild illness in humans.

In tests with monkeys, the vaccine was shown to produce Ebola virus antibodies. Researchers say this was accomplished by altering VSV so that it contained the same protein that Ebola uses to invade cells.

The vaccine is being tested at the National Institute of Allergy and Infectious Diseases and the Walter Reed Army Institute of Research, according to the NIH. One set of tests will involve a two-shot "prime-boost" strategy, while the other will test a single shot technique.

The vaccine has been licensed to Newlink Genetics Corporation of Ames, Iowa.

In September, phase one safety trials began on another vaccine candidate developed by the NIAID and the pharmaceutical company Glaxosmithkline.

The NIH said that initial safety and immune response results for the NIAID-GSK vaccine are expected by the end of this year.

Follow @montemorin for science news

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Human safety trials begin on second experimental Ebola vaccine

PUBLIC RELEASE DATE:

18-Oct-2014

Contact: Nalini Padmanabhan press@ashg.org 301-634-7346 American Society of Human Genetics @GeneticsSociety

BETHESDA, MD Human geneticists have discovered that a region of the genome associated with autism contains genetic variation that evolved in the last 250,000 years, after the divergence of humans from ancient hominids, and likely plays an important role in disease. Their findings were presented today at the American Society of Human Genetics (ASHG) 2014 Annual Meeting in San Diego.

Researchers at the University of Washington analyzed the genomes of 2,551 humans, 86 apes, one Neanderthal, and one Denisovan. They closely examined a region of human chromosome 16 known as 16p11.2, a region prone to genetic changes in which segments of DNA are deleted or duplicated, one of the most common genetic causes of autism, schizophrenia, and other conditions. The geneticists found that certain segments of DNA in this region are repeated a variable number of times in different people and may also be associated with disease.

To trace the origins of this variation, the researchers collaborated with colleagues at the University of Lausanne and the University of Bari to sequence and analyze corresponding regions of ape genomes.

"When we compared the genomes of apes and humans, we found that the humans had evolved complex structural changes at 16p11.2 associated with deletions and duplications that often result in autism. The findings suggest that these changes emerged relatively recently and are unique to humans," explained study author Xander Nuttle, BS, BSE, a graduate student in the Department of Genome Sciences at the University of Washington School of Medicine.

While this genetic variation has likely made humans more vulnerable to disease, the scientists believe it also contributed to the formation of novel genes. One such gene is BOLA2, a gene thought to be important in cell reproduction. The researchers found that while apes, Neanderthals, and Denisovans had only two copies of BOLA2, all modern humans have between three and 14 copies, with an average of six. The team is currently studying the function of BOLA2 to understand the potential significance of additional copies for human evolution.

"Another question we are exploring is why people with the same duplications and deletions at 16p11.2 vary in disease severity," Mr. Nuttle said. "Some people are healthy or have mild illness, while others are severely affected and have multiple clinical diagnoses."

One hypothesis is that differences among people in how the region is organized, such as the number of copies of genes like BOLA2 present and the precise locations at which deletions and duplications start and end, contribute to this variability. To examine this possibility, Mr. Nuttle and colleagues are analyzing DNA and medical data from over 125 individuals with deletions or duplications at 16p11.2.

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Gene duplications associated with autism evolved recently in human history

PUBLIC RELEASE DATE:

19-Oct-2014

Contact: Nalini Padmanabhan press@ashg.org 301-634-7346 American Society of Human Genetics @GeneticsSociety

BETHESDA, MD Scientists studying birth defects in humans and purebred dogs have identified an association between cleft lip and cleft palate conditions that occur when the lip and mouth fail to form properly during pregnancy and a mutation in the ADAMTS20 gene. Their findings were presented today at the American Society of Human Genetics (ASHG) 2014 Annual Meeting in San Diego.

"These results have potential implications for both human and animal health, by improving our understanding of what causes these birth defects in both species," said Zena Wolf, BS, a graduate student at the University of California, Davis School of Veterinary Medicine.

In both humans and dogs, cleft lip and cleft palate occur naturally with varying degrees of severity, and can be caused by various genetic and environmental factors. Since purebred dogs breed only with each other, there is less genetic variation to consider, making cleft lip and cleft palate easier to understand in these populations, Ms. Wolf explained.

From previous studies, the researchers knew that a mutation in the dog genes DLX5 and DLX6, which are involved in face and skull development, explained 12 of 22 cases of cleft palate. However, a mutation in the corresponding human genes accounted for just one of 30 cases in the study sample.

To search for additional genes that may be involved, Ms. Wolf and colleagues performed a genome-wide association study (GWAS), a study that compares the genomes of dogs with cleft lip and cleft palate to those of dogs without it. They found that the conditions were associated with a mutation in the gene ADAMTS20 that caused the protein it encodes to be shortened by 75 percent. Previous studies had shown that ADAMTS20 is involved in the development and shaping of the palate, but no specific mutations that occur in nature had been identified. A similar GWAS in people with cleft lip and cleft palate suggested that mutations in the human version of the ADAMTS20 gene may also increase the risk of these conditions.

"Cleft lip and cleft palate are complex conditions in people, and the canine model offers a simpler approach to study them," Ms. Wolf said. "Not only does this research help people, but it helps dogs, too," she added.

The study was conducted by scientists at the University of California, Davis, along with collaborators at the University of Pittsburgh, the University of Iowa, and the University of Sydney.

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Scientists identify mutation associated with cleft palate in humans and dogs