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Schizophrenia: 30 genes under suspicion -- ScienceDaily

Alex Schier's team has now identified 30 genes in these regions and has been able to show that they have concrete effects on the structure and function of the brain as well as on various behavioral patterns. "Of the 132 suspects, we were ultimately able to establish a more precise perpetrator profile for 30 genes," said Schier. "One of the perpetrators is the transcription factor znf536, which controls the development of the forebrain. This brain region influences our social behavior and the processing of stress." The research team not only deciphered the function of the individual genes, but also generated an atlas of all genes with their respective consequences for the brain

Reference genome is threatening dream of personalized medicine - STAT

On March 23, 1997, the then-nascent Human Genome Project placed an ad in a newspaper in Buffalo, N.Y. (site of a project scientist’s lab), seeking volunteers to donate blood from which they would sequence DNA. Through a quirk of whose DNA got processed when, about 70 percent of the reference genome comes from an anonymous man designated RP11, said UW genome scientist Evan Eichler, with the rest from a few score other volunteers. The reference genome is therefore a mashup of the sequences of these everyday people. As a result, it isn’t a perfectly healthy genome: It has at least 3,556 variants that increase the risk of diseases, including type 1 diabetes and hypertension. Its most serious shortcoming, however, reflects the fact that 1990s Buffalo was not exactly the United Nations. Its ethnic populations are almost all European — German, Irish, Polish, and others. The reference genome, therefore, is as well. That had long been known, but was largely swept under the rug.

Reference genome is threatening dream of personalized medicine - STAT

In other cases, the reference genome is missing vast quantities of the DNA found in non-Europeans. Computational biologist Steven Salzberg of Johns Hopkins University and colleagues sequenced the genomes of 910 African Americans and measured how many pieces are present in all of them but are missing from the reference genome. Their count: 296,485,284 base pairs — nearly 10 percent of the human genome — they reported last November. One missing fragment is 100,000 base pairs long, and millions are at least 1,000 long.

Serotonin can regulate gene expression inside neurons -- ScienceDaily

The study revolves around DNA and how it works to form each person's individual biological map. Each cell in the body contains two meters of DNA, the blueprint for all functions of all cells in the body. This DNA is wound around spools of histone proteins (proteins that package DNA in the nucleus of cells, and are heavily prone to chemical modifications that aid in the regulation of gene expression) into structures referred to as nucleosomes. When DNA encoding a specific gene is wound tightly within the spool, that gene is less likely to be expressed. When the gene is not wound as tightly, it is more likely to be expressed. This can affect many functions of a given cell. Serotonin is a chemical that can transmit signals between neurons in the brain and is involved in the regulation of mood. Selective serotonin reuptake inhibitors, known as SSRIs, alter the amounts of serotonin in the brain, which enables mood changes. When small packages of serotonin are released from a neuron, the resulting signals set up a chain reaction of communication between different parts of the brain. The research team discovered that a protein called tissue transglutaminase 2 can directly attach serotonin molecules to histone proteins (a process called histone serotonylation), which in turn loosens the spool to enable more robust gene expression. Specifically, they found that in developing rodent brains and human neurons, genes near the part of the spool loosened by the serotonin are more likely to be expressed. They also showed that a specific binding complex enables this process.

What controls the tips of our chromosomes? -- ScienceDaily

The researchers also showed that this process is identical both in yeast and in human cells. This means that the regulation of the "S" component has been conserved throughout evolution of species, which somehow reveals the importance of this process for the correct functioning of cells. This opens new avenues to the discovery of therapies capable of dealing with debilitating diseases associated to defects in telomeres. "The unanticipated role of this evolutionary conserved phosphatase is reminiscent of the regulation of the cell cycle by phosphatases that counteract the role of kinases, thus re-establishing the ground state of 'once and only once' cell cycle processes," says the investigator Miguel Godinho Ferreira. "With this work, we now understand better how telomere regulation works, a key process in cancer and ageing," says Jose Escandell, first author of the publication.

How genetic background shapes individual differences within a species: Every genome is different and scientists are beginning to understand what this means for life of an organism -- ScienceDaily

With all this information, Hou was able to scan the genomes of all 1000 yeast isolates and accurately guessed which other strains will act like Sigma or the Sake yeast and be completely reliant on the CYS genes to survive. This is similar to being able to single out, from 1000 patients with the same genetic disorder, those individuals who have a higher chance of developing a more severe form of disease.

Fat cells work different 'shifts' throughout the day -- ScienceDaily

During this unique study seven participants underwent regulated sleep-wake cycles and meal times before entering the laboratory, where they maintained this routine for a further three days. Participants then experienced a 37- hour 'constant routine' during which time they did not experience daily changes in light-dark, feed-fast and sleep-wake cycles. Biopsies of fat tissue were taken at six hourly intervals and then followed by an analysis of gene expression. Researchers identified 727 genes in the fat tissue that express their own circadian rhythm, many carrying out key metabolic functions. A clear separation in gene rhythms was identified with approximately a third peaking in the morning and two thirds in the evening.

Could we soon be able to detect cancer in 10 minutes? | Science | The Guardian

Looking for ctDNA has become a viable proposition in recent years because of improvements in DNA sequencing technologies that make it possible to scan fragments and find those few with alterations that may indicate cancer. While other blood-based biomarkers are being investigated, the advantage of ctDNA is that, because it has a direct link to the tumour, it can be very specific at identifying cancer. For that reason, ctDNA is also showing promise as a way to profile and monitor advanced stage cancers, a “liquid biopsy”. Early detection is a harder problem. Early on, when the tumour is small, there is not as much ctDNA to detect. The women Illumina identified as having cancer were all late, not early stage.

The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated | Genetics in Medicine

Until very recently, the fragmented distribution of patients across institutions hindered the discovery of new rare diseases. Clinicians working with a single, isolated patient could steadily eliminate known disorders but do little more. Families would seek clinicians with the longest history and largest clinic volume to increase their chances of finding a second case, but what does a physician do when N = 1 or if the phenotype is inconsistent across patients? These challenges are driving an increase in the use of NGS. Yet this technological advance presents new challenges of its own. Perhaps the most daunting, in our opinion, is the inability to share sequencing data quickly and universally. Standards and bioinformatic tools are needed that allow for a national repository where families or scientists can bring clinical results and NGS data for comparison. This challenge can be circumvented by tools already created for and by the Internet and social media.

Your genes could impact the quality of your marriage: Specific genes relevant to how partners provide and receive support from each other -- ScienceDaily

"However, what emerged as most relevant to overall marital quality for both partners was genotypic variation among husbands at a specific location on OXTR. Husbands with a particular genotype, which other researchers associated with signs of social deficits, were less satisfied with the support they were provided. Being less satisfied with the support they got from their wives was also associated with being less satisfied with their marriage. The researchers hope their findings provide the foundation for replication and additional study of OXTR as an enduring determinant of marital functioning, as well as encourage research more broadly evaluating the role of genetic factors in interpersonal processes important to overall marital quality. "Genes matter when it comes to the quality of marriage, because genes are relevant to who we are as individuals, and characteristics of the individual can impact the marriage," said Mattson. "Our findings were the first to describe a set of genetic and behavioral mechanisms for one possible route of the genetic influence on marriage. In addition, we added to the increasing awareness that the expression of genotypic variation differs greatly depending on context."

Male Y chromosomes not 'genetic wastelands' -- ScienceDaily

Using sequence data generated by new technology that reads long strands of individual DNA molecules, Chang and Larracuente developed a strategy to assemble a large part of the Y chromosome and other repeat-dense regions. By assembling a large portion of the Y chromosome, they discovered that the Y chromosome has a lot of duplicated sequences, where genes are present in multiple copies. They also discovered that although the Y chromosome does not experience crossing over, it undergoes a different type of recombination called gene conversion. While crossing over involves the shuffle and exchange of genes between two different chromosomes, gene conversion is not reciprocal, Larracuente says. "You don't have two chromosomes that exchange material, you have one chromosome that donates its sequence to the other part of the chromosome" and the sequences become identical.

Myriad Genetics to Acquire Counsyl for $375M | GenomeWeb

Myriad will merge Counsyl's reproductive health tests with its existing preventive care business unit into a new business unit called Myriad Women's Health, which will focus solely on OB-Gyns and reproductive healthcare providers. Myriad will also combine its women's health sales force of approximately 225 representatives with Counsyl's 80 sales professionals, enabling a threefold increase in physician reach for reproductive testing, according to Myriad.

An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell

In summary, many complex traits are driven by enormously large numbers of variants of small effects, potentially implicating most regulatory variants that are active in disease-relevant tissues. To explain these observations, we propose that disease risk is largely driven by genes with no direct relevance to disease and is propagated through regulatory networks to a much smaller number of core genes with direct effects. If this model is correct, then it implies that detailed mapping of cell-specific regulatory networks will be an essential task for fully understanding human disease biology.

An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell

core genes generally contribute just a small part of the total heritability and how most genes expressed in relevant cell types could make non-zero contributions to heritability. To resolve this, we propose that cell regulatory networks are highly interconnected to the extent that any expressed gene is likely to affect the regulation or function of core genes.

An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell

This debate was resolved in a seminal 1918 paper by R.A. Fisher, who showed that, if many genes affect a trait, then the random sampling of alleles at each gene produces a continuous, normally distributed phenotype in the population (Fisher, 1918). As the number of genes grows very large, the contribution of each gene becomes correspondingly smaller, leading in the limit to Fisher’s famous “infinitesimal model” (Barton et al., 2016).

‘Omnigenic’ Model Suggests That All Genes Affect Every Complex Trait | Quanta Magazine

“What we realized was that the signal for height was coming from almost the whole genome,” he said. If the genome were a long string of ornamental lights, and every DNA snippet linked to height were illuminated, more than 100,000 lights would be shining all the way down the string. That result contrasted starkly with the general expectation that GWAS findings would be clustered around the most important genes for a trait.

‘Omnigenic’ Model Suggests That All Genes Affect Every Complex Trait | Quanta Magazine

Starting about 15 years ago, geneticists began to collect DNA from thousands of people who shared traits, to look for clues to each trait’s cause in commonalities between their genomes, a kind of analysis called a genome-wide association study (GWAS). What they found, first, was that you need an enormous number of people to get statistically significant results — one recent GWAS seeking correlations between genetics and insomnia, for instance, included more than a million people. Second, in study after study, even the most significant genetic connections turned out to have surprisingly small effects. The conclusion, sometimes called the polygenic hypothesis, was that multiple loci, or positions in the genome, were likely to be involved in every trait, with each contributing just a small part. (A single large gene can contain several loci, each representing a distinct part of the DNA where mutations make a detectable difference.)

Heavy drinking may change DNA, leading to increased craving for alcohol: Genetic vicious cycle may reinforce risky drinking behavior -- ScienceDaily

Scientists at Rutgers and Yale University School of Medicine focused on two genes implicated in the control of drinking behavior: PER2, which influences the body's biological clock, and POMC, which regulates our stress-response system. By comparing groups of moderate, binge and heavy drinkers, the researchers found that the two genes had changed in the binge and heavy drinkers through an alcohol-influenced gene modification process called methylation. The binge and heavy drinkers also showed reductions in gene expression, or the rate at which these genes create proteins. These changes increased with greater alcohol intake. Additionally, in an experiment, the drinkers viewed stress-related, neutral or alcohol-related images. They also were shown containers of beer and subsequently tasted beer, and their motivation to drink was evaluated. The result: alcohol-fueled changes in the genes of binge and heavy drinkers were associated with a greater desire for alcohol.

BARBARIANS AT THE GATE: CONSUMER-DRIVEN HEALTH DATA COMMONS AND THE TRANSFORMATION OF CITIZEN SCIENCE

This article explores how these mechanisms, imbedded in major federal research and privacy regulations, enshrine institutional data holders—entities such as hospitals, research institutions, and insurers that store people’s health data—as the prime movers in assembling large-scale data resources for research and public health. They rely on approaches—such as de-identification of data and waivers of informed consent—that are increasingly unworkable going forward. They shower individuals with unwanted, paternalistic protections—such as barriers to access to their own research results—while denying them a voice in what will be done with their data.

BARBARIANS AT THE GATE: CONSUMER-DRIVEN HEALTH DATA COMMONS AND THE TRANSFORMATION OF CITIZEN SCIENCE

Data resources are a central currency of twenty-first-century science, and the question is, “Who will control them?”

The F.D.A. vs. Personal Genetic Testing | The New Yorker

A fifty-five-year-old who is confused and depressed and learns that he carries two copies of the risk gene and stands an eighty-per-cent chance of getting Alzheimer’s might reach for a gun, which is the kind of scenario that some genetic counsellors worry about.

23andMe Is Sharing Genetic Data with Drug Giant - Scientific American

Only about 10,000 of the 1 million Americans with Parkinson’s disease have the disease because of LRRK2. So, GlaxoSmithKline has to test about 100 Parkinson’s patients to find just one potential candidate. However, 23andMe has already provided 250 Parkinson’s patients who have agreed to be re-contacted for GlaxoSmithKline’s clinical trials, which may help the pharmaceutical company develop the drug much faster, Forbes reported.

Full transcript: 23andMe CEO Anne Wojcicki answers genetics and privacy questions on Too Embarrassed to Ask - Recode

It’s hard because health care is spectacularly fragmented. An oncology team at Stanford doesn’t do the same things as an oncology team at Memorial Sloan Kettering and to protect it under the Practice of Medicine, and they have different ways that they engage with their patients. Everything is spectacularly fragmented. For us, one of the things that I’m really proud of that we saw is I have millions of people now on a single platform that I know are all interested in their DNA and their health. I think there’s a huge potential for us to help, again, engage all of our customers and potentially work with all of the innovative tech companies out here and give them a platform.

How Fasting Can Improve Overall Health - Neuroscience News

“The reorganization of gene regulation by fasting could prime the genome to a more permissive state to anticipate upcoming food intake and thereby drive a new rhythmic cycle of gene expression. In other words, fasting is able to essentially reprogram a variety of cellular responses. Therefore, optimal fasting in a timed manner would be strategic to positively affect cellular functions and ultimately benefiting health and protecting against aging-associated diseases.”

You become what you believe

A week later, the participants were given a result, based not on their actual data, but rather on one of two groups into which they had been randomly placed. Some were told they had the form of a gene called CREB1 that makes a person tire easily; others were told they had the high-endurance version. Then they ran on the treadmill again. This time, those who had been told they had the low-endurance version of CREB1 did worse on the test, even if they had the other variant. Compared with their results on the first test, on average their bodies removed toxic carbon dioxide less efficiently, their lung capacity dropped, and they stopped running 22 seconds sooner, the team reports today in Nature Human Behavior. And those who thought they had the high-endurance form of the CREB1 gene ran slightly longer on average before feeling hot and tired, regardless of what gene variant they had. “Simply giving people this information changed their physiology,” Turnwald says. The team also tested a second group of 107 people for its version of FTO, a gene that influences how full we feel after eating. Some versions can also predispose people to obesity. Participants ate a small meal and rated their fullness. After being told, at random, that they had a version of FTO that made them hungrier than average or one that made them easily sated, participants ate the same meal. Those told they had the “hungry” version of the gene didn’t feel any different. But those who were told they had the other version felt less hungry on average after eating; they also had higher blood levels of a hormone that indicates a feeling of fullness.

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial | The American Journal of Clinical Nutrition | Oxford Academic

Loge relative weight change over the intervention phase was −7.1% ± 0.7% (mean ± SEM) with ICR, −5.2% ± 0.6% with CCR, and −3.3% ± 0.6% with the control regimen (Poverall < 0.001, PICR vs. CCR = 0.053). Despite slightly greater weight loss with ICR than with CCR, there were no significant differences between the groups in the expression of 82 preselected genes in adipose tissue implicated in pathways linking obesity to chronic diseases. At the final follow-up assessment (week 50), weight loss was −5.2% ± 1.2% with ICR, −4.9% ± 1.1% with CCR, and −1.7% ± 0.8% with the control regimen (Poverall = 0.01, PICR vs. CCR = 0.89). These effects were paralleled by proportional changes in visceral and subcutaneous adipose tissue volumes. There were no significant differences between ICR and CCR regarding various circulating metabolic biomarkers.