Boston University scientists claim to have identified a small set of genetic variants that predicts extreme longevity.

The scientists, Paola Sebastiani and Thomas Perls, examined the DNA of 1,055 centenarians living in New England. They isolated 150 gene variants that were common in this population. They subsequently examined a separate sample of centenarians and found that 77% of them had many of the same genetic variants.

The centenarians in the original cohort had as many disease-associated gene variants as shorter-lived people, so the scientists reasoned that the genes they identified must protect against disease.

This conclusion is at odds with current thinking about extreme longevity which is predicated on the assumption that long life is caused by the absence of disease-causing gene variants, rather than the presence of protective genes.

To find the protective genes, the scientists implemented a genome-wide association study, a technique that has so far failed to meet expectations that it would unlock genetic secrets behind common conditions like diabetes and Alzheimer’s disease.

Some scientists questioned the findings of the BU group. Kari Stefansson, a geneticist who works for Decode Gentics told the New York Times for example, that he was “amazed at how many loci of genome-wide significance have been found in a modest sample size.”

Stefansson’s company has also studied extreme longevity. Apparently, none of the BU group’s 150 genetic variants showed up in the population studied by Decode Genetics.

There are roughly 80,000 centenarians in the US right now. Roughly 15 % of the general population has some or many of the 150 genetic variants found in the BU study. Most of them fail to reach a ripe old age because of accidents or an unhealthy lifestyle.

Their report appears in Thursday’s issue of Science.

Boston University scientists claim to have identified a small set of genetic variants that accurately predicts extreme longevity in humans.

The scientists, Paola Sebastiani and Thomas Perls, examined the DNA of 1,055 centenarians living in New England. They isolated 150 gene variants that were common in this population. They subsequently examined a separate sample of centenarians and found that 77% of them had many of the same genetic variants.

The centenarians in the original cohort had as many disease-associated gene variants as shorter-lived people, so the scientists reasoned that the genes they had identified must protect against disease.

This conclusion is at odds with current thinking about extreme longevity which is predicated on the assumption that long life is caused by the absence of disease-causing gene variants, rather than the presence of protective genes.

To find the protective genes, the scientists implemented a genome-wide association study, a technique that had previously failed to meet expectations that it could unlock genetic secrets behind common conditions like diabetes and Alzheimer’s disease.

Some scientists questioned the findings of the BU group. Kari Stefansson, a geneticist who works for Decode Gentics, told the New York Times for example that he was “amazed at how many loci of genome-wide significance have been found in a modest sample size.”

Stefansson’s company has also studied extreme longevity. Apparently, none of the BU group’s 150 genetic variants showed up in the population studied by Decode Genetics.

There are roughly 80,000 centenarians in the US right now. Roughly 15 % of the general population has some or many of the 150 genetic variants found in the BU study. Most of them fail to reach extreme old age because of accidents or an unhealthy lifestyle.

The report appears in Science.

The NIH has rejected a request to approve several dozen colonies of human embryonic stem cells for use by federally funded researchers. The lines were created by Reproductive Genetics Institute, a private infertility clinic based in Chicago. They contain mutations thought to be linked to several diseases including cystic fibrosis, muscular dystrophy and Huntington’s disease.

Many scientists believe that studies using these lines will reveal new information about the diseases, and perhaps lead to new treatments, but NIH Director Francis Collins nixed the proposal on grounds that the acquisition of the new lines violated his organization’s strict ethical guidelines.

The new stem cell lines were obtained from embryos donated by couples that were receiving treatment for infertility. The company decided against using them after tests revealed the genetic defects.

An NIH advisory panel tasked by Collins to evaluate the situation found however, that the consent forms used by RGI to secure the lines included unacceptably broad language and required couples to give up their right to sue the clinic for any cause.

Collins’ decision will limit research on the valuable cell lines to scientists who have secured private funding. The new NIH director did approve 8 other new stem cell lines, meaning that federally funded scientists have 75 different lines they can use for research.

“The NIH guidelines for reviewing stem cell lines for federal funding were set up to adhere rigorously to the well-established norms for informed consent,” Collins said in a statement. “It was painful for my advisory committee to recommend against approval of additional lines from RGI because of a consent problem, but rigorous guidelines are only meaningful if they are rigorously applied.”

In a truly remarkable scientific breakthrough, researchers at Synthetic Genomics, Inc. have created a living organism that is wholly controlled by man-made genetic instructions.

“We call it the first synthetic cell,” Craig Venter, the company founder who oversaw the project told the Wall Street Journal. “These are very much real cells.”

The unicellular organism can reproduce but has no living ancestors.

The laboratory methods used to create it, which are patented by Synthetic Genomics, appear to be applicable to other bacterial strains with commercial potential. In fact at least 3 companies are using similar methods to create organisms which produce fuels and vaccines and (better late than never) gobble up oil spills.

“This is literally a turning point in the relationship between man and nature,” said molecular biologist Richard Ebright of Rutgers University. “For the first time, someone has generated an entire artificial cell with predetermined properties.”

Synthetic Genomics provided $30 million to fund the work. It owns intellectual-property rights to the entire process.

To create the new life form, Venter and bioengineer Daniel Gibson stripped out the DNA of a bacterium known as Mycoplasma capricolum and replaced it with a genome they built which was a variant of a second species known as Mycoplasma mycoides. The minor variations amount to biochemical signatures of the scientists, essentially proving the creation was theirs.

“We make a genome from four bottles of chemicals; we put that synthetic genome into a cell; that synthetic genome takes over the cell,” Gibson told the Journal. “The cell is entirely controlled by that new genome.”

The incredible work is documented in Science.

Soon after the announcement, the House Energy and Commerce Committee said it would hold public hearings on the matter in the near future.

Responding to criticism from scientists and the FDA, Walgreens has postponed plans to market a personal genetic test kit made by Pathway Genomics

“We’ve elected not to move forward with offering the Pathway product to our customers until we have further clarity on this matter,” a Walgreens statement said.

The Pathway Genomics kit uses saliva samples to assess one’s risk of contracting in excess of 70 diseases including lung cancer, hypertension and heart disease.

The kits cost $20. They include a plastic container, handy instructions and a postage-paid envelope to ship the specimen to a San Diego-based laboratory. Testing costs an additional $79 to $249.

The state-of-the-art in genomic science these days is that it’s easy and inexpensive to obtain genetic markers for a host of diseases, but there is insufficient data to give much credence to the findings…at least for diseases like cancer, diabetes and heart disease which are thought to be influenced by hundreds of different genes.

“Many of these markers are not understood, even what genes they are affecting right now,” Kenneth Offit, the chief of clinical genetics at Memorial Sloan-Kettering Cancer Center in New York told CNN. “It’s a very, very early stage in this level of genomic research.”

For its part, the FDA said, “Pathway Genomics has moved outside of the currently sanctioned boundaries for lab-developed tests by marketing (its) product in a retail store. These kits have not been proven safe, effective or accurate. Patients could be making medical decisions based on data from a test that hasn’t been validated by the FDA.”

Of note, Pathway Genomics has sold these kits online for the last 8 months. In fact, more than 30 companies offer personal genetic tests on line.

Rejection of the donor organ is a frequent and sometimes life-threatening complication of heart transplantation. It is best handled if caught early, and since early rejection is typically asymptomatic, physicians had heretofore been required to perform regular biopsies to screen for rejection of the transplanted heart.

The biopsy is expensive and not without risk however, so scientists have long searched for a non-invasive alternative to diagnose rejection.

That search may have yielded results. In a presentation at last month’s meeting of the International Society for Heart & Lung Transplantation, Michael Pham and colleagues from Stanford University showed that a genetic test reduced the need for biopsies in selected patients.

The gene test is known as Allomap. It is marketed by XDx and has been used on 7,000 transplant recipients so far. It costs about $3,000, or 25-40% less than the biopsy.

The study by Pham’s team included 602 transplant recipients. It showed that Allomap was as effective as routine biopsies in preventing serious episodes of transplant rejection like heart failure, the need for a re-transplant or death.

The study was limited to patients who were at low risk for rejection and had undergone the procedure at least 6 months prior to enrollment. Nineteen months after randomization, 14.5% of patients that were followed with the genetic test and 15.3% of those followed with routine biopsies suffered a major complication.

“You’re not going to harm patients by reducing the number of biopsies,” Pham told the Wall Street Journal.

Pham noted that his team’s findings could not be extrapolated to patients that had received a transplant within the last 6 months or to those at high risk for rejection.

The study appears in the New England Journal of Medicine.

Last week, a federal judge threw out patents on BRCA1 and BRCA2, genes whose mutations are linked to breast and ovarian cancer. The decision casts doubt on patents covering thousands of human genes.

In his decision, US District Court Judge Robert Sweet  ruled the patents were “improperly granted” since they involved a “law of nature.” He rejected the notion that isolating a gene made it patentable, calling that “a ‘lawyer’s trick’” which circumvents the “prohibition on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result.”

The case had been brought by patients and medical organizations last May. They argued that genes, as products of nature, are discoverable and hence fall outside of the universe of things that can be patented. They also argued that patents drive up testing costs and stifle biomedical innovation.

Myriad Genetics is the company that held the BRCA patents. It markets a $3,000 test that scans for mutations in the genes which are associated with a high risk of breast and ovarian cancer.

Nearly 20% of all human genes have been patented. Enormous industries have been created around the intellectual property rights granted by these patents.

If the decision withstands a likely appeal, it might become difficult for companies to raise venture capital to support genomics research. “The industry is going to have to get more creative about how to retain exclusivity and attract capital in the face of potentially weaker patent protection,” said Kenneth Chahine, a law professor who filed an amicus brief for Myriad.

In that instance, “the government is going to become the funder for content discovery because it’s going to be hard to justify it outside of academia,” venture capitalist Bryan Roberts told the New York Times.

Everyone knows that people react differently to pain: the initial jab of Novocain at a dentist’s office causes excruciating discomfort for some, while others barely seem to mind. But is that because some people truly feel more pain than others in a given circumstance (such as an injection) or because some people can just suck it up better?

A new study by Frank Reimann and colleagues at Cambridge Institute for Medical Research suggests the former may be true, even though it doesn’t completely rule-out the whimp factor.

Reimann’s group reported in the Proceedings of the National Academy of Sciences that variations in the SCN9A gene were associated with changes in the perception of pain.

To reach this conclusion, they studied kids with a rare condition characterized by an inability to detect pain. These kids can pass knives through their arms and walk across hot coals without a flinch. Reimann’s group found this extremely maladaptive condition was associated with a nonfunctioning SCN9A gene.

The scientists reasoned that polymorphism at the SCN9A locus could cause differing pain thresholds, and tested their hypothesis by examining DNA from 578 people with osteoarthritis. They found that folks having a common variant of the SCN9A gene had lower pain self-assessment scores than those having a rarer form of the gene.

The scientists reproduced their findings in people with back pain, pancreatitis and phantom limb pain.

The SCN9A gene it turns out, codes for a membrane-bound protein on pain sensory nerve cells. The protein is involved with triggering those cells, which then relay a pain message to the brain. Apparently, the version of the protein created by the rare SCN9A decreases firing thresholds in the cells so they are more likely to relay bad news.

The obesity epidemic has become a major public health concern. The phenomenon is typically attributed to changes in diet and lifestyle, and socioeconomic factors like poverty and poor education.

Genetic factors have been known play a role as well, but a recent study by UK-based scientists suggests they play much more prominent role, at least in a subset of people who become morbidly obese at a young age.

In the study, Sadaf Farooqi of the University of Cambridge and colleagues showed that many such kids are missing a large chunk of DNA, known as SH2B1, from chromosome 16.

The missing genetic code had been known to play a role in regulating weight and blood sugar levels. Kids with the chromosomal abnormality tended to overeat on a massive scale, and gain weight easily. 

To reach these conclusions, the scientists scanned the genomes of 300 morbidly obese kids in search of copy number variants (CNVs), which are lengthy strands of DNA that are either duplicated or missing.
The scientists compared their findings with information from healthy controls.

In their write-up, which appears in Nature, the scientists wrote, “we identified several rare copy number variants that were recurrent in patients but absent or at much lower prevalence in controls.”

“Part of chromosome 16 can be deleted in some families. People with this deletion have severe obesity from a young age,” Farooqi told Medical News Today: “One particular gene on chromosome 16 called SH2B1 plays a key role.”

The finding may have broad social implications, since it is common to blame parents or guardians for morbid obesity in kids. The scientists noted for example, that some kids in the study had been handed over to Social Services because their parents were assumed to have been deliberately overfeeding them.

A multinational group of scientists has concluded that about a third of the genetic underpinnings of schizophrenia are caused by the interactions of many thousand common genetic variants. While each variant may be harmless on its own, the combined impact vastly increases the risk of both schizophrenia and bipolar disorder.

The results imply that the genetic basis of the 2 common psychoses  are more complex than had been thought, and that the conditions can develop not just from a rare, devastating genetic variant, but from dozens or hundreds of common ones.

The write-up is in Nature.
 
“This is an enormous first for our field,” co-author Patrick Sullivan told BurrillReport. “We now have the outline of the puzzle, we just need to… see how (the pieces) fit together,” added the professor of psychiatry at the UNC School of Medicine.
 
Although scientists have long recognized that schizophrenia has a genetic basis, it’s only recently that they’ve started pinpointing offending genetic loci.
 
To reach their conclusions, Sullivan and colleagues isolated 30,000 genetic variants that occurred more frequently in 3,000 people having schizophrenia than in a control group without the condition. The team confirmed the differences in 2 other populations of schizophrenic patients and 2 groups with bipolar disorder.

The genetic link between schizophrenia and bipolar disorder had not previously been recognized.
 
“While our study finds a surprising number of genetic effects, we expect that future work will assemble them into meaningful pathways that will teach us about the biology of schizophrenia and bipolar disorder,” senior author Pamela Sklar told Burrill.
 
The scientists also found that a particular HLA haplotype increased the risk for both psychoses. Since HLA proteins are involved in the immune response to infections, they speculated that an infectious agent might be an etiologic factor.