As more biomarker-based studies open, such testing will increase opportunities to match patients with clinical trials.
Nearly three-quarters of patients with advanced cancer could be referred to a potential targeted treatment based on the results of a comprehensive analysis of their tumour’s genetic landscape, a new analysis finds.
The study suggests the value of so-called next generation sequencing, a sophisticated method of evaluating the DNA and RNA of a tumour to help direct treatment.
In a report on the first 500 patients with advanced solid tumours to go through the University of Michigan Comprehensive Cancer Center’s sequencing program, 72 percent qualified for a clinical trial based on a genetic marker in their tumour.
Although not all of those patients were able to enroll in a trial based on other eligibility factors and trial location, the number who did enroll doubled from about 5 percent of patients in 2012 to 11 percent in 2016. Increased trial enrollment occurred as several major national biomarker-based studies opened.
“Availability of biomarker trials is crucial for being able to act on these results. Over time, we became better at matching patients to clinical trials as more of these basket trials opened,” says Erin Cobain, M.D., clinical lecturer of haematology/oncology at the University of Michigan Medical School.
As part of the sequencing program, patients with stage 4 cancer undergo a biopsy and provide a blood sample to test their normal DNA. Patients also receive genetic counselling.
Results of the sequencing are discussed by a team of oncologists, genetics specialists, pathologists, bioinformatics specialists and genetic counsellors, among others, at a precision medicine tumour board. This group discusses all results and assesses the feasibility of pursuing treatment options based on the genomic findings.
Genetic sequencing involves looking at all of the DNA and RNA expressed within a tumor. Scientists comb through this enormous amount of data to identify anomalies that may prove to be targets for existing approved or experimental therapies.
In addition, the program sequences patients’ normal genome. This means it’s able to identify hereditary genetic variations, or those inherited from a mother or father and potentially passed down to children.
Researchers found these hereditary variations in 11 percent of patients, none of which had been previously identified through family history.
“That was a major surprise — that 11 percent of patients had a genetic change that increases cancer risk is much higher than we would expect. This has significant impact not only on the patients, but also on their families, who may carry a genetic susceptibility to cancer,” Cobain says.
MI-ONCOSEQ requires a fresh biopsy, whereas many commercial sequencing tools can use frozen tissue samples. This ensures the U-M researchers can perform a more comprehensive analysis. Commercial tests analyse only about 350 genes while MI-ONCOSEQ’s more thorough analysis of both DNA and RNA covers at least 1,700 genes.
This means many anomalies were identified that would not have been found on panel-based tests. Because MI-ONCOSEQ is run as a research study, patients do not pay for sequencing.
Cobain cites an example of a patient with cholangiocarcinoma, a cancer of the bile duct. Sequencing revealed a novel gene fusion that would not have been identified through panel-based tests. The patient was able to enroll on a clinical trial targeting the gene fusion and had an excellent response to that therapy.
“This would not have been found by a commercial assay,” Cobain says. “Sequencing is beginning to have a real impact on treatment recommendations. It’s important to consider this testing early in the patient’s clinical course in order to improve our ability to act on the results and impact the patient’s course.”

Michigan University
labblog.uofmhealth.org/rounds/genetic-sequencing-can-influence-treatment-for-advanced-cancer

Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.

A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.

“Most of the variation between individuals is in noncoding regions of the genome,” says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk’s Genomic Analysis Laboratory. “These regions don’t code for proteins, but they still contain genetic variants that cause disease. We just haven’t had very effective tools to locate these areas in a variety of tissues and cell types—until now.”

Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous “junk.” But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called “enhancers” dictate where and when the gene information is read out.

Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker’s new system, called REPTILE (for “regulatory-element prediction based on tissue-specific local epigenomic signatures”), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team’s experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.

 “The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data,” says Yupeng He, a Salk graduate student and first author of the paper. “We were then able to test REPTILE’S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm’s ability to find enhancers.”

Salk Institute www.salk.edu/news-release/finding-way-around-dna/

Recent advances in large-scale clinical DNA sequencing have led to genetic diagnoses for many rare disease patients, but the diagnosis rate based on these approaches is still far from perfect. On average, clinicians are unable to provide a genetic diagnosis for over half of patients in the clinic. The lack of a clear genetic diagnosis can lead to profound uncertainty about patients’ long-term prognoses, treatment options, and family planning decisions.
In a new Science Translational Medicine study, a team led by researchers from the Broad Institute of MIT and Harvard and the National Institute of Neurological Disorders and Stroke adds RNA sequencing to the diagnostic toolkit to identify disease-causing mutations buried inside the genome.
The researchers sequenced the RNA from muscle samples of 50 patients with undiagnosed genetic muscle disorders — who had undergone extensive genetic testing — and, in conjunction with DNA sequence information and a reference database, successfully located pathogenic mutations that had previously gone undetected in one-third of the patients. The study firmly positions RNA sequencing as a tool that adds additional power to the existing set of technologies deployed to solve genetic disease mysteries.
“For some patients, we know that there is variation in the human genome, with an effect on the transcript, that we just haven’t been capturing with our traditional genetic sequencing methods,” says senior author Daniel MacArthur, co-director of the Medical and Population Genetics Program at the Broad Institute and group leader at Massachusetts General Hospital. “With RNA sequencing, we were able to take a set of patients who had gone through diagnostic odysseys — often lasting many years, where many methods had been used to try to detect the cause of their disease without success — and find the biological answers that previous technologies had missed.”
Having a molecular diagnosis in-hand is a medical milestone for some patients and their families, and opens the door to potential therapies while offering some peace of mind. “For example, one patient’s family had opted to delay having other children until they knew the genetic basis of her condition,” MacArthur adds. “Our clinical collaborators were able to report that they had found the genetic cause, and now the parents have the option of prenatal testing for that mutation.”
The study demonstrates that RNA sequencing, or RNA-seq, applied to relevant tissue samples and coupled with genetic analysis, can detect pathogenic mutations hidden in the noncoding sections of a gene, highlight relevant mutations missed in the noise of whole-genome analysis, and rule out other genetic variants suspected to cause disease. Previously, the technology was rarely applied in a clinical setting, and then only for single patients when specific mutations were already suspected — but the research team saw the potential for RNA-seq to augment other clinical tools earlier in diagnostics.

Broad Institute of MIT and Harvard
www.broadinstitute.org/news/rna-sequencing-applied-tool-solve-patients%E2%80%99-diagnostic-mysteries

Loss of a key protein leads to defects in skeletal development including reduced bone density and a shortening of the fingers and toes — a condition known as brachydactyly. The discovery was made by researchers at Penn State University who knocked out the Speckle-type POZ Protein (Spop) in the mouse and characterized the impact on bone development. The research redefines the role of Spop during bone development and provides a new potential target for the diagnosis and treatment of bone diseases such as osteoporosis.
“The Spop protein is involved in Hedgehog signalling — a well-studied cell-tocell communication pathway that plays multiple roles during development,” said Aimin Liu, associate professor of biology at Penn State and the corresponding author of the study. “Previous studies done in cell culture suggested that Spop negatively regulates or ‘turns down’ Hedgehog signalling. However, in our study, we show that Spop positively regulates the pathway downstream of a member of the Hedgehog family, a protein called Indian Hedgehog, during bone development. This new understanding adds to our knowledge of the genetic basis of bone development and could open new avenues to study bone disease.”
Indian Hedgehog (Ihh) plays an essential role in bone development. It is near the top of a hierarchical cascade of genes that program cells to produce cartilage and bone. Ihh controls gene expression by regulating the activity of the transcription factors — proteins that control the expression of other genes — Gli2 and Gli3. Gli2 acts mainly as an activator of gene expression and Gli3 acts mainly to repress gene expression. The Spop protein tags the Gli proteins to be degraded in the cell. “Previous studies led to a hypothesis that a loss of Spop function would increase Hedgehog signalling because the Gli activators were no longer being degraded,” said Hongchen Cai, a graduate student at Penn State and an author of the paper. “We were surprised to see in our study the repressor of gene expression, Gli3, built up in developing bone, but not the activator of gene expression, Gli2. This imbalance led to an overall decrease in Hedgehog signalling.”
In order to study the role of Spop in bone development more closely, the researchers knocked the gene out specifically in the limb. Limbs that lacked Spop had less dense bone, mimicking osteopenia — a human condition characterized by low bone density, but not as severe as osteoporosis. The limbs also had shorter than normal fingers and toes. The researchers also showed that the effects of losing Spop could be mitigated by simultaneously reducing the amount of Gli3 in the limbs.

Penn State http://tinyurl.com/jx3y6nj