Scientists at Baylor College of Medicine, Baylor Genetics, the University of Texas Health Science Center at Houston and Texas Children’s Hospital are combining descriptions of patients’ clinical features with their complex genetic information in a unified analysis to obtain more precise diagnoses of complex diseases, particularly those that involve more than one gene causing the condition.
The researchers anticipate that improved clinical and genetic diagnoses could lead to patients receiving more effective treatments and families benefiting from needed counselling.
“One of the main interests of our lab is to better understand the impact of genetic variation on human health and disease,” said co-first author Dr. Jennifer Posey, assistant professor of molecular and human genetics at Baylor.
“Traditionally, physicians have spoken of a unifying diagnosis, meaning that genetic conditions are due to mutations in only one gene,” said co-first author Dr. Tamar Harel, who was a genetics fellow at Baylor when she was working on this study and currently is a geneticist at Hadassah Medical Center in Israel. “Yet, we see here that two or more genes can be involved in a disease and produce a complex clinical picture. For many in the field, this is a revolutionary idea.”

The challenge of diagnosing diseases with multiple genetic causes
The researchers used whole exome sequencing to analyse all the genes in the genomes of nearly 7,400 unrelated patients with the goal of identifying the genetic cause of their conditions. They found a genetic cause in 2,076 of the 7,374 patients (28 percent); among these patients, 101 (approximately 5 percent) had two or more disease genes involved. If an individual has multiple defective genes, he or she may present with a complex set of clinical features that may lead to an imprecise diagnosis.
“Clinically, multiple genetic causes can be missed because a patient may present with characteristics that overlap those of two different conditions, so the patient can be diagnosed with one or the other,” said Posey. “Alternatively, a patient’s clinical characteristics may not match those of any described condition, so the patient may be diagnosed with what is thought to be a new condition.”
“In these situations, we, as physicians, have to think of the possibility that more than one gene might be involved in the patient’s disease,” said senior author Dr. James R. Lupski, Cullen Professor of Molecular and Human Genetics at Baylor. “Our study shows the limitations of defining a disease according to what we see in the clinic alone. Our work shows the need to consider that a patient may have two or more genetic diseases, not one, and to send for a genomic test to help sort out the patient’s condition and causes of it.”

Paving a future toward more precise multiple genetic diagnoses
“One of the contributions of our work involves utilization of a structured phenotype ontology,” said Posey. “This computational tool allows us to model complex clinical features (phenotypes) that can result when more than one gene is involved, in order to better understand, from the perspective of the physician, how such cases may present in the clinic.”
Furthermore, Dr. Regis James, now at Regeneron Pharmaceuticals, previously created OMIM Explorer while training as a graduate student at BCM. OMIM Explorer is a tool that helps analyse genomic data in the context of the clinical characteristics of the patient. Both James and his thesis advisor and mentor, Dr. Chad Shaw, director of bioinformatics at Baylor Genetics and associate professor of molecular and human genetics at Baylor, were contributors to this work.
“It provides a more complete perspective of how genes and physical traits relate to each other,” said Lupski.
“My colleagues and I anticipate that in the future, geneticists, clinicians and mathematicians will work together using genetic and clinical information to make diagnostic and therapeutic decisions,” said Harel.

Baylor College of Medicine http://tinyurl.com/jm44mr5

Genomic testing of biopsies from patients with deadly, treatment-resistant cancerous blood syndromes called histiocytoses allowed doctors to identify genes fuelling the ailments and use targeted molecular drugs to successfully treat them.

Researchers from the Cincinnati Children’s Cancer and Blood Diseases Institute have recently report their data.  They recommend the regular use of comprehensive genomic profiling at diagnosis to positively impact clinical care, as well as rigorous clinical trials to verify and extend the diagnostic and treatment conclusions in their study.

Histiocytoses are a group of disorders in which abnormal accumulations of white blood cells form tumours on vital organs, leading to systemic organ damage or death. About half of the patients can be treated successfully with chemotherapy, but others are treatment resistant.

Study authors conducted genomic profiling of biopsies from 72 child and adult patients with a variety of treatment-resistant histiocytoses, including the most common one in children, Langerhans cell histiocytosis (LCH), according to the lead investigator, Ashish Kumar, MD, PhD.

Twenty-six patients with treatment-resistant disease had gene mutations involving either BRAF or MAP2K1 that directly activate the MAP-kinase cancer pathway. Researchers determined such patients would benefit from the targeted molecular therapies dabrafenib or trametinib, which block the MAP kinase pathway. The approved cancer drugs were prescribed off label to the histiocytosis patients.

‘In the last year, three patients we treated were infants with disease that was resistant to several rounds of intense chemotherapy. In the past, these children either would have suffered serious complications including death or would have had to endure more intensive treatments and the ensuing toxicities, including the risk of death,” Kumar said. “All three are thriving now on one oral medication that put their disease into remission.”

In one case a 22-month-old child was referred to Cincinnati Children’s for treatment-resistant LCH that was complicated by a secondary diagnosis of HLH (hemophagocytic lymphohistiocytosis). HLH is a difficult-to-treat and often-fatal autoimmune disorder in which an overheated immune system causes uncontrolled inflammation and organ damage. The little girl, whose condition was worsening with organ failure, had a mutation in the BRAF gene. 

Two days after starting targeted treatment with oral dabrafenib (which blocks the MAP-kinase pathway) the little girl’s fever disappeared and a week later her organ function returned to normal, according to study authors.

Previous studies, future directions
For their JCI Insight research project, in addition to their own laboratory tests, study authors drew from data in previous research papers by a number of institutions, which examined genetic and molecular processes affecting white blood cell expansion in different types of histiocytosis.

As Kumar and his colleagues continue their research, they plan to test methodologies that could expand the use of genomic profiling of patient biopsies and targeted molecular therapies in more patients with recurrent, treatment-resistant disease.

Cincinnati Children’s www.cincinnatichildrens.org/news/release/2017/treating-deadly-disorders

Siemens Healthineers has recently been commissioned to take over the clinical laboratory service operations for two new hospitals in Turkey built and operated as Public Private Partnership (PPP) of DiA Holding and Turkish Ministry of Health. The five-year contract grants a minimum of close to 30 million Euros in revenues. The amount is based on a guaranteed annual test volume, and is expected to reach up to over 100 million Euros revenue based on the anticipated test volumes. Siemens Healthineers will assume the laboratory services for all medical laboratory disciplines (Biochemistry, Microbiology, Hematology, Immunology, Emergency, Genetics, Pathology and Point of Care testing) within these hospitals. Siemens Healthineers also will provide the design, medical and technical equipment, appliances, consumables, service and maintenance, in addition to laboratory technical staff. “This project combines our expertise in equipping laboratories with our service portfolio. It is a proof point for how we enable our customers to meet their current challenges and to excel in their respective environments. The new business model is designed to support our customers in increasing efficiency and containing costs right from the beginning,” said Bernd Montag, Chief Executive Officer, Siemens Healthineers. This order will strengthen our portfolio and is consistent with our strategy.”
Siemens Healthineers will operate the laboratories at the hospitals in Bilkent, Ankara, and in Mersin in partnership with lab doctors from Turkey’s Ministry of Health. Both hospitals are being built by DiA Construction, a subsidiary of DiA, for the Turkish Ministry of Health as a public-private partnership.  The new hospitals are intended to improve healthcare as part of a Turkish government programme to restructure the country’s healthcare system, which was initiated in 2003. It is expected that around 92 million patients will benefit from the partnership over the next five years”.
According to the Turkish government, the Bilkent health campus — with almost 3,800 beds and an affiliated hotel, congress centre and commercial area — is the largest project in the healthcare sector ever constructed from scratch in the country. Beginning in mid-2018, more than 10,000 medical staff will be responsible for nearly 25,000 patients there on a daily basis. The new hospital in Mersin will hold about 1,300 beds and has become operational at the end of January 2017.
www.siemens.com/healthineers

Single-stranded, noncoding micro-ribonucleic acids (microRNAs), consisting of 18-23 nucleotides, play a key role in regulating gene expression. Levels of microRNAs circulating within blood can be correlated to different states of diseases such as cancer, neurodegenerative disorders and cardiovascular conditions. Many microRNAs within the blood are encapsulated within exosomes, nanoscale vesicles released by the cells.

Accurate measurement of the quantity of microRNAs circulating within the blood is extremely challenging because of their short lengths, similar sequences and low concentration levels. Due to their small number of nucleotides, traditional polymerase chain reaction (PCR) detection methods must necessarily involve a ligation, or linking, step to produce longer complementary DNA strands. Such ligation often produces large biases.

Consequently, large volumes of clinical samples typically required to obtain accurate measurements, but few conventional detection systems can handle this directly without proper sample preparation and volume reduction.
A team of researchers in Italy from the Istituto Italiano di Tecnologia and the University of Naples Federico II, both in Naples, set out to develop a simple, ultrasensitive fluorescence detection system of in-flow microRNAs that uses spectrally encoded microgels.

As the team reports in Biomicrofluidics until now such a multiplexed barcode detection approach has only been performed in time-consuming observation procedures, significantly hindering its possible diagnostic performance.
‘Our technological achievement rests upon the straightforward implementation of a seemingly real-time, microfluidic-based readout of microRNA sequences of interest, handling down to a few microliters of target volume,’ explained Filippo Causa, an associate professor of industrial bioengineering in the Department of Chemical, Materials Engineering, and Industrial Production at the University of Naples Federico II. ‘No previous RNA sequence amplification is required, which reduces evident sources of measurement errors.’
To do this, the researchers first explored a cost-effective and biocompatible non-Newtonian fluid to create the optimal 3-D alignment of microgels in the center of a square-shaped glass capillary.
They then used a simple microfluidic layout to flow the microgel and allow a continuous measurement of the fluorescence signal with several emission wavelengths for the multiplexed barcode detection.

‘We chose microgels with non-overlapping fluorescence-emitting molecules designed to distinguish spectral barcodes for multiplex analysis … and to obtain an absolute quantification of microRNA sequences,’ said Causa. ‘The precise microgel alignment at various throughput rates and an automatic microRNA sequence intensity normalization in flow gives us an opportunity to obtain reliable measurements, similar to quiescent measurement results, without any fundamental pretreatments of the measurement sample.’

To prove their concept of this multiplex spectral microgel analysis within a microfluidic flow, the team used ‘different barcodes corresponding to different emissions at specific wavelengths and the fluorescence intensity of known microRNA concentration,’ which was measured for calibrations of the specific microRNA being explored. Causa said, ‘So far, nine different microgel barcodes have been tested in flow with our detection approach, and more codes are being prepared to multiplex it further.’

As a proof of principle, the team explored microRNA based on its significance to the pathogenesis of various malignant tumors including prostate, gastric, colon, breast and lung cancers.
‘We were able to specifically detect, count and identify in a quasi-real-time manner hundreds of microgels (~80 microgel particles per minute) at sample volumes of only a few microliters,’ said Causa. ‘Our system achieved a microRNA detection limit of 202 femtoMolars in microfluidic flow conditions.’

Measurements were performed with different microgel barcodes and one in particular focused on specific microRNA targets, demonstrating the specificity of the assay for multiplex measurement conditions.
‘A microRNA 21 concentration of 0.74 picoMolars was detected in flow, which is consistent with the initial sample concentration level,’ Causa said. ‘Out of such fluorescence acquisitions, an absolute quantification of the microRNA 21 concentration level was possible.’

In terms of applications for the system, since the specific target detection of microgels can be easily tuned, it can be applied to a wide range of different biomarkers thanks to its barcode structure.
‘Users can also easily adjust its readout speed specifically for any microscopic system,’ said Causa. ‘This means that the system will open up new options for biosensing particles within microfluidic devices.’

PHYS.ORG phys.org/news/2016-12-biomolecules-barcoded-microgels.html

Most prostate cancer (Pca) is diagnosed through a blood test, serum PSA testing. The well appreciated down-side of PSA testing is the diagnosis of a considerable proportion of indolent cancers that are highly unlikely to progress to clinically significant, lethal disease. Our limited ability to accurately identify men destined to suffer and die from the disease from the majority of indolent cases is a major concern and contributes to the dilemma regarding Pca screening and its genetic testing. There is therefore an unmet need to develop genetic tests that can predict whether a man specifically is highly susceptible to the aggressive form of prostate cancer. In some other cancers, such as breast and ovarian cancer, certain predictors of aggressiveness (e.g. BRCA gene mutations) have proven effective in identifying subsets of patients for specific interventions.
In prostate cancer, genetic testing to predict the individual risk to Pca is not performed routinely because of the absence of a marker which accurately identifies aggressive prostate cancer. In a new study, Dr. Alex Zlotta and colleagues identified a new region within the Kallikrein gene, the Kallikrein 6 gene region, detectable in the blood, that is strongly associated with aggressive prostate cancer (defined as Gleason Score ?8) in a cohort of 1858 men from three continents. The team developed a blood test at the Lunenfeld-Tanenbaum Research Institute which detects variants of this Kallikrein 6 gene. The test was validated in three independent cohorts including unique cohorts from large international screening studies for prostate cancer.
The Kallikrein 6 gene variants identified also independently predicted treatment failure after surgery or radiation for prostate cancer in a fourth independent cohort. The frequency of the gene variants varied from 6 to 14% in the population and the increased risk of aggressive prostate cancer was multiplied by almost 3 times in men who harboured the mutations.
Most studies to date have focused on the risk of prostate cancer, not the specific risk of aggressive lethal prostate cancer. The demonstration that germline variants of a new gene, Kallikrein 6, are strongly associated with aggressive prostate cancer, may be of high value in the management of the most common cancer in men.

Lunenfeld-Tanenbaum Research Institute
research.lunenfeld.ca/rssnews/?page=2165