Partnership Aims to Expand Access to NGS Newborn Screening Panels in Canada

Newborn Screening Ontario (NSO) has partnered with Tute Genomics and UNIConnect to establish an informatics infrastructure for NSO’s new next-generation sequencing (NGS) testing panels. NSO operates the highest sample volume laboratory in Canada for molecular testing, and is also the most comprehensive newborn screening program in the country. The Ontario Ministry of Health and Long Term Care have contracted NSO to offer NGS panels and a multiple ligation-dependent probe amplification assay for the diagnostic confirmation of a variety of congenital disorders. The move is the latest in a series of efforts by the Ontario government aimed at increasing genetic testing capacity in Ontario and lowering costs for tests that are currently performed largely outside Canada.

NSO initially aims to prove the clinical utility of its NGS panels by offering confirmatory diagnostic testing for the subset of newborns who screen positive for congenital disorders using traditional biochemical testing. Once the clinical utility of the NGS panels is confirmed, NSO hopes to expand diagnostic testing to all newborns who screen positive, and in the future may explore the possibility of NGS as a screening test for all of the babies born annually in Ontario.

To enable the delivery of these services, Tute Genomics will deploy its cloud-based informatics and genome interpretation platform in conjunction with partner UNIConnect’s Precision Molecular Diagnostics laboratory information management system. NSO will use the combined solution to manage bioinformatics pipelines in support of all NGS data generated, enabling the organization to identify clinically actionable variants and generate reports from raw sequencing data in an efficient manner.

Zika RUO Assays, Reagents Surge in Response to Growing Epidemic

With Zika infections on the rise, numerous companies have launched research use only (RUO) tests for the virus. The MultiFlex Mosquito-borne Panel developed by Luminex partner GenArraytion is now available as a multi-analyte RUO assay that can detect multiple disease agents, including Zika, and Luminex has partnered with the University of Sao Paulo, Brazil to validate it. Thermo Fisher has begun offering the Euroimmun Ag, an RUO test kit for the serological detection of Zika that can differentiate between the Zika, dengue, and chikungunya viruses. Additionally, Siemens has released the Versant kPCR Zika 1.0 assay, an RUO genetic test for Zika that runs on the Siemens Versant kPCR molecular system or other commercially available PCR systems.

Like many of these companies, Siemens took the RUO route to speed the availability of its assay for critical research. “We hope the Siemens Healthcare assay will help researchers identify the Zika virus, assist in the development of a vaccine, and ultimately help find a cure,” said Fernando Beils, head of Siemens Healthcare, Molecular Diagnostics. “Our aim is to help researchers fight the Zika outbreak in any way we can.”

Aalto Bio Reagents has also jumped on the Zika bandwagon and created the first mouse monoclonal antibodies to Zika NS1 protein and envelope protein to support the development of Zika diagnostic assays.

Center for Infectious Disease Research, SATVI Develop Test for TB Risk

The Center for Infectious Disease Research and the University of Cape Town’s South African Tuberculosis Vaccine Initiative (SATVI) have developed a blood test that is intended to predict whether a latent Mycobacterium tuberculosis infection is likely to develop into active tuberculosis disease (TB). Findings published in The Lancet show that this test can identify, with a 10–20% false positive rate the majority of individuals who will progress to active TB more than 1 year before the disease manifests.

To develop the test, scientists studied RNA expression patterns in blood samples obtained from a study of more than 6,000 teenagers infected with Mycobacterium tuberculosis from South Africa, who were followed for more than 2 years to identify which individuals progressed to active TB disease. They identified RNA biomarkers that predicted disease progression that were then confirmed using samples obtained from a study of 4,500 adults. The organizations believe that the test could eventually be developed into a diagnostic for large-scale efforts to screen and preventatively treat the disease. They now plan to evaluate the test in a clinical trial to determine if targeted therapy can halt the development of TB in at-risk individuals.

IBM, New York Genome Center to Build Genetic Database for Cancer Research

The New York Genome Center and IBM plan to use IBM’s Watson—a technology platform that analyzes big data—to create a comprehensive and open repository of genetic data to accelerate cancer research. The two organizations will work together to build the capacity to house contributed data, train Watson’s cognitive computing capabilities for genomic analysis, and enable the Center’s member institutions and other research collaborators to sequence and analyze DNA and RNA from patients’ tumors.

In the first phase of the project, the two organizations will examine genetic information from 200 cancer patients to compare how different types of sequencing might impact possible treatment options—examining whole genome and whole exome sequencing as well as clinical panels currently in wide use. Sequencing and clinical data will be fed into Watson to accelerate and focus reviews of massive amounts of medical evidence to help identify existing drugs that might target patients’ cancer-causing mutations. Clinically relevant insights will then be returned to each patient’s physician to potentially support the physician’s treatment decisions.

InSilixa, DNA Software Collaborate on Infectious Diseases Panels

InSilixa and DNA Software have teamed to develop infectious diseases assays for InSilixa’s sample-to-answer complementary metal-oxide-semiconductor (CMOS) biochip platform. The proprietary CMOS biochip technology enables rapid detection, quantification, and genotyping of viruses and bacteria in clinical samples while simultaneously identifying their drug resistance profiles using a highly-multiplexed targeted mutation detection technique. The first generation of InSilixa’s products will focus on molecular diagnostics applications in near-patient and point-of-care settings, including analyzing seasonal respiratory infection outbreaks, rapidly detecting multiple-drug resistant bacteria in urgent care settings, and detecting, quantifying, and performing drug resistance genotyping of HIV in blood samples. Under the terms of the agreement, DNA Software will provide multiplexed PCR designs, algorithms for signature sequence identification, ThermoBlast for scanning oligonucleotides against collections of genomic sequences, and PCR design software.

CHOP, Seven Bridges Partner on Data Platform for Pediatric Oncology

The Children’s Hospital of Philadelphia (CHOP) and Seven Bridges, a biomedical data analysis company, have jointly developed Cavatica, a new cloud-based environment for securely storing, sharing, and analyzing large volumes of pediatric cancer patient genomics data. Cavatica will support CHOP’s commitment to the White House Precision Medicine Initiative through the newly launched Center for Data Driven Discovery in Biomedicine, which is located at CHOP. The Cavatica system is designed to aid researchers in using a growing body of curated pediatric genomic data to make discoveries that will help doctors match cancer therapies more precisely to individual children. To start, Cavatica will support the data sharing and large-volume genomic analyses needs of two integrated consortia: the Children’s Brain Tumor Tissue Consortium and Pacific Pediatric Neuro-Oncology Consortium, both of which are dedicated to the study of childhood brain tumors.