Boston Children’s Enlists Watson in Efforts to Diagnose Rare Childhood Diseases

IBM and Boston Children’s Hospital have teamed to use IBM’s Watson cognitive platform to help clinicians identify possible options for the diagnosis and treatment of children with rare genetic diseases. Currently, genetic sequencing results often present an overload of information, without yielding a definitive causative variant. The goal of the new collaboration is to create a cognitive tool that helps clinicians interpret a child’s genome sequencing data, compare this with medical literature, and quickly identify anomalies that might be responsible for the unexplained symptoms.

Watson will initially focus on nephrology, and will aggregate information on causative mutations for steroid-resistant nephrotic syndrome, a rare genetic form of kidney disease. Then, experts at Boston Children’s plan to train Watson by feeding it genomic sequencing data from retrospective patients. Following the kidney project’s completion, Boston Children’s plans to expand the effort into undiagnosed neurologic disorders and other disease areas studied by the hospital’s Manton Center for Orphan Disease Research.

“One of Watson’s talents is quickly finding hidden insights and connecting patterns in massive volumes of data,” said Deborah DiSanzo, general manager of IBM Watson Health. “Rare disease diagnosis is a fitting application for cognitive technology that can assimilate different types and sources of data to help doctors solve medical mysteries. For the kids and their families suffering without a diagnosis, our goal is to team with the world’s leading experts to create a cognitive tool that will make it easier for doctors to find the needle in the haystack, uncovering all relevant medical advances to support effective care for the child.”

Thermo Fisher, Singapore General to Identify Asian-Specific Oncogenic Mutations

Thermo Fisher Scientific and Singapore General Hospital are collaborating to identify genetic cancer mutations linked with Asian populations using Thermo Fisher’s Ion Torrent next-generation sequencing (NGS) platform. The partnership’s research will analyze retrospective samples from cancer patients with Asian ancestry to identify their mutational profiles and how they differ from existing data of reference populations, which principally contain individuals of Caucasian ancestry.

"Investigating the differences in cancer gene mutations among different populations is an essential factor in advancing healthcare in a multiracial and multicultural society,” said Tan Puay Hoon, MD, head of the Department of Pathology at Singapore General Hospital.

In the first phase of the project, Singapore General Hospital will perform a validation study using Thermo Fisher’s Ion PGM platform and Oncomine Comprehensive assay. The project will then move to NGS-based prospective data analysis of multiple cancers by using formalin-fixed paraffin-embedded tissues and, potentially, other types of clinical samples.

Baylor Miraca Signs Deal for SNP Probe Technology

Baylor Miraca Genetics Laboratories has licensed the use of Oxford Gene Technology’s proprietary single nucleotide polymorphism (SNP) array probe. This technology overcomes the limitations of restriction enzyme-based SNP probe approaches previously employed at Baylor for loss of heterozygosity (LOH) detection, enabling more accurate array-based analysis of low-input DNA samples. Based in Texas, Baylor provides genomic services across the U.S. and to more than 16 countries worldwide. As part of its offerings, Baylor uses array comparative genomic hybridization methods containing both copy number variation and SNP probes to identify a broad range of genetic syndromes. Oxford Gene Technology’s intensity-based SNP probe technology will now provide Baylor with an alternative to restriction enzyme-based approaches that are unable to analyze small amounts of DNA accurately. The probes designed by Oxford Gene Technology target each SNP allele, with the intensity ratio following hybridization enabling detection of LOH.

Institut Pasteur, Chan Soon-Shiong Institute to Create Global Genomic Research Center

France’s Institut Pasteur and the Los Angeles-based Chan Soon-Shiong Institute for Molecular Medicine have entered a partnership to establish The Pasteur Global Health Genomics Center (PGHGC). The aim of PGHGC is to accelerate genomic research using next-generation patient information systems to support the acquisition and usage of high-quality sequencing data. Building on the Institut Pasteur International Network, an existing network of national research institutes, PGHGC will upgrade laboratories on five continents. Six of these facilities are projected to launch in 2017 and 2018, and by 2020, a total of 12 global resource hubs for data intensive and high throughput based precision medicine are expected to be fully operational. PGHGC also plans to invest in data acquisition, education, basic research, and training. The Chan Soon-Shiong Institute has made an initial commitment of $1 million to fund the design phase of the project.

Agilent Buys Cell Metabolism, Bioenergetics Firm

Agilent Technologies has acquired Seahorse Bioscience, a developer of instruments and assay kits for measuring cell metabolism and bioenergetics. Seahorse’s proprietary XF technology provides real-time kinetics data and is designed to enable a better understanding of cell function and signaling, as well as how the cell may be impacted by the introduction of a specific drug. Researchers currently use XF technology to investigate the role of cell metabolism in numerous conditions, including neurodegeneration, cancer, cardiovascular disease, infectious diseases, mitochondrial diseases, diabetes, and metabolic disorders. Agilent believes this technology complements its separations and mass spectrometry solutions, in particular for metabolomics and disease research in pharma.

U Penn, Epic Sciences Partner on Liquid Biopsy Research

The Abramson Cancer Center of the University of Pennsylvania has joined forces with Epic Sciences to investigate biomarkers identified by analyzing circulating tumor cells (CTCs) at a single cell resolution that are predictive of response to personalized cancer therapeutics. Under the terms of the partnership, Abramson will leverage Epic’s No Cell Left Behind CTC detection and characterization platform to explore the cellular heterogeneity of numerous different cancer types, with a focus on genomic and phenotypic markers that could improve understanding of the utility of existing therapies and potential new therapies.

The No Cell Left Behind platform quantifies the proteomic and genomic changes that accumulate in tumor cells over time and in response to successive rounds of therapy. It detects all categories of CTCs in the blood and identifies, on a single cell basis, subpopulations of metastatic cancer cells that might be resistant or susceptible to cancer therapeutics. Unlike similar technologies, Epic’s platform also analyzes all nucleated cells and does not exclude CTCs based on assumptions about size or surface markers, thereby providing a more comprehensive view of the variation among a patient’s tumor cells that might affect therapeutic response.