News from Day 3 of ASHG17

October 20, 2017
News from Day 3 of ASHG17
Bionano Genomics’ Saphyr System (pictured) will be used by Beijing GrandOmics to develop novel assays for genetic diseases in China, the companies said at ASHG [Source: Bionano Genomics].

Following are further product and service announcements made at the American Society of Human Genetics 2017 Annual Meeting, held Oct. 17-21 in Orlando, FL.

CombiMatrix Presents Data from Genomic Abnormalities Study

CombiMatrix presented new data at ASHG from a large-scale, first-of-its kind study showing that genomic alterations decrease in frequency and severity from conception through development into childhood.  

The study—which analyzed nearly 32,000 samples—was intended to provide a comprehensive assessment of chromosomal imbalances and their adverse impact upon human growth and development from conception to childhood.

“These results support the importance of genomic testing for different abnormalities that may occur at distinct development stages,” CombiMatrix President and CEO Mark McDonough said in a statement. “We now have even more compelling evidence of the importance of the genetic information produced from this testing from preconception through early childhood.”

Investigators explored and catalogued the frequency, severity and complex evolution of genomic abnormalities with adverse effects on human conception, pregnancy and childhood growth and development. The researchers obtained data from CombiMatrix's exclusive data collected over a multi-year period. 

An abstract of the study, "Large-scale cytogenomic analysis of samples from conception to childhood: a comprehensive assessment of the landscape of unbalanced genomic abnormalities," is available at http://combimatrix.com/providers/educational-references.

The abstract reviewed outcomes from preimplantation genetic screening (PGS) of 6,883 embryos and chromosomal microarray analysis testing of 12,324 pregnancy loss samples, 4,176 prenatal samples, 1,564 neonatal samples and 7,047 pediatric samples. 

A spectrum of unbalanced genomic abnormalities was detected in each sample type. Among key findings of the study:

  • Embryo or early pregnancy loss samples showed the highest abnormality rates and a predictable correlation between the severity of chromosomal abnormalities, primarily aneuploidies, with unsuccessful implantation or progression to viable pregnancy. 
  • Prenatal and neonatal samples showed that the frequency of significant genomic alterations correlated with the incidence of significant physical and developmental abnormalities, but were not necessarily incompatible with life. 
  • Pediatric samples were predominantly deletions and duplications rather than aneuploidy and had less drastic adverse effects.

“This is the first study to provide a comprehensive overview of the nature and frequency of cytogenomic abnormalities with adverse effects from the earliest post-conception developmental stages (i.e., embryos) through pregnancy and into childhood,” stated Trilochan Sahoo, M.D., FACMG, CombiMatrix VP of clinical affairs and director of cytogenetics.

“Analysis of this larger sample set validates our previous findings that showed an interesting pattern elucidating genomic alterations of decreasing severity as human growth progresses these developmental stages,” Dr. Sachoo added. “This opens a new window into the errors and corrective mechanisms at play at a cellular level during various stages of human development.”

 

GrandOmics to Use Bionano’s Saphyr System

Beijing GrandOmics said it intends to develop novel assays for genetic diseases in China using Bionano Genomics’ Saphyr System for genome mapping, through a collaboration whose value was not disclosed.

Beijing-based GrandOmics positions itself as China's first third-generation sequencing service provider and the first third-generation sequencing based precision medicine company. GrandOmics began building its capacity for generating Bionano data earlier this year when it acquired its first Saphyr, in addition to its six PacBio Sequel and six Oxford Nanopore GridION platforms.

One of Bionano’s first indications for the Saphyr platform has been the neuromuscular disease facioscapulohumeral muscular dystrophy (FSHD). FSHD is tied to variation in the size of the D4Z4 arrays, in which a 3.3 kbp unit on chromosomes 4 and 10 is repeated multiple times, but only permissive alleles with low copy numbers in chromosome 4 are pathogenic.

While Southern blot is used to characterize array sizes above and below a threshold level and to identify permissive alleles today, more precise information such as the specific number of D4Z4 repeats and the mosaic level of variation hold diagnostic value that according to GrandOmics is not captured by current methods, including second or third generation sequencing technologies.

“The Bionano Saphyr System is uniquely suited for detecting the complex structural variations (SVs) associated with FSHD in a way that will improve patient management,” GrandOmics CEO Depeng Wang said in a statement. “We are very pleased to have Bionano’s support for this project.”

Saphyr is Bionano’s third-generation optical mapping solution, designed to enable visualization of whole genomes with long-range reads from 100,000 bp to megabase pair lengths.

According to Bionano, Saphyr offers much higher resolution than available through karyotyping or fluorescence in situ hybridization (FISH)—as well as assembly and discovery algorithms that offer greater sensitivity than sequencing-based technologies.

The company says its solution offers 99% sensitivity for large homozygous insertions/deletions, 98% sensitivity for translocations, and 87% sensitivity for large heterozygous insertions/deletions. Saphyr is one of Bionano’s two systems for next-generation mapping (NGM); the other is Irys®.

Added Bionano CSO Cao Han, Ph.D.: “(GrandOmics’) recognition that Saphyr solves the technical unmet need for FSHD is part of a broader global recognition of Bionano’s utility for detecting SVs in translational research and clinical applications as well as in de novo genome assembly applications for countless plants and animals.”

Bionano is at Booth #555 at ASHG.

 

Phosphorus Launches Genetic Testing SaaS Platform

Phosphorus, a computational genomics company, has launched its Elements software suite, a software-as-a-solution (SaaS) platform designed to power diagnostic genetic testing for laboratories, hospital networks, and other healthcare users.

The Elements platform consists of six distinct modules—one each for managing logistics, accessioning, lab tracking, bioinformatics, variant curation, and reporting. The suite is part of Phosphorus’ broader in-house testing partnership, which includes predesigned sequencing assays, reimbursement consulting, and operational assistance.

According to Phosphorus, Elements features full HIPAA compliance, scalability, security, intuitive dashboards, and highly customizable algorithms, forms, and workflows. Elements is also designed to be integrated easily with existing workplace systems, such as legacy variant data annotations, EMR systems, and more. Elements also includes customer service for users seeking guidance on SOPs, billing assistance and more.

“Implementation of a Precision Medicine strategy is still a huge challenge for most hospitals and health systems,” Alexander Bisignano, Phosphorus co-founder and CEO, said in a statement. “A strong genomics core at the center of any strategy is really important, and with our Elements software, the challenges and costs of bringing clinical testing in-house are significantly reduced.”

In addition to the software suite, New York-based Phosphorus also markets a catalogue of compatible specialty diagnostic genetic tests. The tests offer what Phosphorus says are expert-curated panels, powerful data analytics, a simple testing workflow, and rigorous variant interpretations to ensure the most accurate results for patients.

“Our portfolio of diagnostic products, paired with Phosphorus Elements software, is the first end-to-end solution enabling laboratories and medical centers to easily build and expand their precision medicine capabilities,” Bisignano added.

Phosphorus is at Booth #1005 at ASHG.

 

LifeOmic to Use Genomenon’s Mastermind Search Engine

LifeOmic said it will streamline clinical interpretation of its genome sequencing data using Genomenon’s Mastermind Genomic Search Engine, through a partnership whose value was not disclosed. LifeOmic plans to automate prioritization of its genome sequencing data for clinical patients by annotating disease-causing variants with citations from relevant biomedical literature.

Mastermind is designed to link data on DNA mutations from patients with citations from scientific publications, with the goal of understanding the clinical impact of each mutation. Mastermind aims to comprehensively identify all clinically relevant and prioritized articles, and to date has indexed more than 5.5 million scientific articles covering every disease, gene and variant.

By providing immediate insight into published scientific literature, LifeOmic said, Genomenon’s Mastermind search engine accelerates the variant interpretation process by helping pathologists and geneticists decide which variants are likely associated with disease and important for clinical care, and which are likely benign and can be safely ignored.

LifeOmic has built the LifeOmic Precision Medicine Platform™, an analytic platform with advanced informatics designed to process and analyze a patient's whole genome. The platform has been designed as a secure cloud service for the long-term storage, retrieval, analysis and clinical use of genomic and other medical information.

The companies sponsored a presentation at ASHG.