Published study shows that novel algorithm and use of two different NGS systems deliver confirmed diagnoses with greater sensitivity and efficiency than traditional single platform NGS with Sanger confirmation

April 19, 2016

Boston, Massachusetts ? April 19, 2016 – Claritas Genomics today announced the publication of a study demonstrating the superior sensitivity and speed of its proprietary orthogonal sequencing process compared to industry standard practice.  The study, ‘Orthogonal Next Generation Sequencing (NGS) for High Throughput Clinical Diagnostics’  was published today in the online edition of Scientific Reports.  Orthogonal sequencing is the practice of running two gene sequencing technologies in parallel to assist with the diagnosis of more complex genetic diseases. The report shows how the company’s enhanced process provides high quality and more complete exome data, i.e.; data from the coding part of the genome; providing superior validated results to physicians and patients, much faster than with standard orthogonal sequencing processes. This is because the results from standard processes need to be verified in a second test.[1]

The enhanced speed and accuracy of the novel orthogonal sequencing process is due to the use of two separate NGS systems. Claritas developed an algorithm, the Combinator, to allow the output (DNA variant calls) from two NGS systems to be combined into a single set of calls in an automated manner. Because every sequencing platform provides variant calls in a slightly different way, it can be difficult to compare complex variation between them. Combinator allows a unified set of variant calls that can then be evaluated for disease impact.

“The benefits of broad genetic testing for patients with previously undiagnosed diseases are clear,” said John Thompson, Chief Technology Officer for Claritas Genomics, “but the speed and diagnostic yield have been problems.  By using two independent systems, we can detect more variants and confirm more than 90% of them immediately. This improves both speed and diagnostic yield so that patients and their families are more likely to get an answer and to get that answer faster.”

Technologies Used
The novel orthogonal sequencing process was run using the Illumina and Ion Torrent NGS technologies. For Illumina-based sequencing, DNA was targeted using the Agilent Clinical Research Exome kit. DNA sequenced on the Ion Torrent Proton was targeted using the Life Technologies AmpliSeq Exome kit. Variant calls (DNA changes) from Illumina and Ion Torrent were combined using a custom algorithm, Combinator, developed by Claritas for integrating multi-platform Variant Call Files (VCFs). Combinator was necessary because each platform uses a slightly different VCF format. This made identifying equivalent data challenging and time consuming. 

Accessible Clinical Use
In order to provide maximum flexibility for patients providing biological fluids for DNA extraction, multiple sample collection methods were examined. DNA collected from cell lines, from blood, and from saliva all performed identically. While the initial cost of sequencing two exomes is higher, the ultimate savings in confirmatory sequencing as well as the improved sensitivity makes up for that expense.

Orthogonal sequencing is available to patients (via their health care providers) in two forms, the Claritas Clinical Exome and Regions of Interest. The Claritas Clinical Exome examines all coding regions. The Regions of Interest (ROIs) focus on genes known to be involved in particular diseases. The advantage of the ROIs is the ability to incorporate newly discovered genes into gene lists in a rapid manner as well as the ability to expand to the whole exome if diagnostics findings are not identified in the initial gene list and those results are already confirmed. The orthogonal exome is also available for research use.

Report Authors
Orthogonal NGS for High Throughput Clinical Diagnostics
Niru Chennagiri1, Eric J. White1, Alexander Frieden1, Edgardo Lopez1, Daniel S. Lieber1, Anastasia Nikiforov1, Tristen Ross1, Rebecca Batorsky1, Sherry Hansen1, Va Lip1, Lovelace J. Luquette2, Evan Mauceli1, David Margulies1,2,3, Patrice M. Milos1, Nichole Napolitano1, Marcia M. Nizzari1, Timothy Yu1, John F. Thompson1

1Claritas Genomics, Cambridge MA
2Harvard Medical School, Boston MA
3Boston Children’s Hospital, Boston MA

About Claritas Genomics
Claritas Genomics serves children affected with complex genetic disorders by providing timely and accurate results, resolving families’ long search for answers. By combining clinical expertise of the world’s best pediatric specialists with innovative platform solutions, Claritas is working to improve patient care and enable new discoveries.  For more information about Claritas Genomics, visit

Betsy Stevenson
Director of Corporate Communications
[email protected]
Tel: (860) 984-1424

[1] The American College of Medical Genetics recommends “that all disease-focused and/or diagnostic testing include confirmation of the final result using a companion technology.” Most laboratories use the lower throughput Sanger sequencing method that is not well suited to whole genome scale.