Lineagen Announces Launch of Proprietary Variant Index to Improve Interpretation of Genetic Basis for Childhood Developmental Delay

October 19, 2016
SALT LAKE CITY--(PRNewswire)--Lineagen, Inc., an innovative genetics diagnostic company focused on advanced genetic testing and clinical information services for complex neurodevelopmental disorders, today announced a presentation at ASHG on new methods of interpreting findings for its FirstStepDx PLUS® chromosomal microarray (CMA) test. Lineagen also announced commercial launch of the presentation subject, a variant index which will provide improved clarity of interpretation. When applied to findings from FirstStepDx PLUS, the variant index assigns greater clinical importance to genetic variants that are known to be causal for these disorders and, importantly, to findings known as variants of unknown significance (VOUS). This will furnish clinicians with the most comprehensive results for the possible underlying genetic basis in individuals with autism spectrum disorder (ASD), developmental delay (DD), intellectual delay (ID), and multiple congenital anomalies (MCA).

CMA is recommended as a first-tier test by multiple medical society guidelines in identifying deletions and duplications in the genetic material to diagnose chromosomal disorders underlying ASD, DD, ID and MCA. One of the key challenges of CMA testing for both laboratories and healthcare providers is the detection and interpretation of VOUS findings, since they create diagnostic ambiguity for both the provider and the family. The new variant index has been demonstrated to clarify VOUS results in about 40% of clinical cases to date, and adds increased clinical significance in about 70% of causal findings.

Lead author Dr. Karen Ho, Principal Scientist of Translational Research at Lineagen, presented a paper at the Annual Meeting of ASHG today in Vancouver, B.C., entitled "Clinical Application of a Critical Exon Mapper to Aid in Determining Pathogenicity of Copy Number Variants of Unknown Significance," in conjunction with members of The Centre for Applied Genomics at The Hospital for Sick Children (SickKids) of Toronto, Canada. The technology underlying the critical exon mapper, or variant index, has been licensed from SickKids by Lineagen.

Dr. Stephen Scherer, Senior Scientist and Director of The Centre for Applied Genomics, and his renowned team at SickKids, assembled a variant index that identifies gene regions that are highly expressed and highly conserved (i.e., not frequently mutated) in the brain and, when disrupted, are likely causal for ASD and DD[1]. Use of the variant index in interpreting findings of FirstStepDx PLUS unveils meaningful information about CMA test results, especially VOUS, which brings more clinical insight to providers and may lead directly to a change in medical management of patients with ASD and DD.

"We're very excited by the data presented in the paper, as well as the launch of clinical use of the variant index," noted Dr. Robert Wassman, Chief Medical Officer for Lineagen and senior author of the presentation. "We reported here on our real world clinical experience using the variant index as part of our PrismDx Variant Information ProgramSM, in a series of 5518 individuals, in which we reported clinically relevant findings in 40% of the VOUS and incremental clinical information in 70% of abnormal findings. Further insights from the medical literature on these specific genes allow us to provide physicians with richer information for better medical management. We present several cases which illustrate how the variant index might impact clinical interpretation of VOUS and help identify critical regions that are likely pathogenic, but previously undetectable."

About Lineagen
Lineagen helps physicians personalize medical management for individuals with developmental delay and autism spectrum disorder by providing advanced genetic testing and clinical information services.

Lineagen makes genetic testing accessible to everyone, from patient to provider, by combining simple non-invasive sampling and advanced testing and information technology with dedicated service and support. Lineagen's FirstStepDx PLUS chromosomal microarray (CMA) testing service helps providers pinpoint the cause of delay and develop a personalized healthcare management program for their patient.

FirstStepDx PLUS can detect hundreds of genetic conditions and is recommended as the first-tier test for autism spectrum disorder, developmental delay and intellectual delay according to nationally accepted guidelines. The FirstStepDx PLUS test has the highest reported detection rate of any CMA.

FirstStepDx PLUS uses a painless cheek swab for DNA sampling, with a detailed and personalized report that presents results in plain English. Families and providers can contact Lineagen's team of certified genetic counselors for help prior to testing and for aid in interpreting results. Additionally, the Lineagen team of specialists handles everything related to reimbursement, from pre-authorizations to appeals. For additional information, visit

Lineagen Contact:
David Jansen

1. Uddin M, et al. Sci Rep. 2016 Jul 1;6:28663