Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Abstract

Objective: Whole Exome Sequencing (WES) is an effective diagnostic method for complicated and multi-system involved rare diseases. However, annotation and analysis of the WES result, especially for single case analysis still remain a challenge. Here, we introduce a method called phenotype-driven designing “virtual panel” to simplify the procedure and assess the diagnostic rate of this method.Methods: WES was performed in samples of 30 patients, core phenotypes of probands were then extracted and inputted into an in-house software, “Mingjian” to calculate and generate associated gene list of a virtual panel. Mingjian is a self-updating genetic disease computer supportive diagnostic system that based on the databases of HPO, OMIM, HGMD. The virtual panel that generated by Mingjian system was then used to filter and annotate candidate mutations. Sanger sequencing and co-segregation analysis among the family were then used to confirm the filtered mutants.Result: We first used phenotype-driven designing “virtual panel” to analyze the WES data of a patient whose core phenotypes are ataxia, seizures, esotropia, puberty and gonadal disorders, and global developmental delay. Two mutations, c.430T > C and c.640G > C in PMM2 were identified by this method. This result was also confirmed by Sanger sequencing among the family. The same analysing method was then used in the annotation of WES data of other 29 neurological rare disease patients. The diagnostic rate was 65.52%, which is significantly higher than the diagnostic rate before.Conclusion: Phenotype-driven designing virtual panel could achieve low-cost individualized analysis. This method may decrease the time-cost of annotation, increase the diagnostic efficiency and the diagnostic rate.

Molecular diagnosis of muscular diseases in outpatient clinics

“…The number of VUS might be much more increased in the regular laboratory setting with limited clinical information. Overall, our results support the use of an exome-based panel for muscular disorders, although several considerations must be taken into account when introducing exome-based panel in the laboratory [38][39][40] (table e-6, links.lww.com/NXG/A239).…”

Next-Generation Sequencing Technologies and Neurogenetic Diseases

“…WES employs NGS platforms, such as Illumina, to sequence the protein-coding regions of the genome. Although initial sequencing and analysis of the human genome revealed that less than 2% of the genome comprises exons, approximately 85% of the DNA variations responsible for highly penetrant genetic diseases lie in this small fraction of the genome [ 6 , 7 ]. Currently, WES is the most commonly used mainstream sequencing method in clinical applications due to its low associated cost and turnaround time, compared with WGS.…”

“…Thus, WES facilitated landmark changes in the management and treatment of diseases based on the identification of causal genetic factors. With further development of sequencing technology, the diagnostic rate across diverse clinical laboratories increased to 65.52% [ 7 ]. However, the overall diagnosis rate remains low, primarily due to challenges associated with the detection of pathogenic mutations, which may be classified as a VUS or appear within the noncoding region, thus escaping capture by WES.…”

Clinical and Genetic Study on a Chinese Patient with Infantile Onset Epileptic Encephalopathy carrying a PPP3CA Null Variant: a case report

“…Whole-exome sequencing (WES) and Sanger sequencing were performed by Running Gene Inc. (Beijing, China) using their standard process, which is available in the previous report [8]. The variant c.1283insC (GRCh37/ hg19, NM_000944) of PPP3CA was identified in the proband.…”