Interpretation of standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology / 中华实验眼科杂志

Sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing (NGS). By adopting NGS, more and more ophthalmologists and medical institutions are now performing genetic testing for molecular diagnosis and genetic research in genetic ocular disorders.Genetic testing has gradually become an indispensable test item in the diagnosis and treatment of patients with monogenetic ocular diseases and has been accompanied by new challenges in sequence interpretation due to increased complexity.As we know, NGS can detect a large number of the genetic variation data.Without strict standards to distinguish pathogenic variation from many potential functional variations in the human genome, false positive judgments of causality may be accelerated, which may hind the application and promotion of genetic diagnosis in clinical diagnosis as well as the biological understanding of diseases.The American College of Medical Genetics and Genomics (ACMG) has developed guidances for the interpretation of sequence variants and the Chinese Branch of Genetic Counseling has organized some experts in the field of genetic compiled the Chinese version of the ACMG Standards and Guidelines, which is one of the reference bases to help us interpret genetic variation.This article interpreted the ACMG Standards and Guidelines in order to provide reference for Chinese ophthalmologists in the classification of genetic variation, determination of pathogenic variation, application in clinical diagnosis and related genetic research.

Comparison study of whole exome sequencing and targeted panel sequencing in molecular diagnosis of inherited retinal dystrophies / 北京大学学报(医学版)

OBJECTIVE@#To evaluate and compare whole exome sequencing (WES) and targeted panel sequencing in the clinical molecular diagnosis of the Chinese families affected with inherited retinal dystrophies (IRDs).@*METHODS@#The clinical information of 182 probands affected with IRDs was collected, including their family history and the ophthalmic examination results. Blood samples of all probands and their relatives were collected and genomic DNA was extracted by standard protocols. The first 91 cases were subjected to the WES and the other 91 cases were subjected to a specific hereditary eye disease enrichment panel (HEDEP) designed by us. All likely pathogenic and pathogenic variants in the candidate genes were determined by Sanger sequencing and co-segregation analyses were performed in available family members. Copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA). As PRGR ORF15 was difficult to capture by next generation sequencing (NGS), all the samples were subjected to Sanger sequencing for this region. All sequence changes identified by NGS were classified according to the American College of Medical Gene-tics and Genomics and the Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines. In this study, only variants identified as pathogenic or likely pathogenic were included, while those variants of uncertain significance, likely benign or benign were not included.@*RESULTS@#In 91 cases with WES, pathogenic or likely pathogenic variants were determined in 30 cases, obtaining a detection rate of 33.00% (30/91); While in 91 cases with HEDEP sequencing, pathogenic or likely pathogenic variants were determined in 51 cases, achieving the diagnostic rate of 56.04% (51/91), and totally, the diagnostic rate was 44.51%. HEDEP had better sequencing coverage and read depth than WES, therefore HEDEP had higher detection rate. In addition, HEDEP could detect CNVs. In this study, we detected disease-causing variants in 29 distinct IRD-associated genes, USH2A, ABCA4 and RPGR were the three most common disease-causing genes, and the frequency of these genes in Chinese IRDs population was 11.54% (21/182), 6.59% (12/182) and 3.85% (7/182), respectively. We found 43 novel variants and 6 cases carried variants in RPGR ORF15.@*CONCLUSION@#NGS in conjunction with Sanger sequencing offers a reliable and effective approach for the genetic diagnosis of IRDs, and after evaluating the pros and cons of the two sequencing methods, we conclude that HEDEP should be used as a first-tier test for IRDs patients, WES can be used as a supplementary molecular diagnostic method due to its merit of detecting novel IRD-associated genes if HEDEP or other methods could not detect disease-causing va-riants in reported genes. In addition, our results enriched the mutational spectra of IRDs genes, and our methods paves the way of genetic counselling, family planning and up-coming gene-based therapies for these families.

Clinical phenotype assessment is very important in mutation analysis for patients with hereditary eye disease / 中华实验眼科杂志

Sanger sequencing technology is the most commonly used method for genetic analysis in inherited eye disease in the past few decades on account of its long DNA sequencing read length and high accuracy.However,application of this method is limited in genetically heterogeneous diseases because of the high economic and time cost.Next generation sequencing (NGS) technology is a high-throughput,cost-effective,and highly automated method which has been widely used since 2005.Although NGS is especially suitable for studies on genetically heterogeneous inherited eye disease,overdependence on the technique itself and neglect of the assessment of the phenotype may lead to misjudgment of the testing results and higher economic burden for the patients.So far,the most common method on researches of monogenic inherited eye disease is to combine NGS and Sanger sequencing technique.Precise evaluation of the clinical phenotype of patients is very important,as it is related with selection of detection methods and determination of disease-causing mutations.