Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases

Abstract

Background: Targeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis.

Methodology/principal findings: We designed a capture array to mainly capture all the coding sequence (CDS) of 2,181 genes associated with 561 Mendelian diseases and conducted NGS to detect mutations. The accuracy of NGS was 99.95%, which was obtained by comparing the genotypes of selected loci between our method and SNP Array in four samples from normal human adults. We also tested the stability of the method using a sample from normal human adults. The results showed that an average of 97.79% and 96.72% of single-nucleotide variants (SNVs) in the sample could be detected stably in a batch and different batches respectively. In addition, the method could detect various types of mutations. Some disease-causing mutations were detected in 69 clinical cases, including 62 SNVs, 14 insertions and deletions (Indels), 1 copy number variant (CNV), 1 microdeletion and 2 microduplications of chromosomes, of which 35 mutations were novel. Mutations were confirmed by Sanger sequencing or real-time polymerase chain reaction (PCR).

Conclusions/significance: Results of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases.

Fig 1. Flowchart for the process of bioinformatic analysis.

Fig 2. Evaluation of the accuracy of our method.

Venn diagrams of the number of genotypes detected by targeted NGS and SNP Array in four samples (S1-1, S2, S3 and S4).

Fig 3. Evaluation of the stability of our method.

(A) Venn diagram of S1 sequenced three times in a same batch. (B) Venn diagram of S1 sequenced three times in different batches.

Fig 4. Identification and confirmation of heterozygous duplications involved in CMT in P57.

(A) Diagram of the average sequencing depth and coverage for CDS1-4 in the PMP22 gene. (B) Quantitative real-time PCR analysis. Relative amplification value calculated from the data of quantitative real-time PCR for detecting possible duplications in the PMP22 gene of patient P57.

Fig 5. Confirmation of inconsistent genotypes detected by targeted NGS and Snp Array using Sanger sequencing.

(A) A heterozygous substitution of G with A was confirmed in the TET2 gene in sample S1-1. (B) A Homozygous substitution of C with T was confirmed in the KAL1 gene in sample S1-1. (C) A Homozygous substitution of C with T was confirmed in the KAL1 gene in sample S4.