Challenges in detecting genomic copy number aberrations using next-generation sequencing data and the eXome Hidden Markov Model: a clinical exome-first diagnostic approach

• Published in: Human genome variation Vol. 3; no. 1; p. 16025
• Main Authors: Yamamoto, Toshiyuki, Shimojima, Keiko, Ondo, Yumiko, Imai, Katsumi, Chong, Pin Fee, Kira, Ryutaro, Amemiya, Mitsuhiro, Saito, Akira, Okamoto, Nobuhiko
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.08.2016; Springer Nature B.V; Nature Publishing Group
• Subjects: 631/208/2489/144; 692/308/2056; Biomedical and Life Sciences; Biomedicine; Gene Expression; Gene Function; Gene Therapy; Human Genetics; Molecular Medicine
• ISSN: 2054-345X; 2054-345X
• DOI: 10.1038/hgv.2016.25

Next-generation sequencing (NGS) is widely used for the detection of disease-causing nucleotide variants. The challenges associated with detecting copy number variants (CNVs) using NGS analysis have been reported previously. Disease-related exome panels such as Illumina TruSight One are more cost-effective than whole-exome sequencing (WES) because of their selective target regions (~21% of the WES). In this study, CNVs were analyzed using data extracted through a disease-related exome panel analysis and the eXome Hidden Markov Model (XHMM). Samples from 61 patients with undiagnosed developmental delays and 52 healthy parents were included in this study. In the preliminary study to validate the constructed XHMM system (microarray-first approach), 34 patients who had previously been analyzed by chromosomal microarray testing were used. Among the five CNVs larger than 200 kb that were considered as non-pathogenic CNVs and were used as positive controls, four CNVs was successfully detected. The system was subsequently used to analyze different samples from 27 patients (NGS-first approach); 2 of these patients were successfully diagnosed as having pathogenic CNVs (an unbalanced translocation der(5)t(5;14) and a 16p11.2 duplication). These diagnoses were re-confirmed by chromosomal microarray testing and/or fluorescence in situ hybridization. The NGS-first approach generated no false-negative or false-positive results for pathogenic CNVs, indicating its high sensitivity and specificity in detecting pathogenic CNVs. The results of this study show the possible clinical utility of pathogenic CNV screening using disease-related exome panel analysis and XHMM. Medical genetics: A test for disease-related structural alterations Targeted sequencing of clinically relevant genes can reveal large structural anomalies responsible for undiagnosed diseases. A team led by Toshiyuki Yamamoto from Tokyo Women’s Medical University, Japan, investigated whether a DNA test that reads all the protein-coding regions of 4,813 genes with known health impacts could be combined with a statistical tool to find genomic duplications or other large structural rearrangements — so-called copy number variants, or CNVs — that explain mysterious ailments. The researchers validated the approach in 34 patients with CNVs that don’t cause disease. They then turned to 27 patients with undiagnosed developmental problems, and successfully discovered disease-related CNVs in two subjects, with no false results or misdiagnoses (as confirmed by other genetic methods). The technique provides a cost-effective means of screening for disease-related copy number aberrations in the genome.