Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins
Targeted panel, whole exome, or whole genome DNA sequencing using next-generation sequencing (NGS) allows for extensive high-throughput investigation of molecular machines/systems such as the LINC complex. This includes the identification of genetic variants in humans that cause disease, as is the case for some genes encoding LINC complex proteins. The relatively low cost and high speed of the sequencing process results in large datasets at various stages of analysis and interpretation. For those not intimately familiar with the process, interpretation of the data might prove challenging. This review lays out the most important and most commonly used materials and methods of NGS. It also discusses data analysis and potential pitfalls one might encounter because of peculiarities of the laboratory methodology or data analysis pipelines.
Key wordsDNA sequencing DNA sequence analysis LINC complex Mutation Next-generation sequencing Polymorphism Sequence variants
H.J.W. is supported by National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under award numbers R01AR048997 and R01AR068636. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
P.L.N. is an employee of MNG Laboratories and owns equity in the company. H.J.W. serves on the scientific advisory board of MNG Laboratories and receives fees for this service.
- 13.Puckelwartz MJ, Kessler E, Zhang Y et al (2009) Disruption of nesprin-1 produces an Emery Dreifuss muscular dystrophy-like phenotype in mice. Disruption of nesprin-1 produces an Emery Dreifuss muscular dystrophy-like phenotype in mice. Hum Mol Genet 18:607–620CrossRefPubMedPubMedCentralGoogle Scholar
- 27.Van der Auwera GA, Carneiro MO et al (2013) From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11.10.1–11.1033Google Scholar
- 30.Richards S, Aziz N, Bale S et al (2015) 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. Genet Med 17:405–423CrossRefPubMedPubMedCentralGoogle Scholar