Next Generation Sequencing Platforms and Bioinformatics Pipelines for Variant Calling and Analysis

Next generation sequencing (NGS) is the latest diagnostic screening method with high accuracy for comprehensive testing of chromosomal abnormalities. Preimplantation genetic screening (PGS) in conjunction with NGS has revolutionized the world of infertility. PGS helps determine genetic disorders of embryos before being transferred to uterus. Couples with idiopathic inheritance disorders or women who have a history of recurrent miscarriage are good candidates for PGS-NGS. The aim of this review study is to provide an overview of NGS strategies to analyze genetic variants in mendelian and rare complex genetic diseases and also assessment bioinformatics pipelines for variant calling and analysis. We reviewed available NGS platforms including Roche 454, Illumina, SOLiD and Ion Torrent. The bioinformatic pipelines for variant calling workflow using whole genome sequencing and whole exome sequencing data including quality control of fastq files, alignment to reference genome, mark duplication, variant calling, filtration, annotation, and clinical report were also discussed. The quality of data achieved by NGS integrated with affordable costs, improved data handling capabilities, enhanced computational power and efficient bioinformatics analysis tools, revolutionized clinical genetic diagnostic testing and research approaches to identify associated mutation causing mendelian or complex genetic diseases. NGS-based methods could lead to representation de novo mutations with significant association or in the absence of association. In this review study, we highlighted NGS strategies combined with bioinformatic analysis programs to detect genetic variants involved in Mendelian and uncommon genetic diseases in research and clinical settings. This fast-progressing approach can help future studies to identify novel variants and genetic medicine. Keywords * High-throughput nucleotide sequencing * Genetic testing, infertility * Genome