BACKGROUND Next-Generation Sequencing (NGS) has made genomic mutation-driven therapy feasible for metastatic breast cancer (MBC) patients. We frequently submit tumor tissue from MBC patients for targeted NGS of tumor using the Illumina HiSeq 2000 platform (FoundationOne®, Foundation Medicine, MA). Herein, we report the results and clinical impact of this test in MBC patients. PATIENTS AND MET...

SUMMARY NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, fo...

In this issue of the Journal, Schumacher and colleagues1 describe important principles to consider when applying nextgeneration sequencing (NGS) for the identification of clonal sequences to support the diagnosis of T-cell neoplasms. NGS has been shown to be clinically useful in identifying germline mutations in hereditary conditions and somatic mutations in numerous cancers. In 2009, one of th...

Cystic fibrosis (CF) is a multisystemic disease but without a classical disease-specific renal phenotype. A 32-year-old male patient with CF (ΔF508/ΔF508) presented with a nephrotic syndrome. Renal biopsy revealed nodular glomerulosclerosis (NGS) occurring in the absence of diabetes mellitus, amyloidosis and any other known common cause of NGS. He had a progressive decline in estimated glomerul...

OBJECTIVE To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected CNS infections. METHODS In a prospective pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord ...

Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detect...

Next-generation sequencing (NGS) technology, with its high-throughput capacity and low cost, has developed rapidly in recent years and become an important analytical tool for many genomics researchers. New opportunities in the research domain of the forensic studies emerge by harnessing the power of NGS technology, which can be applied to simultaneously analyzing multiple loci of forensic inter...

High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries fro...

The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL Minimal residual disease (MRD) monitoring via antigen receptor quantitative polymerase chain reaction (qPCR) is an important pre-dictor of outcome in childhood acute lymphoblastic leukemia (ALL), is rigorously standardized within the EuroMRD consortium and has a greater...

The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing ...