Clinical validation of targeted next-generation sequencing for inherited disorders.

CONTEXT: Although next-generation sequencing (NGS) can revolutionize molecular diagnostics, several hurdles remain in the implementation of this technology in clinical laboratories. OBJECTIVES: To validate and implement an NGS panel for genetic diagnosis of more than 100 inherited diseases, such as neurologic conditions, congenital hearing loss and eye disorders, developmental disorders, nonmalignant diseases treated by hematopoietic cell transplantation, familial cancers, connective tissue disorders, metabolic disorders, disorders of sexual development, and cardiac disorders. The diagnostic gene panels ranged from 1 to 54 genes with most of panels containing 10 genes or fewer. DESIGN: We used a liquid hybridization-based, target-enrichment strategy to enrich 10 067 exons in 568 genes, followed by NGS with a HiSeq 2000 sequencing system (Illumina, San Diego, California). RESULTS: We successfully sequenced 97.6% (9825 of 10 067) of the targeted exons to obtain a minimum coverage of 20× at all bases. We demonstrated 100% concordance in detecting 19 pathogenic single-nucleotide variations and 11 pathogenic insertion-deletion mutations ranging in size from 1 to 18 base pairs across 18 samples that were previously characterized by Sanger sequencing. Using 4 pairs of blinded, duplicate samples, we demonstrated a high degree of concordance (>99%) among the blinded, duplicate pairs. CONCLUSIONS: We have successfully demonstrated the feasibility of using the NGS platform to multiplex genetic tests for several rare diseases and the use of cloud computing for bioinformatics analysis as a relatively low-cost solution for implementing NGS in clinical laboratories.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

BACKGROUND: The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories. FINDINGS: To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample. CONCLUSIONS: We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.

Sclerosing spindle cell rhabdomyosarcoma in an adult: report of a new case and review of the literature.

Sclerosing spindle cell rhabdomyosarcoma (SSRMS) is a newly recognized entity in adults. The authors report a new case of SSRMS in a 31-year-old woman who presented with a large right leg mass. Biopsy revealed a malignant spindle cell neoplasm with focal sclerotic areas. A diagnosis of monophasic synovial sarcoma was favored initially. The tumor cells in the resection specimen were positive for myosin, myogenin, and MyoD1. Fluorescence in situ hybridization performed on the resection specimen showed no evidence of SYT gene rearrangement in the neoplastic cells, ruling out monophasic synovial sarcoma. A diagnosis of SSRMS was established. The patient succumbed to widely metastatic disease 16 months after initial diagnosis. This case highlights the utility of skeletal muscle markers and cytogenetic testing in distinguishing SSRMS from its mimic, monophasic synovial sarcoma. It is hoped that this case will expand the literature on adult SSRMS and help clinicians and pathologists better understand this newly described entity.