Fengqi Chang

Clinical application of amplicon-based next-generation sequencing in cancer

Next-generation sequencing (NGS) technology has revolutionized genomic research by decreasing the cost of sequencing while increasing the throughput. The focus now is on potential clinical applications of NGS technology for diagnostics and therapeutics. Clinical applications of NGS in cancer can detect clinically actionable genetic/genomic alterations that are critical for cancer care. These alterations can be of diagnostic, prognostic, or therapeutic significance. In certain cancers, patient risk and prognosis can be predicted based on the mutation profile identified by NGS. Many targeted therapies have been developed for cancer patients who bear specific mutations; however, choosing the right NGS technique for the appropriate clinical application can be challenging, especially in clinical oncology, where the material for NGS tests is often limited and the turnaround time (TAT) for cancer tests is constrained to a few days. Currently, amplicon-based NGS approaches have emerged as the best fit for clinical oncology. In this review, we focus on amplicon-based library preparation, sequencing, sequence data alignment and annotation, and post-analytic interpretation and reporting.

Prenatal diagnosis of CLOVES syndrome confirmed by detection of a mosaic PIK3CA mutation in cultured amniocytes.

Congenital lipomatous asymmetric overgrowth of the trunk, lymphatic, capillary, venous, and combined‐type vascular malformations, epidermal nevi, skeletal and spinal anomalies (CLOVES) syndrome, a segmental overgrowth syndrome, is caused by post zygotic somatic mutations in PIK3CA, a gene involved in the receptor tyrosine kinase phosphatidylinositol 3‐kinase (PI3)‐AKT growth‐signaling pathway. Prenatal ultrasound findings of lymphovascular malformations, segmental overgrowth and skeletal defects can raise suspicion for CLOVES syndrome, but molecular confirmation of PIK3CA mutations on prenatally obtained samples is challenging because of somatic mosaicism. We detected a mosaic disease‐causing mutation in PIK3CA by sequencing of DNA extracted from cultured amniotic cells, but not from DNA directly prepared from an amniotic fluid sample in a fetus with prenatally suspected CLOVES syndrome. The infant was born prematurely and displayed severe lymphovascular malformations and segmental overgrowth consistent with a clinical diagnosis of CLOVES syndrome; he passed away at 29 days of life. We discuss the complexities and limitations of genetic testing for somatic mosaic mutations in the prenatal period and highlight the potential need for multiple approaches to arrive at a molecular diagnosis.

The Genomic Era of Clinical Oncology: Integrated Genomic Analysis for Precision Cancer Care

Genomic alterations are important biological markers for cancer diagnosis and prognosis, disease classification, risk stratification, and treatment selection. Chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are superb new tools for evaluating cancer genomes. These state-of-the-art technologies offer high-throughput, highly accurate, targeted and whole-genome evaluation of genomic alterations in tumor tissues. The application of CMA and NGS technologies in cancer research has generated a wealth of useful information about the landscape of genomic alterations in cancer and their implications in cancer care. As the knowledge base in cancer genomics and genome biology grows, the focus of research is now shifting toward the clinical applications of these technologies to improve patient care. Although not yet standard of care in cancer, there is an increasing interest among the cancer genomics communities in applying these new technologies to cancer diagnosis in the Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories. Many clinical laboratories have already started adopting these technologies for cancer genomic analysis. We anticipate that CMA and NGS will soon become the major diagnostic means for cancer genomic analysis to meet the increasing demands of precision cancer care.

Clinical efficacy of ruxolitinib and chemotherapy in a child with Philadelphia chromosome-like acute lymphoblastic leukemia with GOLGA5-JAK2 fusion and induction failure

Patients with Philadelphia chromosome-like B-cell lymphoblastic leukemia (Ph-like or BCR-ABL1 -like BALL) experience high relapse rates and are difficult to cure with conventional chemotherapy.[1][1],[2][2] The Ph-like ALL subtype comprises 15-25% of B-ALL in older children and adolescents/young

Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing

The focus of next-generation sequencing (NGS) technology is now shifting to include clinical applications owing to the major advantage of NGS, decreasing of sequencing cost while increasing throughput. Clinical applications of NGS in cancer can detect clinically actionable genetic/genomic alterations that are critical for cancer care. In certain cancers, patient risk and prognosis can be predicted based on the mutation profile identified by NGS. Many targeted therapies have been developed for cancer patients who bear specific mutations; however, choosing the right NGS technique for the appropriate clinical application in cancer can be challenging because of the limited material and short turnaround time for such cancer tests. Currently, amplification-based NGS approaches have emerged as one of the best fits for clinical oncology. In this review, we focus on NGS platforms that are suitable for targeted deep sequencing, amplification-based NGS technologies, and clinical applications of amplification-based NGS in cancer.