The evolving potential of companion diagnostics

Abstract

The scope of companion diagnostics in cancer has undergone significant shifts in the past few years, with increased development of targeted therapies and novel testing platforms. This has provided new opportunities to effect unprecedented paradigm shifts in the application of personalized medicine principles for patients with cancer. These shifts involve assay platforms, analytes, regulations, and therapeutic approaches. As opportunities involving each of these facets of companion diagnostics expand, close collaborations between key stakeholders should be enhanced to ensure optimal performance characteristics and patient outcomes.     

Update on molecular companion diagnostics - a future in personalized medicine beyond Sanger sequencing

ABSTRACT

Introduction

The merging of molecular diagnostics with personalized medicine has led to a surge in development of molecular-based companion diagnostics. Companion diagnostics, defined as ‘a medical device, often an in vitro device, which provides information that is essential for the safe and effective use of a corresponding drug or biological product’, are key to the appropriate utilization of several pharmacotherapies; primarily in the area of oncology.     

Regulatory perspectives on next-generation sequencing and complementary diagnostics in Japan

ABSTRACT

Introduction

The ‘one biomarker/one drug’ scenario is unsustainable because cancer is a complex disorder that involves a number of molecular defects. In the past decade, major technological advances have lowered the overall cost and increased the efficiency of next-generation sequencing (NGS).     

腮腺病变的CT诊断

目的 :探讨腮腺病变中的CT表现 ,为临床诊治提供可靠依据。方法 :回顾性分析经病理证实的 2 2例腮腺肿块的CT表现 ,并与病理检查进行对照研究。结果 :2 2例腮腺肿块中 ,3例双侧呈弥漫性肿大 ,密度增高 ,19例单侧腮腺内有软组织块影 ,其中 11例肿块较弥漫 ,密度不均 ,边界模糊 ,4例肿块较局限 ,密度均匀 ,边缘模糊 ,2例腮腺体积缩小。结论 :CT对大部分腮腺炎能作出正确诊断 ,对治疗方案的选择有指导意义     

下一代测序技术在分子诊断中的应用

DNA测序是破译人类疾病的一种强大技术,尤其在癌症方面。飞速发展的下一代测序（next—generation sequencing,NGS）极大降低了测序成本,并且实现了高通量,这使我们可以获得整个基因组的序列,以及那些临床上确诊病人的全部基因组信息。然而下一代测序技术带来诸多益处的同时也带来了挑战,那就是怎样使这个技术在临床诊断中成为常规手段。本文就目前NGS的几大技术平台原理,在临床诊断中的应用,以及目前面临的挑战等进行综述。     

Nucleic acid detection technologies and marker molecules in bacterial diagnostics

There is a growing need for quick and reliable methods for microorganism detection and identification worldwide. Although traditional culture-based technologies are trustworthy and accurate at a relatively low cost, they are also time- and labor-consuming and are limited to culturable bacteria. Those weaknesses have created a necessity for alternative technologies that are capable for faster and more precise bacterial identification from medical, food or environmental samples. The most common current approach is to analyze the nucleic acid component of analyte solution and determine the bacterial composition according to the specific nucleic acid profiles that are present. This review aims to give an up-to-date overview of different nucleic acid target sequences and respective analytical technologies.     

Molecular diagnostics for hereditary hearing loss in children

Introduction: Hearing loss (HL) is the most common birth defect in industrialized countries with far-reaching social, psychological and cognitive implications. It is an extremely heterogeneous disease, complicating molecular testing. The introduction of next-generation sequencing (NGS) has resulted in great progress in diagnostics allowing to study all known HL genes in a single assay. The diagnostic yield is currently still limited, but has the potential to increase substantially.

Areas covered: In this review the utility of NGS and the problems for comprehensive molecular testing for HL are evaluated and discussed.

Expert commentary: Different publications have proven the appropriateness of NGS for molecular testing of heterogeneous diseases such as HL. However, several problems still exist, such as pseudogenic background of some genes and problematic copy number variant analysis on targeted NGS data. Another main challenge for the future will be the establishment of population specific mutation-spectra to achieve accurate personalized comprehensive molecular testing for HL.     

Next-generation sequencing applied to rare diseases genomics

Genomics has revolutionized the study of rare diseases. In this review, we overview the latest technological development, rare disease discoveries, implementation obstacles and bioethical challenges. First, we discuss the technology of genome and exome sequencing, including the different next-generation platforms and exome enrichment technologies. Second, we survey the pioneering centers and discoveries for rare diseases, including few of the research institutions that have contributed to the field, as well as an overview survey of different types of rare diseases that have had new discoveries due to next-generation sequencing. Third, we discuss the obstacles and challenges that allow for clinical implementation, including returning of results, informed consent and privacy. Last, we discuss possible outlook as clinical genomics receives wider adoption, as third-generation sequencing is coming onto the horizon, and some needs in informatics and software to further advance the field.     

New generation sequencing in pathogen discovery and microbial surveillance

23rd European Congress of Clinical Microbiology and Infectious Diseases (ECCMID).

Berlin, Germany, 27–30 April 2013

The annual congress of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) is recognized as the largest European congress for the presentation and discussion of the key priorities and more recent scientific developments in the fields of clinical microbiology and infection. This year, it attracted almost 10,000 participants from all over the world. Keynote lectures, symposia, meet-the-expert sessions, educational workshops, poster and oral sessions covered the diagnosis, treatment, epidemiology and prevention of infectious diseases, as well as related basic microbiology. Moreover, interactive sessions addressing specific subjects underlined the important educational aspect of the ECCMID’s congress. The scientific program, abstracts, oral presentations are available at their website . This meeting report is focused on one of the several challenging and one of the most transversal topics of the meeting: the application of the next-generation sequencing (NGS) to the microbial world.     

Clinical investigational studies for validation of a next-generation sequencing in vitro diagnostic device for cystic fibrosis testing

Purpose: Clinical investigational studies were conducted to demonstrate the accuracy and reproducibility of the Illumina MiSeqDx CF System, a next-generation sequencing (NGS) in vitro diagnostic device for cystic fibrosis testing. Methods: Two NGS assays – a Clinical Sequencing Assay (Sequencing Assay) and a 139-Variant Assay (Variant Assay) – were evaluated in both an Accuracy Study and a Reproducibility Study, with comparison to bi-directional Sanger sequencing and PCR as reference methods. For each study, positive agreement (PA), negative agreement (NA), and overall agreement (OA) were evaluated. Results: In the Accuracy Study, the Sequencing Assay achieved PA of 99.7% including the polyTG/polyT region and PA of 100% excluding the region. The Variant Assay achieved PA of 100%. NA and OA were >99.99% for both Assays. In the Reproducibility Study, the Sequencing Assay achieved PA of 99.2%; NA and OA were both 99.7%. The Variant Assay achieved PA of 99.8%; NA and OA were both 99.9%. Sample pass rates were 99.7% in both studies for both assays. Conclusion: This is the first systematic evaluation of a NGS platform for broad clinical use as an in vitro diagnostic, including accuracy validation with multiple reference methods and reproducibility validation at multiple clinical sites. These NGS-based Assays had accurate and reproducible results which were comparable to or better than other methods currently in clinical use for clinical genetic testing of cystic fibrosis.     

The impact of sequencing on diagnosis and treatment of malignant melanoma

Melanoma is one of the clinically most important cancer types considering its high mortality rate and that it is commonly diagnosed in relatively young people. With the advent of targeted therapies and, more recently, immune checkpoint inhibitors, more treatment options are available resulting in higher patient survival rates. However, the successful application of these targeted therapies critically depends on the reliable detection of molecular aberrations. Today, massively parallel sequencing techniques enable us to analyze large sets of genes in a relatively short time. It has allowed increased knowledge of acquired somatic mutations in melanoma and has helped to identify new targets for personalized therapy, and potentially may help to predict response to immune therapies. Described here are the development of sequencing techniques, how their improvement has changed diagnosis, prognosis and management of malignant melanoma and the future perspectives of melanoma diagnostics in the routine clinical setting.     

Combination of real-time PCR and sequencing to detect multiple clinically relevant genetic variations in the lactase gene

Background: Lactase persistence is an autosomal dominant trait commonly distributed in Europe as well as some parts of east Africa and the Arabian Peninsula. Using real-time PCR to detect the ?13910C?>?T variant common in the European population is a reliable analysis although other variants in the probe-binding site may cause errors in analysis. The aim of this study was to determine the prevalence of the variants in a Danish cohort examined for lactose intolerance as well as to improve the real-time PCR analysis for detection of the different variants.

Methods: We genotyped 3395 routine samples using real-time PCR for the ?13910C?>?T-variant. All consecutive samples identified as ?13910CC were sequenced using Sanger Sequencing. Using the SDS software we examined various quality value settings to improve on the genetic analysis.

Results: Using real-time PCR resulted in 100% successful genotyping of the ?13910C?>?T variant. By using a quality value of 99% and sequencing the undetermined samples we improved the ability of the assay to identify variants other than ?13910C?>?T. This resulted in a reduction of the diagnostic error rate by a factor of 2.4 while increasing the expenses only 3%.

Conclusions: We conclude that using a quality value of 99% in the SDS software significantly improves the diagnostic efficiency of the real-time PCR assay for detecting variants associated to lactase persistence.