scholarly journals 2443 Attitudes and preferences for return of results from next-generation sequencing

2018 ◽  
Vol 2 (S1) ◽  
pp. 79-79
Author(s):  
Matthew Neu ◽  
Jaimie Richards ◽  
Sara J. Knight
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Incidental Findings ◽  
Return Of Results ◽  
Medical Setting ◽  
Specific Gene ◽  
Next Generation ◽  
Inclusion Criteria ◽  
Secondary Findings ◽  
Generation Sequencing

OBJECTIVES/SPECIFIC AIMS: Objectives: Decreasing costs and increasing evidence for clinical utility have contributed to whole genome sequencing (WGS) becoming a clinical reality. While previous studies have surveyed the attitudes of patients and community members towards specific gene tests, an emerging literature has begun to describe the preferences of diverse recipients for WGS results. In this study, we sought to identify and synthesize the quantitative evidence on preferences for results from WGS using a systematic review of the literature. METHODS/STUDY POPULATION: We conducted a search of articles on PubMed including subject index terms WGS, whole exome sequencing, genome sequencing, secondary findings, incidental findings, attitudes, preferences, choices, utilities, stated-preferences, discrete choice experiment, and willingness-to-pay. We conducted 11 formal searches to refine the strategy and conducted a final search in December 2017. Duplicates were eliminated and a title and abstract review was conducted to select articles meeting inclusion criteria. RESULTS/ANTICIPATED RESULTS: Our search strategy identified 79 publications meeting initial search criteria with 30 manuscripts meeting inclusion criteria. Of these, most studies were conducted with patient-participants enrolled in existing sequencing studies, while few engaged members of the general public. Of the studies conducted on patients, most were on the medical setting of cancer and related syndromes. The earliest publication date of a manuscript meeting our inclusion criteria was in 2012, yet the majority were published in 2015 or later. DISCUSSION/SIGNIFICANCE OF IMPACT: Between 2012 and 2015, we saw an increasing focus in the medical literature on understanding public and patient preferences for return of results from WGS and WES. Both public and patient populations participating in surveys expressed preferences for receiving results from next-generation sequencing, even if the results are secondary or incidental findings unrelated to the primary indication for sequencing. A primary factor related to patient interest in incidental or secondary findings is the extent to which these results can inform medical intervention. Few studies surveyed representative population-based samples, and this may be an area for future investigation.

scholarly journals Incidental findings from cancer next generation sequencing panels

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Nika Maani ◽  
Karen Panabaker ◽  
Jeanna M. McCuaig ◽  
Kathleen Buckley ◽  
Kara Semotiuk ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Incidental Findings ◽  
Complete Blood Count ◽  
Hematologic Malignancy ◽  
Retrospective Chart Review ◽  
Hematologic Malignancies ◽  
Next Generation ◽  
Inclusion Criteria ◽  
Pathogenic Variants ◽  
Generation Sequencing

AbstractNext-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Power and Promise of Next-Generation Sequencing in Liquid Biopsies and Cancer Control

2020 ◽  
Vol 27 (3) ◽  
pp. 107327482093480
Author(s):  
Ting-Miao Wu ◽  
Ji-Bin Liu ◽  
Yu Liu ◽  
Yi Shi ◽  
Wen Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Treatment Plan ◽  
Genetic Mutations ◽  
Specific Gene ◽  
Specific Situation ◽  
Next Generation ◽  
Early Screening ◽  
Liquid Biopsies ◽  
Cancer Management ◽  
Generation Sequencing

Traditional methods of cancer treatment are usually based on the morphological and histological diagnosis of tumors, and they are not optimized according to the specific situation. Precision medicine adjusts the existing treatment regimen based on the patient’s genomic information to make it most suitable for patients. Detection of genetic mutations in tumors is the basis of precise cancer medicine. Through the analysis of genetic mutations in patients with cancer, we can tailor the treatment plan for each patient with cancer to maximize the curative effect, minimize damage to healthy tissues, and optimize resources. In recent years, next-generation sequencing technology has developed rapidly and has become the core technology of precise targeted therapy and immunotherapy for cancer. From early cancer screening to treatment guidance for patients with advanced cancer, liquid biopsy is increasingly used in cancer management. This is as a result of the development of better noninvasive, repeatable, sensitive, and accurate tools used in early screening, diagnosis, evaluation, and monitoring of patients. Cell-free DNA, which is a new noninvasive molecular pathological detection method, often carries tumor-specific gene changes. It plays an important role in optimizing treatment and evaluating the efficacy of different treatment options in clinical trials, and it has broad clinical applications.

scholarly journals Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jin Sun No ◽  
Won-Keun Kim ◽  
Seungchan Cho ◽  
Seung-Ho Lee ◽  
Jeong-Ah Kim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Samples ◽  
Whole Genome ◽  
Target Enrichment ◽  
Next Generation ◽  
Apodemus Agrarius ◽  
Target Capture ◽  
Generation Sequencing

Abstract Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus agrarius lung tissues containing up to 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.

scholarly journals Next generation sequencing (NGS) in oncology: lights and shadows

2016 ◽  
Vol 4 (1) ◽  
pp. 17-19
Author(s):  
Margherita Nannini ◽  
Maria A. Pantaleo
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Next Generation ◽  
Coding Regions ◽  
Oncology Research ◽  
Potential Applications ◽  
Functional Consequences ◽  
Next Generation Sequencing Ngs ◽  
Tumor Genome ◽  
Generation Sequencing

Advances in tumor genome sequencing using next generation sequencing (NGS) technologies have facilitated a greater understanding of the genetic abnormalities involved in cancer development and progression, dramatically changing oncology research. There are several different types of NGS technologies. Whole genome sequencing (WGS) determines the sequence of the complete genome, providing information on both coding and non-coding regions and structural variants. However, use is limited by the large volume of data generated, and associated time and resource costs. Whole exome sequencing (WES) determines the sequence of coding regions only, making it faster and cheaper than WGS, and the functional consequences of variants are easier to interpret. However, all variations in non-coding regions are missed. WGS and WES are often used together to maximize detection of variants. A less costly approach is the use of targeted sequencing, which focuses on particular regions of interest, based on their biological relevance. NGS technologies can also be used to sequence RNA, referred to as RNA-Seq. All these NGS technologies, individually or in combination, have a number of potential applications, including identification of biomarkers, and development of diagnostic and therapeutic strategies. However, although advances have been made, there are a number of limitations to be overcome before NGS technologies are routinely applied in both research and clinical practice.

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