scholarly journals Sequencing your genome: your future is here, but are you sure you want to know it?

2014 ◽  
Vol 96 ◽  
Author(s):  
NIR PILLAR ◽  
OFER ISAKOV ◽  
NOAM SHOMRON
Keyword(s):  
Next Generation Sequencing ◽  
Research Laboratory ◽  
High Throughput Sequencing ◽  
Genomic Research ◽  
Sequencing Technology ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
The Past ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS; also known as deep sequencing or ultra-high throughput sequencing) has probably been the most important tool for genomic research over the past few years. NGS has led to numerous discoveries and scientific breakthroughs in the genetic field. The sequencing technology that has entered the research laboratory in the past decade is now being introduced into the clinical diagnostic laboratory. Consequently, NGS results are becoming available in the medical arena as abundance of clinically relevant variants, conferring predisposition to disease, are being discovered at a growing rate (Stanley, 2014).

The efficacy of targeted next-generation sequencing for detection of clinically actionable mutations in cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10598-10598
Author(s):  
Yu-Ye Wen ◽  
Erica Fang ◽  
Yanchun Li ◽  
Condie Edwin Carmack ◽  
Marilyn M. Li
Keyword(s):  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Cancer Gene ◽  
Cancer Genes ◽  
Next Generation ◽  
Clinical Diagnostic Laboratory ◽  
Kras Mutations ◽  
Diagnostic Laboratory ◽  
Turn Around Time ◽  
Generation Sequencing

10598 Background: The emergence of next-generation sequencing (NGS) technologies has significantly accelerated the identification of cancer-causing mutations and the development of personalized cancer care. However, the clinical application of these technologies to detect cancer gene mutations has been extremely limited due to the long turn around time, the high cost, and large amount of input DNA required by existing NGS-based tests. Methods: We have assessed the performance of a novel NGS technology that merges multiplex PCR with ion semiconductor sequencing (AmpliSeq, Life Technologies, Inc.) in our clinical diagnostic laboratory. The test interrogates 739 common mutations in 46 cancer genes including many clinically actionable mutations concurrently. First, we studied 12 tumor samples including 4 archived FFPE, 4 blood/bone marrow, and 4 cell line samples with known mutations to evaluate the sensitivity and specificity of the test. We then studied 34 de-identified, archived FFPE tumor samples of unknown genotype to further evaluate the efficacy of the test. Results: We successfully identified all known mutations previously detected by Pyposequencing or Sanger sequencing technologies. Multiple serial dilution studies showed that the test could detect mutations at frequencies as low as 5% with 99% confidence. For the samples of unknown genotype, we detected 23 COSMIC mutations in 16 samples including HRAS, BRAF, MET, TP53 mutations in lung cancer, KRAS, PIK3CA, TP53, APC, BRAF, ERBB2 mutations in colon cancer, TP53 and KRAS mutations in breast cancer, and KIT and PDGFRA mutations in GIST. Analysis of the variant call data showed that a minimum of 100X coverage is required in order to detect mutations at 10% frequency or above; a minimum 300K final library reads are necessary in order to minimize/eliminate amplicon dropout. Conclusions: The targeted NGS test can effectively detect cancer gene mutation with input DNA as low as a few nanograms, turn around time can be as short as two days, and can significantly lower cost compared to traditional Sanger sequencing. Our experience demonstrates that this technology holds great potential for clinical use, including diagnostic and therapeutic applications.

scholarly journals Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing

2019 ◽  
Vol 221 (Supplement_3) ◽  
pp. S289-S291 ◽  
Author(s):  
Mariana Leguia ◽  
Anton Vila-Sanjurjo ◽  
Patrick S G Chain ◽  
Irina Maljkovic Berry ◽  
Richard G Jarman ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Infectious Diseases ◽  
Next Generation ◽  
The Past ◽  
Infectious Disease Research ◽  
History Of ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Health Applications

Abstract This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled “Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research.” We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.

scholarly journals Guidelines for diagnostic next-generation sequencing

2015 ◽  
Vol 24 (1) ◽  
pp. 2-5 ◽  
Author(s):  
Gert Matthijs ◽  
Erika Souche ◽  
Mariëlle Alders ◽  
Anniek Corveleyn ◽  
Sebastian Eck ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Tests ◽  
Human Genetics ◽  
Genetic Disorders ◽  
Next Generation ◽  
The Past ◽  
Supplementary Material ◽  
New Feature ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract We present, on behalf of EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of next-generation sequencing (NGS) applications for the diagnosis of genetic disorders. The work was performed by a group of laboratory geneticists and bioinformaticians, and discussed with clinical geneticists, industry and patients’ representatives, and other stakeholders in the field of human genetics. The statements that were written during the elaboration of the guidelines are presented here. The background document and full guidelines are available as supplementary material. They include many examples to assist the laboratories in the implementation of NGS and accreditation of this service. The work and ideas presented by others in guidelines that have emerged elsewhere in the course of the past few years were also considered and are acknowledged in the full text. Interestingly, a few new insights that have not been cited before have emerged during the preparation of the guidelines. The most important new feature is the presentation of a ‘rating system’ for NGS-based diagnostic tests. The guidelines and statements have been applauded by the genetic diagnostic community, and thus seem to be valuable for the harmonization and quality assurance of NGS diagnostics in Europe.

scholarly journals Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies

2017 ◽  
Vol 141 (6) ◽  
pp. 759-775 ◽  
Author(s):  
Mariam Thomas ◽  
Mahadeo A. Sukhai ◽  
Tong Zhang ◽  
Roozbeh Dolatshahi ◽  
Djamel Harbi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rare Variants ◽  
Gc Content ◽  
Hematologic Malignancies ◽  
Performance Characteristics ◽  
Next Generation ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Genomic Regions ◽  
Generation Sequencing

Context.— Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes. Objective.— To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics. Data Sources.— Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified. Conclusions.— We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 500×. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non–next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone.

scholarly journals RETRACTED: LFQC: a lossless compression algorithm for FASTQ files

2014 ◽  
Vol 35 (9) ◽  
pp. e1-e7
Author(s):  
Sudipta Pathak ◽  
Sanguthevar Rajasekaran
Keyword(s):  
State Of The Art ◽  
Compression Algorithm ◽  
Genomic Research ◽  
Sequencing Technology ◽  
Compression Algorithms ◽  
Average Improvement ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Motivation Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques. Results We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz, fqzcomp, G-SQZ, SCALCE, Quip, DSRC, DSRC-LZ etc. This comparison reveals that our algorithm achieves better compression ratios. The improvement obtained is up to 225%. For example, on one of the datasets (SRR065390_1), the average improvement (over all the algorithms compared) is 74.62%. Availability and implementation The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/FastqPrograms.zip.

NGS for prenatal diagnosis of fetal anomalies

2020 ◽  
pp. 65-66
Author(s):  
Т.И. Янова ◽  
И.В. Канивец ◽  
С.А. Коростелев ◽  
Д.В. Пьянков ◽  
В.Ю. Удалова ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Fetal Anomalies ◽  
Fetal Dna ◽  
Pathogenic Variants ◽  
Monogenic Diseases ◽  
Fetal Malformations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Использование высокопроизводительного секвенирования в пренатальной диагностике позволило значительно увеличить выявляемость причин аномалий развития плода, определенных при УЗИ. Установление релевантного варианта является важным для постановки диагноза и оценки прогноза. Цель настоящей работы - определить распространенность и структуру моногенных заболеваний, являющихся причиной пороков развития плода при использовании секвенирования нового поколения (NGS). В нашем исследовании было проанализировано 60 образцов ДНК плодов, аномалии развития которых были выявлены при УЗИ во время беременности. Патогенные варианты, являющиеся причиной аномалий развития были найдены у 71% плодов. The use of high-throughput sequencing in prenatal diagnostics has significantly increased the detection of the causes of fetal abnormalities identified by ultrasound. Establishing a relevant option is important for making a diagnosis and evaluating the prognosis. The purpose of this work is to determine the prevalence and structure of monogenic diseases that cause fetal malformations using next generation sequencing (NGS). In our study, we analyzed 60 samples of fetal DNA whose abnormalities were detected by ultrasound during pregnancy. Pathogenic variants were found in 71% of fetuses.

ABCs of genomics

Hematology ◽  
2013 ◽  
Vol 2013 (1) ◽  
pp. 316-323 ◽  
Author(s):  
Stefan K. Bohlander
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Analysis ◽  
High Throughput ◽  
Patient Management ◽  
Genetic Basis ◽  
Day Treatment ◽  
Malignant Diseases ◽  
The Past ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Our genome, the 6 billion bp of DNA that contain the blueprint of a human being, has become the focus of intense interest in medicine in the past two decades. Two developments have contributed to this situation: (1) the genetic basis of more and more diseases has been discovered, especially of malignant diseases, and (2) at the same time, our abilities to analyze our genome have increased exponentially through technological breakthroughs. We can expect genomics to become ever more relevant for day-to-day treatment decisions and patient management. It is therefore of great importance for physicians, especially those who are treating patients with malignant diseases, to become familiar with our genome and the technologies that are currently available for genomics analysis. This review provides a brief overview of the organization of our genome, high-throughput sequence analysis methods, and the analysis of leukemia genomes using next-generation sequencing (NGS) technologies.

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