scholarly journals An archaeogenetic approach to identify the remains of the Hungarian Kings. Working Plan

2021 ◽  
Vol 1 (2) ◽  
pp. 333-342
Author(s):  
Gergely I. B. Varga ◽  
Kitti Maár ◽  
Alexandra Ginguta ◽  
Bence Kovács ◽  
Balázs Tihanyi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Analysis ◽  
Genetic Information ◽  
Sequence Data ◽  
Rapid Development ◽  
Personal Identification ◽  
Library Preparation ◽  
Working Plan ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The Royal Basilica of Székesfehérvár was the burial place of fifteen Hungarian kings. Unfortunately, the anthropological findings excavated at the site of the Basilica were mixed up during the tumultuous centuries of Hungary, hence the royal remains still lie unidentified in a charnel-house. The appearance and rapid development of archaeogenetics now allows the personal identification of the royal skeletons from among the remains of the Basilica. The genetic information necessary for the identification of the Árpád dynasty members is accessible, while sequence data of the non-Árpádian kings’ relatives still need to be obtained by further genetic analysis. Here we provide an outline of the investigation for the identity of the royal skeletons: we sketch the process of sample preparation and DNA extraction, the steps of library preparation for next-generation sequencing (NGS) and give a brief report of the current progressions.

The applications of next-generation sequencing (NGS) in drug development for cancer therapy

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Cancer Therapy ◽  
Target Identification ◽  
Rapid Development ◽  
Next Generation ◽  
Biomedical Sciences ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

scholarly journals Pharmacogenomics in Children: Advantages and Challenges of Next Generation Sequencing Applications

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
O. M. Vanakker ◽  
A. De Paepe
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Next Generation ◽  
Clinical Implementation ◽  
Ethical Aspects ◽  
Number Of Genes ◽  
Working Groups ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Single Reaction

Pharmacogenetics is considered as a prime example of how personalized medicine nowadays can be put into practice. However, genotyping to guide pharmacological treatment is relatively uncommon in the routine clinical practice. Several reasons can be found why the application of pharmacogenetics is less than initially anticipated, which include the contradictory results obtained for certain variants and the lack of guidelines for clinical implementation. However, more reproducible results are being generated, and efforts have been made to establish working groups focussing on evidence-based clinical guidelines. For another pharmacogenetic hurdle, the speed by which a pharmacogenetic profile for a certain drug can be obtained in an individual patient, there has been a revolution in molecular genetics through the introduction of next generation sequencing (NGS), making it possible to sequence a large number of genes up to the complete genome in a single reaction. Besides the enthusiasm due to the tremendous increase of our sequencing capacities, several considerations need to be made regarding quality and interpretation of the sequence data as well as ethical aspects of this technology. This paper will focus on the different NGS applications that may be useful for pharmacogenomics in children and the challenges that they bring on.

scholarly journals Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Biology ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 295
Author(s):  
Girum Fitihamlak Ejigu ◽  
Jaehee Jung
Keyword(s):  
Next Generation Sequencing ◽  
Genome Annotation ◽  
Sequence Data ◽  
Genetic Disorders ◽  
Next Generation ◽  
Functional Annotations ◽  
General Aspects ◽  
Tools And Techniques ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.

scholarly journals Case Report: Effectiveness of Targeted Treatment in a Patient With Pancreatic Cancer Harboring PALB2 Germline Mutation and KRAS Somatic Mutation

2022 ◽  
Vol 8 ◽  
Author(s):  
Wei Wu ◽  
Yu Liu ◽  
Yuzhi Jin ◽  
Lulu Liu ◽  
Yixuan Guo ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Next Generation Sequencing ◽  
Somatic Mutation ◽  
Germline Mutation ◽  
Tissue Sample ◽  
Rapid Development ◽  
Parp Inhibitor ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Pancreatic cancer is one of the most leading causes of cancer death worldwide. The rapid development of next-generation sequencing (NGS) and precision medicine promote us to seek potential targets for the treatment of pancreatic cancer. Here, we report a female pancreatic cancer patient who underwent radical surgical excision after neoadjuvant chemotherapy. After the surgery, the patient underwent gemcitabine + S-1 therapy, capecitabine + albumin paclitaxel therapy and irinotecan therapy successively, however, MRI review revealed tumor progression. The surgical tissue sample was subjected to next-generation sequencing (NGS), and PALB2 germline mutation and KRAS somatic mutation were identified. The patient then received olaparib (a PARP inhibitor) + irinotecan and the disease stabilized for one year. Due to the increased CA19-9, treatment of the patient with a combination of trametinib (a MEK inhibitor) and hydroxychloroquine resulted in stable disease (SD) with a significant decrease of CA19-9. This case demonstrated that the NGS may be a reliable method for finding potential therapeutic targets for pancreatic cancer.

scholarly journals SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat

2016 ◽  
Vol 2016 ◽  
pp. 1-10
Author(s):  
Zhong-Xu Chen ◽  
Mei Deng ◽  
Ji-Rui Wang
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Low Cost ◽  
Functional Genes ◽  
Accurate Information ◽  
Next Generation ◽  
Polynomial Fitting ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

As plenty of nonmodel plants are without genomic sequences, the combination of molecular technologies and the next generation sequencing (NGS) platform has led to a new approach to study the genetic variations of these plants. Software GATK, SOAPsnp, samtools, and others are often used to deal with the NGS data. In this study, BLAST was applied to call SNPs from 16 mixed functional gene’s sequence data of polyploidy wheat. In total 1.2 million reads were obtained with the average of 7500 reads per genes. To get accurate information, 390,992 pair reads were successfully assembled before aligning to those functional genes. Standalone BLAST tools were used to map assembled sequence to functional genes, respectively. Polynomial fitting was applied to find the suitable minor allele frequency (MAF) threshold at 6% for assembled reads of each functional gene. SNPs accuracy form assembled reads, pretrimmed reads, and original reads were compared, which declared that SNPs mined from the assembled reads were more reliable than others. It was also demonstrated that mixed samples’ NGS sequences and then analysis by BLAST were an effective, low-cost, and accurate way to mine SNPs for nonmodel species. Assembled reads and polynomial fitting threshold were recommended for more accurate SNPs target.

scholarly journals Next-generation sequencing technologies: breaking the sound barrier of human genetics

Mutagenesis ◽  
2014 ◽  
Vol 29 (5) ◽  
pp. 303-310 ◽  
Author(s):  
El Mustapha Bahassi ◽  
Peter J. Stambrook
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Biological Networks ◽  
New Technologies ◽  
Sequence Data ◽  
Rapid Development ◽  
Relevant Information ◽  
Model Organisms ◽  
Next Generation ◽  
Generation Sequencing

Abstract Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of advances in next-generation sequencing (NGS). The generation of large volumes of sequence data and the speed of data acquisition are the primary advantages over previous, more standard methods. In 2013, the Food and Drug Administration granted marketing authorisation for the first high-throughput NG sequencer, Illumina’s MiSeqDx, which allowed the development and use of a large number of new genome-based tests. Here, we present a review of template preparation, nucleic acid sequencing and imaging, genome assembly and alignment approaches as well as recent advances in current and near-term commercially available NGS instruments. We also outline the broad range of applications for NGS technologies and provide guidelines for platform selection to best address biological questions of interest. DNA sequencing has revolutionised biological and medical research, and is poised to have a similar impact on the practice of medicine. This tool is but one of an increasing arsenal of developing tools that enhance our capabilities to identify, quantify and functionally characterise the components of biological networks that keep us healthy or make us sick. Despite advances in other ‘omic’ technologies, DNA sequencing and analysis, in many respects, have played the leading role to date. The new technologies provide a bridge between genotype and phenotype, both in man and model organisms, and have revolutionised how risk of developing a complex human disease may be assessed. The generation of large DNA sequence data sets is producing a wealth of medically relevant information on a large number of individuals and populations that will potentially form the basis of truly individualised medical care in the future.

scholarly journals Can Genomics Remove Uncertainty from Adoption? Social Workers’ and Medical Advisors’ Accounts of Genetic Testing

2021 ◽  
Author(s):  
Michael Arribas-Ayllon ◽  
Katherine Shelton ◽  
Angus Clarke
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Social Workers ◽  
Genetic Information ◽  
Medical Professionals ◽  
High Quality ◽  
Genome Wide ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Wide Testing

Abstract Genetic testing is controversial in adoption with professionals taking different positions on whether children should be protected from genetic information or whether it can be used to assist adoption. In this article, we argue that advances in ‘genome-wide’ testing add further complications to these debates. Although next-generation sequencing (NGS) and microarray-based technologies can offer high-quality molecular diagnoses for a variety of conditions, they also increase the burden of interpretation. For these reasons, adoption professionals will need to understand the relevance and complexity of biomedical information. Our study explores the accounts of social workers’ and medical advisors’ knowledge and reasoning about genetic testing in adoption. Twenty participants, including social workers, managers, medical advisors and paediatricians, were recruited from adoption services in England and Wales. A key finding revealed that medical professionals reported increasing pressure to test children prior to adoption, whilst social workers justified testing on the basis that it reduced uncertainty and therefore assisted adoption. Professionals’ accounts of genetic testing suggest that social workers may not be aware of the potential indeterminacy of microarray and NGS technologies. This has important implications for adoption because increases in genomic uncertainty can stigmatise children and disadvantage their prospects for adoption.

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