Review on the Computational Genome Annotation of Sequences Obtained by Next-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.

Download Full-text

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

International Journal of Pediatrics ◽

10.1155/2013/136524 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 4

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.

Download Full-text

Guidelines for diagnostic next-generation sequencing

European Journal of Human Genetics ◽

10.1038/ejhg.2015.226 ◽

2015 ◽

Vol 24 (1) ◽

pp. 2-5 ◽

Cited By ~ 209

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.

Download Full-text

Problems of unknown significance: Counseling in the era of next generation sequencing

Balkan Journal of Medical Genetics ◽

10.2478/bjmg-2018-0003 ◽

2018 ◽

Vol 21 (1) ◽

pp. 73-76 ◽

Cited By ~ 2

Author(s):

U Fahrioğlu

Keyword(s):

Next Generation Sequencing ◽

Genetic Disorders ◽

New Technology ◽

Cost Effective ◽

Next Generation ◽

Effective Manner ◽

Unknown Significance ◽

Technical Issues ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Dear Editor Next generation sequencing (NGS) has changed the way we approach the diagnosis, prognosis and treatment of genetic disorders. It gave us base pair (bp) precision, multi-gene approach that can be executed in a timely and cost-effective manner. Despite some minor technical issues in NGS, it comes with great advantages. However, the clinical, and especially, genetic counseling profession will need to rise to the challenge to face some of the new issues, dilemmas and problems this new technology is bringing to the table. Some of the counseling guidelines predate the NGS era and will urgently need to be brought up to par with the technology.

Download Full-text

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

BioMed Research International ◽

10.1155/2016/3524908 ◽

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.

Download Full-text