New Generation Of Sequencing Technologies Research Articles

The Emerging Landscape and Application of Protein Sequencing

Proteins play an indispensable role in all cells and tissues in all living creatures especially the human body. To determine the protein primary structure, also known as protein sequencing, is an important subject in life science and medicine. Scientists have tried chemical reactions such as Edman degradation, as well as instrument analysis like mass spectrometry. These mainstream methods can effectively determine the sequence of protein and are widely used. On the other hand, the new method like nanopore sequencing shows the single molecule level sequencing sensitivity and has great emerging landscape. The development of protein sequencing technology will help people better understand the laws of life activities and achieve early diagnosis and precise treatment of diseases. This paper will briefly summarize the traditional protein sequencing methods, focus on the introduction of the new generation of sequencing technology represented by nanopore sequencing. Meanwhile, after comparing those advantages and disadvantages, its future research direction could be found. More cheap, high-throughput and highly sensitive protein sequencing methods and instruments will be discovered and popularized in the near future.

Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2.

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short-read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the rolling circle to concatemeric consensus (R2C2) method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, and regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.

Big Data and its Future in Computational Biology: A Literature Review

Big data technologies are used majorly for computational biology research nowadays due to the emerge of massive amounts of biological data that have been generated and collected at an unprecedented speed and scale and with different structures. As an example, the processing of billions of DNA sequence data per day represents the new generation of sequencing technologies. It is expected that the cost of acquiring and analyzing biomedical data will decrease with the assistance of technology upgrades in the computational biology field. The application of big data in health care is a fast-growing field, with many new discoveries and methodologies. In this study, an overview of recent developments and technologies in big data in the computational biology field. Moreover, in this study, we summarize and highlight the challenges, gaps and opportunities to improve and advance big data applications in computational biology. Also, this review presents a useful starting point for the application of Big Data in future Bioinformatics research. Finally, some of the Big Data sources in computational biology that help in applying these new emerging technologies are mentioned.

Advances in molecular genetics of intelligence disability or developmental delay

Intelligence disorder or developmental delay is the defect of cognitive function and social adaptation function as the main clinical features, two-thirds of the etiology is unknown.Clinical manifestations, high morbidity, and low treatment outcome are the major challenge for us.In recent years, with the application of the new generation of sequencing technology, We have gained further understanding of the etiology and pathogenesis of intelligent disorder or developmental delay.It has been found that multiple copies of chromosomal copies can lead to it.This paper summarizes the clinical, imaging and etiology of intelligent disorder or developmental delay, especially the recent advances in molecular genetics. Key words: Developmental delay; Etiology; Mutation

Whole Genome Sequencing Progress in Medical Application

At present, there are still a lot of diseases pathogenesis not clear, but making use of a new generation of sequencing technology to organisms conduct whole genome sequencing, which for the pathogenesis of many diseases provide a new theoretical basis. So, Which aspects the whole genome sequencing in medical use? In this article, I got through reading the whole genome sequencing of research papers about abroad nearly five years finding that the whole genome sequencing could be widely used in genetic disease, tumor, infectious diseases, infectious epidemic, judge the individual susceptibility to disease, the diagnosis and treatment of a variety of diseases such as biological evolution. This paper reviewed the whole genome sequencing progress in medical application from a genetic disease, tumor, infectious diseases, infectious epidemic, determine the individual susceptibility and biological evolution.

Next-generation resequencing the complete mitochondrial genome of Japanese quail (Coturnix japonica)

As the development of the new generation of sequencing (NGS) technologies, it has been used for standard sequencing applications more and more popular. We used NGS technologies to resequence the complete mitochondrial genome of Japanese quail. The complete mitochondrial genome of Japanese quail is a 16,668 bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, 2 rRNAs, and 22 tRNAs) and a 1156 bp D-loop. Its gene arrangement pattern is identical with typical other Galliformes. All protein-coding genes start with an ATG codon except COI, which start with GTG. TAA is the most frequent stop codon, although ND2 end with TAG, and COI and ND6 end with AGG, COIII and ND4 end with TGC. The mtDNA sequence contains 12S rRNA and 16S rRNA of rRNA. Except for tRNASer(AGY) and tRNALeu(CUN) without the dihydrouridine (DHU) arm, all tRNAs could be folded into canonical cloverleaf secondary structures. Coturnix japonica has close relative with C. chinensis.

Big Data Application in Biomedical Research and Health Care: A Literature Review.

Big data technologies are increasingly used for biomedical and health-care informatics research. Large amounts of biological and clinical data have been generated and collected at an unprecedented speed and scale. For example, the new generation of sequencing technologies enables the processing of billions of DNA sequence data per day, and the application of electronic health records (EHRs) is documenting large amounts of patient data. The cost of acquiring and analyzing biomedical data is expected to decrease dramatically with the help of technology upgrades, such as the emergence of new sequencing machines, the development of novel hardware and software for parallel computing, and the extensive expansion of EHRs. Big data applications present new opportunities to discover new knowledge and create novel methods to improve the quality of health care. The application of big data in health care is a fast-growing field, with many new discoveries and methodologies published in the last five years. In this paper, we review and discuss big data application in four major biomedical subdisciplines: (1) bioinformatics, (2) clinical informatics, (3) imaging informatics, and (4) public health informatics. Specifically, in bioinformatics, high-throughput experiments facilitate the research of new genome-wide association studies of diseases, and with clinical informatics, the clinical field benefits from the vast amount of collected patient data for making intelligent decisions. Imaging informatics is now more rapidly integrated with cloud platforms to share medical image data and workflows, and public health informatics leverages big data techniques for predicting and monitoring infectious disease outbreaks, such as Ebola. In this paper, we review the recent progress and breakthroughs of big data applications in these health-care domains and summarize the challenges, gaps, and opportunities to improve and advance big data applications in health care.

Prenatal screening for Down’s syndrome: recent progress

Down's syndrome is an autosomal disease and its prenatal screening is particularly important.In recent years, clinical application of serological screening markers has been widely used,which improved the detection rate of Down's syndrome,but still remained at about 60%.The new generation of sequencing technology for direct analysis of nucleic acids, which can be used for fetal chromosomal aneuploidy detection,can detect Down's syndrome more accurately.In this paper,we compared the prenatal screening methods for Down's syndrome in recent decades,and reviewed the new screening markers based on proteomics and bioinformatics technology for clinical application.

Detección de mutaciones de resistencia en ADN proviral en infección por VIH-1

Analysis of proviral DNA in HIV infection may have useful applications if techniques that are sufficiently sensitive to detect minor variants, such as single genome sequencing (SGS), are used. This technology, which is performed in DNA from whole blood, improves determination of co-receptor tropism and the detection of both circulating and archived resistance mutations (RM) that are undetectable in plasma. Many of these RM have clinical relevance and their identification could be useful in specific situations, such as the start of antiretroviral therapy to exclude the transmission of resistant strains, as information to be weighed in simplification strategies in patients with undetectable viral loads, and in antiretroviralexperienced patients with limited availability of clinical reports. Clonal analysis using SGS has yielded useful information on the pathogenesis and diagnosis of HIV-1 infection but, in its current design, is inappropriate for the clinical laboratory. The new generation of sequencing technology, which allows the simultaneous analysis of a large number of sequences, has begun to be applied in the analysis of the diversity of plasma HIV-1. The use of these highly sensitive, automated techniques in the analysis of HIV-1 cellular reservoirs will potentially allow all variants recorded during the history of the disease to become available. This information would be highly useful for the clinical management of HIV-1 infection at the individual and population level.

New insights into the diagnosis of lymphomas

The current diagnosis of lymphoid neoplasias is based on the criteria of the World Health Organization (WHO) classification. This framework is built on two major principles: the stratification of neoplasms according to their derivation from precursor or mature cells and the definition of clinically relevant nonoverlapping diseases. The diagnosis is established by integrating the clinical, morphological, phenotypic, genetic and molecular characteristics of the tumors. This approach is reproducible, clinically relevant and scientifically sound. The elucidation of the human genome a decade ago and the development of high-throughput technologies have opened the possibility to search for comprehensive views of the genomic alterations of the tumors that are starting to influence our current approach to diagnosis. The new generation of sequencing technologies and their systematic application to human cancer and in particular to lymphoid neoplasms are revealing a landscape of somatic mutations of unprecedented complexity. These studies have already provided a number of important findings with functional and clinical implications. The translation of all this knowledge into the clinic is challenging and offers relevant perspectives.

Key Principles and Clinical Applications of “Next-Generation” DNA Sequencing

Demand for fast, inexpensive, and accurate DNA sequencing data has led to the birth and dominance of a new generation of sequencing technologies. So-called "next-generation" sequencing technologies enable rapid generation of data by sequencing massive amounts of DNA in parallel using diverse methodologies which overcome the limitations of Sanger sequencing methods used to sequence the first human genome. Despite opening new frontiers of genomics research, the fundamental shift away from the Sanger sequencing that next-generation technologies has created has also left many unaware of the capabilities and applications of these new technologies, especially those in the clinical realm. Moreover, the brisk evolution of sequencing technologies has flooded the market with commercially available sequencing platforms, whose unique chemistries and diverse applications stand as another obstacle restricting the potential of next-generation sequencing. This review serves to provide a primer on next-generation sequencing technologies for clinical researchers and physician scientists. We provide an overview of the capabilities and clinical applications of DNA sequencing technologies to raise awareness among researchers about the power of these novel genomic tools. In addition, we discuss that key sequencing principles provide a comparison between existing and near-term technologies and outline key advantages and disadvantages between different sequencing platforms to help researchers choose an appropriate platform for their research interests.

Abstract 4967: Array-based genomic resequencing of acute myeloid leukemia

Abstract Somatic mutations within cancer-related genes play a central role in the pathogenesis of many human malignancies, as clearly demonstrated for the cases with mutated RAS and EGFR. Although a new generation of sequencing technologies is now available, whole-genome resequencing of many samples remains a demanding task. DNA microarray-based sequencing is suitable for analysis of multiple samples. However, currently available platforms are limited in the number of nucleotides that each array is able to probe. To overcome such limitations, we have now developed extra-large DNA arrays (“wafers”) for resequencing the human genome, in a collaborative study with Perlegen Sciences, Inc. With its capacity to assay ∼9 Mbp, we could place, on the array, oligonucleotides to interrogate sequence alterations at protein-coding exons and exon-intron boundaries for 5648 human genes that are possibly involved in malignant transformation mechanism. To identify transforming mutations in acute myeloid leukemia (AML), hybridization of genomic DNA from CD34-positive blasts of AML (n = 19) or myeloproliferative disorder (MPD) (n = 1) to the arrays revealed a total of 9148 nonsynonymous nucleotide changes on 3403 independent genes in this cohort (Phase I). To discriminate somatic changes from germ-line polymorphisms, we developed a second array for a direct analysis of the 9148 nucleotide changes, which was hybridized with genomic DNA from the leukemic blasts as well as with that from CD4-positive T cell fractions (paired controls) from the same cohort (Phase II). Analysis of CD4-positive fractions revealed that most of these nucleotide changes in Phase I were also present in the paired control genome, leaving only 11 somatic, nonsynonymous mutations among 11 genes. One of these somatic changes results in a Met-to-Ile substitution at amino-acid position 511 of Janus kinase 3 (JAK3), and the JAK3(M511I) protein exhibited transforming potential both in vitro and in vivo. Further screening for JAK3 mutations showed novel and known transforming changes in 9 out of 286 cases with leukemia. Our experiments also showed a somatic change responsible for the Arg-to-His substitution at amino-acid position 882 of DNA methyltransferase 3A, which results in a loss of >50% of the catalytic activity. Our data have thus revealed a unique profile of gene mutations in human leukemias. Given that only a small number of sequence alterations were proved to be “somatic” after Phase II selection, it would be important to use appropriate paired control samples in the search for somatic mutations in the cancer genome. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4967. doi:10.1158/1538-7445.AM2011-4967

What Lies in the Future of Tea Science in the Era of Genomics?

Human being has been using tea as a beverage for thousands of years. Chinese tea is made of dried leaves from tea plants ( Camellia sinensis (L.) Kuntze ), while the British tea, which is called herbal tea, is a mixture of dried herbs from a variety of plants. Countless plants are used to make tea, but do the active compounds in these plants serve the same functions as typical tea leaves do? In fact, it is not yet known what exactly a cup of herbal tea contains. With the development of biotechnology and the arrival of the era of genomics, what lies in the path in the future development of tea science? In this paper, the author would like to propose some directions as the following: 1) the exploration at molecular level of what is inside a tea bag; 2) the study of a typical tea plant ( Camellia sinensis ) as a model plant for tea study; 3) Tea-nomics study based on new-generation of sequencing technology; 4) comparative metabolomics studies on biologically active compounds in tea; 5) identification based on pharmacology and toxicology. With the advent of the genomics era, the mysteries in tea bags will slowly be deciphered; whether it is Chinese tea or English tea, tea will still be the most popular drink.

The “What If Challenge of Plant Genomics” 2010

The Plant GenomeVolume 3, Issue 2 EditorialOpen Access The “What If Challenge of Plant Genomics” 2010 First published: 01 September 2010 https://doi.org/10.3835/plantgenome2010.06.0002ed All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Welcome to the second 2010 issue of The Plant Genome. For this editorial, I am going to rejuvenate what I called the “What If Challenge of Plant Genomics” that ran in 2009. This is timely because over two years have passed since this challenge was initiated and as predicted remarkable advances in sequencing technology have been achieved that have accelerated all aspects of plant genomics. What I wrote in the 2009 issue still stands. We all know that genomics is in an era of accelerating sequence data acquisition and analysis. Many of us remember when sequencing a single 2 or 3 kb of DNA was a major, costly undertaking including both the lab work and data analysis. The establishment of sequencing centers accompanying the paradigm shift brought about by the automated sequencers made single gene and small genome sequencing easily feasible resulting in the complete sequencing of the Arabidopsis and rice genomes in 2000 and 2005, respectively, and many other crops are following suit. More recently, we have experienced another jump in sequencing productivity from a new generation of sequencing technologies that dovetails nicely with standard sequencing closing in on the NIH sponsored target of the $1000 genome. This revolution in sequencing represents a reduction from $10.00 to a few cents per finished bp in less than 20 years (Service, 2006). While this is incredible progress, there are indications that a next generation of technologies promise to cheaply sequence multiple gigabase runs in just hours. Accompanied with the requisite data analysis advances, these technologies promise to again shift our genome sequencing paradigm making it feasible to sequence the large genomes of most crop plants rapidly and at low cost. Without promoting any particular technical approach or company involved in these next generation sequencing technologies, these advances are beginning to be implemented. As I stated in my previous editorial on this topic, it is a wonderful time to be a plant genomics researcher but… are we ready for this next paradigm shift in sequencing? The “What If Challenge of Plant Genomics”—because it now seems likely that sequencing a crop genome for under $1000 will become a reality sooner than later, it is important that the plant genomics community is prepared to benefit. For our next issues of The Plant Genome, an open forum series of short “Vision” articles will be invited that address how ultra high throughput genome sequencing will impact plant breeding, functional genomics, systems biology, and related fields. To ensure that “The What if Challenge” reviews are not obsolesced due to further advances in sequencing technology before they are published, I am setting the costs of sequencing a typical crop genome at $1, three orders of magnitude lower than the $1000 target. For the purpose of the intellectual exercise that “Challenge” represents, this makes sequence capacity and acquisition unlimited. Authors will be “challenged” to forecast the impacts on crop improvement, biology, and how we will do research, all towards closing the gap in knowledge between the genotype and phenotype. For articles to be featured in the next issue, authors will be invited, but in the spirit of the open source world we are interested in a diversity of visions and opinions. If you are interested in submitting an article, please send your proposed topic to [email protected]. Sincerely, Dr. David A. Somers Editor, The Plant Genome References Service, R.F.. 2006. Gene sequencing: The race for the $1000 genome. Science 17 Mar. 2006, 311: 1544– 1546.10.1126/science.311.5767.1544. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000236029500014&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4 Volume3, Issue2September 2010 ReferencesRelatedInformation

De novo assembly of short sequence reads

A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a perceived limitation of these ultra-high-throughput technologies is their short read-lengths. De novo assembly of sequence reads generated by classical Sanger capillary sequencing is a mature field of research. Unfortunately, the existing sequence assembly programs were not effective for short sequence reads generated by Illumina and SOLiD platforms. Early studies suggested that, in principle, sequence reads as short as 20-30 nucleotides could be used to generate useful assemblies of both prokaryotic and eukaryotic genome sequences, albeit containing many gaps. The early feasibility studies and proofs of principle inspired several bioinformatics research groups to implement new algorithms as freely available software tools specifically aimed at assembling reads of 30-50 nucleotides in length. This has led to the generation of several draft genome sequences based exclusively on short sequence Illumina sequence reads, recently culminating in the assembly of the 2.25-Gb genome of the giant panda from Illumina sequence reads with an average length of just 52 nucleotides. As well as reviewing recent developments in the field, we discuss some practical aspects such as data filtering and submission of assembly data to public repositories.

Functional analysis of novel SNPs and mutations in human and mouse genomes

BackgroundWith the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating.ResultsFANS harnesses the power of public information databases and powerful tools from six well established websites to enhance the efficiency of analysis of novel variations. FANS can process any point change in any coding region or GT-AG splice site to provide a clear picture of the disease risk of a prioritized variation by classifying splicing and functional alterations into one of nine risk subtypes with five risk levels.ConclusionFANS significantly simplifies the analysis operations to a four-step procedure while still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize the variations and select the ones with most functional impact for validation. Additionally, the program offers a distinct improvement in efficiency over manual operations in our benchmark test.