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Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, Sutton VR, Beaudet AL, Muzny D, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, Plon SE. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med 2016; 18:678-85. [PMID: 26633545 PMCID: PMC4892996 DOI: 10.1038/gim.2015.142] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 08/31/2015] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults. METHODS We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. RESULTS Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18-30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. CONCLUSION Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678-685.
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Affiliation(s)
- Jennifer E. Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jill A. Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Regis A. James
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX
| | - Matthew Bainbridge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Zhiyv Niu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Xia Wang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Shweta Dhar
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Wojciech Wiszniewski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Zeynep H.C. Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Fan Xia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Richard E. Person
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Magdalena Walkiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Chad A. Shaw
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - V. Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Arthur L. Beaudet
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
| | - Donna Muzny
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children’s Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Human Genetics Center, University of Texas Health Science Center, Houston, TX
| | - Sharon E. Plon
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children’s Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX
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202
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Chaitankar V, Karakülah G, Ratnapriya R, Giuste FO, Brooks MJ, Swaroop A. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res 2016; 55:1-31. [PMID: 27297499 DOI: 10.1016/j.preteyeres.2016.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.
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Affiliation(s)
- Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Felipe O Giuste
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
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203
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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204
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Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E. Recommendations on e-infrastructures for next-generation sequencing. Gigascience 2016; 5:26. [PMID: 27267963 PMCID: PMC4897895 DOI: 10.1186/s13742-016-0132-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/23/2016] [Indexed: 11/21/2022] Open
Abstract
With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations based on the collective experiences from participants in the EU COST Action SeqAhead for the tasks of data preprocessing, upstream processing, data delivery, and downstream analysis, as well as long-term storage and archiving. We cover demands on computational and storage resources, networks, software stacks, automation of analysis, education, and also discuss emerging trends in the field. E-infrastructures for NGS require substantial effort to set up and maintain over time, and with sequencing technologies and best practices for data analysis evolving rapidly it is important to prioritize both processing capacity and e-infrastructure flexibility when making strategic decisions to support the data analysis demands of tomorrow. Due to increasingly demanding technical requirements we recommend that e-infrastructure development and maintenance be handled by a professional service unit, be it internal or external to the organization, and emphasis should be placed on collaboration between researchers and IT professionals.
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Affiliation(s)
- Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, P.O. Box 591, SE-75124, Sweden.
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Dahlberg
- National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Stockholm, P.O. Box 1031, SE-17121, Sweden
| | - Martin Dahlö
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, P.O. Box 591, SE-75124, Sweden.,Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, SE-75123, Sweden
| | - Aleksi Kallio
- CSC - IT Center for Science Ltd., Espoo, P.O. Box 405, FI-02101, Finland
| | - Luca Pireddu
- CRS4, Polaris, Loc. Piscina Manna Ed. 1, Pula, 09010, Italy.,University of Cagliari, Cagliari, 09124, Italy
| | - Francesco Vezzi
- Science for Life Laboratory, Stockholm University, Stockholm, SE-17121, Sweden
| | - Eija Korpelainen
- CSC - IT Center for Science Ltd., Espoo, P.O. Box 405, FI-02101, Finland
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205
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Draft Genome Sequence of Bacillus cereus 905, a Plant Growth-Promoting Rhizobacterium of Wheat. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00489-16. [PMID: 27257205 PMCID: PMC4891651 DOI: 10.1128/genomea.00489-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus cereus 905 is a plant growth-promoting rhizobacterium, isolated from wheat rhizosphere. The draft genome sequence of this strain is 5.39 Mb and harbors 5,412 coding sequences.
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206
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Marian AJ. Genetic Causality in Complex Traits: The Case of Uric Acid. J Am Coll Cardiol 2016; 67:417-419. [PMID: 26821630 DOI: 10.1016/j.jacc.2015.09.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/29/2015] [Indexed: 12/09/2022]
Affiliation(s)
- A J Marian
- Center for Cardiovascular Genetics, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center and Texas Heart Institute, Houston, Texas.
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207
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Lupski JR. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 2016; 135:591-601. [PMID: 27221143 DOI: 10.1007/s00439-016-1682-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 12/23/2022]
Abstract
The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 604B, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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208
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The A, C, G, and T of Genome Assembly. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6329217. [PMID: 27247941 PMCID: PMC4877455 DOI: 10.1155/2016/6329217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022]
Abstract
Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.
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209
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Lee YS, Kim BH, Kim BC, Shin A, Kim JS, Hong SH, Hwang JA, Lee JA, Nam S, Lee SH, Bhak J, Park JW. SLC15A2 genomic variation is associated with the extraordinary response of sorafenib treatment: whole-genome analysis in patients with hepatocellular carcinoma. Oncotarget 2016; 6:16449-60. [PMID: 25965825 PMCID: PMC4599281 DOI: 10.18632/oncotarget.3758] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/10/2015] [Indexed: 12/13/2022] Open
Abstract
Reliable biomarkers are required to predict the response to sorafenib. We investigated genomic variations associated with responsiveness to sorafenib for patients with unresectable hepatocellular carcinoma (HCC). Blood samples from 2 extreme, 2 strong and 3 poor responders to sorafenib were subjected to whole-genome analysis. Then, we validated candidate genomic variations with another 174 HCC patients, and performed in vitro functional analysis and in silico analyses. Genomic data of >96 gigabases/sample was generated at average of ~34X sequencing depth. In total, 1813 genomic variations were matched to sorafenib responses in clinical data; 708 were located within regions for sorafenib-target genes or drug absorption, distribution, metabolism, and excretion (ADME)-related genes. From them, 36 variants were within the coding regions and 6 identified as non-synonymous single-nucleotide variants from 4 ADME-related genes (ABCB1, FMO3, MUSK, and SLC15A2). Validation genotyping confirmed sequencing results and revealed patients genotype for rs2257212 in SLC15A2 showed longer progression-free survival (HR = 2.18). In vitro study displayed different response to sorafenib depending on the genotype of SLC15A2. Structural prediction analysis revealed changes of the phosphorylation levels in protein, potentially affecting sorafenib-associated enzymatic activity. Our finding using extreme responder seems to generate robust biomarker to predict the response of sorafenib treatment for HCC.
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Affiliation(s)
- Yeon-Su Lee
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Bo Hyun Kim
- Center for Liver Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Byung Chul Kim
- The Genomics Institute, Biomedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Aesun Shin
- Molecular Epidemiology Branch, National Cancer Center, Goyang, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin Sook Kim
- Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
| | - Seung-Hyun Hong
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Jung-Ah Hwang
- Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Jung Ahn Lee
- Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
| | - Seungyoon Nam
- New Experimental Therapeutics Branch, National Cancer Center, Goyang, Republic of Korea
| | - Sung Hoon Lee
- Personal Genomics Institute, Genome Research Foundation, TheragenEtex, Suwon, Republic of Korea.,Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea
| | - Jong Bhak
- The Genomics Institute, Biomedical Engineering, UNIST, Ulsan, Republic of Korea.,Personal Genomics Institute, Genome Research Foundation, TheragenEtex, Suwon, Republic of Korea
| | - Joong-Won Park
- Center for Liver Cancer, National Cancer Center, Goyang, Republic of Korea.,Liver and Pancreatobiliary Cancer Branch, National Cancer Center, Goyang, Republic of Korea
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210
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Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine. Pharmaceutics 2016; 8:E15. [PMID: 27110816 PMCID: PMC4932478 DOI: 10.3390/pharmaceutics8020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.
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Affiliation(s)
- Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Leihong Wu
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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211
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A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nat Commun 2016; 7:11101. [PMID: 27089393 PMCID: PMC4837449 DOI: 10.1038/ncomms11101] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring 'allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable 'allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org).
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212
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Li J, Batcha AMN, Grüning B, Mansmann UR. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology. Cancer Inform 2016; 14:87-107. [PMID: 27081306 PMCID: PMC4827795 DOI: 10.4137/cin.s30793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.
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Affiliation(s)
- Jian Li
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aarif Mohamed Nazeer Batcha
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.; Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
| | - Ulrich R Mansmann
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany
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213
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214
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215
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Linderman MD, Nielsen DE, Green RC. Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium. J Pers Med 2016; 6:E14. [PMID: 27023617 PMCID: PMC4932461 DOI: 10.3390/jpm6020014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Thousands of ostensibly healthy individuals have had their exome or genome sequenced, but a much smaller number of these individuals have received any personal genomic results from that sequencing. We term those projects in which ostensibly healthy participants can receive sequencing-derived genetic findings and may also have access to their genomic data as participatory predispositional personal genome sequencing (PPGS). Here we are focused on genome sequencing applied in a pre-symptomatic context and so define PPGS to exclude diagnostic genome sequencing intended to identify the molecular cause of suspected or diagnosed genetic disease. In this report we describe the design of completed and underway PPGS projects, briefly summarize the results reported to date and introduce the PeopleSeq Consortium, a newly formed collaboration of PPGS projects designed to collect much-needed longitudinal outcome data.
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Affiliation(s)
- Michael D Linderman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Daiva E Nielsen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Partners Personalized Medicine, Cambridge, MA 02139, USA.
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Sun X, Sui W, Wang X, Hou X, Ou M, Dai Y, Xiang Y. Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes. Mol Med Rep 2016; 13:3735-46. [PMID: 27035118 PMCID: PMC4838165 DOI: 10.3892/mmr.2016.5014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 01/21/2016] [Indexed: 12/20/2022] Open
Abstract
There is increasing evidence that several genes are associated with an increased risk of type 2 diabetes (T2D); genome-wide association investigations and whole-genome re-sequencing investigations offer a useful approach for the identification of genes involved in common human diseases. To further investigate which polymorphisms confer susceptibility to T2D, the present study screened for high-contribution susceptibility gene variants Chinese patients with T2D using whole-genome re-sequencing with DNA pooling. In total, 100 Chinese individuals with T2D and 100 healthy Chinese individuals were analyzed using whole-genome re-sequencing using DNA pooling. To minimize the likelihood of systematic bias in sampling, paired-end libraries with an insert size of 500 bp were prepared for in T2D in all samples, which were then subjected to whole-genome sequencing. Each library contained four lanes. The average sequencing depth was 35.70. In the present study, 1.36 GB of clean sequence data were generated, and the resulting calculated T2D genome consensus sequence covered 99.88% of the hg19 sequence. A total of 3,974,307 single nucleotide polymorphisms were identified, of which 99.88% were in the dbSNP database. The present study also found 642,189 insertions and deletions, 5,590 structure variants (SVs), 4,713 copy number variants (CNVs) and 13,049 single nucleotide variants. A total of 1,884 somatic CNVs and 74 somatic SVs were significantly different between the cases and controls. Therefore, the present study provided validation of whole-genome re-sequencing using the DNA pooling approach. It also generated a whole-genome re-sequencing genotype database for future investigations of T2D.
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Affiliation(s)
- Xiaojuan Sun
- Department of Social Medicine and Health Service Management, College of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Weiguo Sui
- Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Xiaobing Wang
- Department of Health Management Center, 181st Hospital, Guilin, Guangxi 541002, P.R. China
| | - Xianliang Hou
- Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yueying Xiang
- Department of Health Management Center, 181st Hospital, Guilin, Guangxi 541002, P.R. China
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217
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Zhang CZ, Pellman D. From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:117-37. [PMID: 26968629 DOI: 10.1101/sqb.2015.80.027623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analysis of mutations in thousands of cancer genomes has revealed many characteristic patterns of mutagenesis. The search for the molecular mechanisms underlying these mutational patterns has not only generated novel biological insight but also led to the development of new experimental strategies to study cell-to-cell variation and genome evolution. In this essay, we discuss recent progress in the study of mutational mechanisms with a particular emphasis on the analysis of mutagenesis at the single-cell level.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 Howard Hughes Medical Institute, Boston, Massachusetts 02115
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218
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De Paoli-Iseppi R, Johansson PA, Menzies AM, Dias KR, Pupo GM, Kakavand H, Wilmott JS, Mann GJ, Hayward NK, Dinger ME, Long GV, Scolyer RA. Comparison of whole-exome sequencing of matched fresh and formalin fixed paraffin embedded melanoma tumours: implications for clinical decision making. Pathology 2016; 48:261-6. [PMID: 27020503 DOI: 10.1016/j.pathol.2016.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 12/22/2015] [Accepted: 01/03/2016] [Indexed: 12/15/2022]
Abstract
The identification of recurrent driver mutations by whole-exome sequencing (WES) of fresh-frozen human cancers and the subsequent development of novel targeted therapies have recently transformed the treatment of many cancers including melanoma. In routine clinical practice, fresh-frozen tissue is rarely available and mutation testing usually needs to be carried out on archival formalin fixed, paraffin embedded (FFPE) tissue, from which DNA is typically fragmented, cross-linked and of lower quality. In this study we aimed to determine whether WES data generated from genomic DNA (gDNA) extracted from FFPE tissues can be produced reliably and of clinically-actionable standard. In this study of ten melanoma patients, we compared WES data produced from analysis of gDNA isolated from FFPE tumour tissue with that isolated from fresh-frozen tumour tissue from the same specimen. FFPE samples were sequenced using both Illumina's Nextera and NimbleGen SeqCap exome capture kits. To examine mutations between the two tissue sources and platforms, somatic mutations in the FFPE exomes were called using the matched fresh tissue sequence as a reference. Of the 10 FFPE DNA samples, seven Nextera and four SeqCap samples passed library preparation. On average, there were 5341 and 2246 variants lost in FFPE compared to matched fresh tissue utilising Nextera and SeqCap kits, respectively. In order to explore the feasibility of future clinical implementation of WES, FFPE variants in 27 genes of important clinical relevance in melanoma were assessed. The average concordance rate was 43.2% over a total of 1299 calls for the chosen genes in the FFPE DNA. For the current clinically most important melanoma mutations, 0/3 BRAF and 6/8 (75%) NRAS FFPE calls were concordant with the fresh tissue result, which was confirmed using a Sequenom OncoCarta Panel. The poor performance of FFPE WES indicates that specialised library construction to account for low quality DNA and further refinements will be necessary before this approach could be used for routine clinical decision making over currently preferred techniques.
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Affiliation(s)
| | - Peter A Johansson
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Kerith-Rae Dias
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Gulietta M Pupo
- Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia.
| | - Graham J Mann
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Medicine, Sydney Medical School, The University of Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, Australia; Discipline of Pathology, Sydney Medical School, The University of Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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Bermudez-Santana CI. APLICACIONES DE LA BIOINFORMÁTICA EN LA MEDICINA: EL GENOMA HUMANO. ¿CÓMO PODEMOS VER TANTO DETALLE? ACTA BIOLÓGICA COLOMBIANA 2016. [DOI: 10.15446/abc.v21n1supl.51233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p lang="es-ES" align="JUSTIFY">La bioinformática es un campo novedoso que soporta parte de la investigación biológica dirigida a la identificación de variantes génicas que pueden ser descubiertas desde los estudios de genomas completos. Basados en esta motivación se presenta el panorama general de los aportes principales de la bioinformática en el desarrollo del secuenciamiento del primer genoma humano. Adicionalmente se resumen los principales avances en cómputo desarrollados para responder a las demandas requeridas por los métodos de secuenciamiento de última generación para lograr re-secuenciar un genoma humano. Finalmente se introducen algunos de los nuevos retos que deben asumirse para aplicar la genómica personalizada en el desarrollo de la medicina. </p><p lang="es-ES" align="JUSTIFY"> </p><p lang="es-ES" align="JUSTIFY">Abstract</p><p lang="es-ES" align="JUSTIFY">Bioinformatics is a new field that supports part of the biological research aimed at identifying gene variants that can be discovered from studies of whole genomes. Based on this motivation the overview of the main contributions of bioinformatics in the development of sequencing the first human genome is presented. Additionally it is summarized the main advances in computing developed to meet the demands to re-sequence a human genome by using the next generation sequencing technologies. Finally some new challenges that must be faced to apply the personalized genomics into the medicine development are introduced.</p>
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220
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Gunawardena S, Karunaweera ND. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. Pathog Glob Health 2016; 109:123-41. [PMID: 25943157 DOI: 10.1179/2047773215y.0000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals.
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221
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Mapping and differential expression analysis from short-read RNA-Seq data in model organisms. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0060-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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222
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Jo H, Park M, Woo H, Han M, Kim B, Choi B, Chung K, Koo S. Application of whole‐exome sequencing for detecting copy number variants in CMT1A/HNPP. Clin Genet 2016; 90:177-81. [DOI: 10.1111/cge.12714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 11/26/2022]
Affiliation(s)
- H.‐Y. Jo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.‐H. Park
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - H.‐M. Woo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.H. Han
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐Y. Kim
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐O. Choi
- Department of Neurology, Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea
| | - K.W. Chung
- Department of Biological Sciences Kongju National University Gongju South Korea
| | - S.K. Koo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
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223
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de Leng WWJ, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FAS, Koudijs MJ, Nijman I, Hinrichs JWJ, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MHG, Sleijfer S, Willems SM, Lolkema MP. Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material. PLoS One 2016; 11:e0149405. [PMID: 26919633 PMCID: PMC4769293 DOI: 10.1371/journal.pone.0149405] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5% concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detection of low-frequency variants. The reliability of mutation analysis could be further improved with manual inspection of sequence data. Conclusion Targeted NGS can be reliably implemented in cancer diagnostics using both FFPE and FF tissue when using appropriate analysis settings, even with low input DNA.
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Affiliation(s)
- Wendy W. J. de Leng
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Christa G. Gadellaa-van Hooijdonk
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Françoise A. S. Barendregt-Smouter
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marco J. Koudijs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Ies Nijman
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - John W. J. Hinrichs
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stef van Lieshout
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Robert D. Loberg
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, 91320–1799, United States of America
| | - Maja de Jonge
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Emile E. Voest
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Roel A. de Weger
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Neeltje Steeghs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Marlies H. G. Langenberg
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stefan Sleijfer
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Martijn P. Lolkema
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
- * E-mail:
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224
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Salgado D, Desvignes JP, Rai G, Blanchard A, Miltgen M, Pinard A, Lévy N, Collod-Béroud G, Béroud C. UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution. Hum Mutat 2016; 37:439-46. [PMID: 26842889 PMCID: PMC5067603 DOI: 10.1002/humu.22965] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/11/2016] [Indexed: 01/18/2023]
Abstract
Whole‐exome sequencing (WES) is increasingly applied to research and clinical diagnosis of human diseases. It typically results in large amounts of genetic variations. Depending on the mode of inheritance, only one or two correspond to pathogenic mutations responsible for the disease and present in affected individuals. Therefore, it is crucial to filter out nonpathogenic variants and limit downstream analysis to a handful of candidate mutations. We have developed a new computational combinatorial system UMD‐Predictor (http://umd‐predictor.eu) to efficiently annotate cDNA substitutions of all human transcripts for their potential pathogenicity. It combines biochemical properties, impact on splicing signals, localization in protein domains, variation frequency in the global population, and conservation through the BLOSUM62 global substitution matrix and a protein‐specific conservation among 100 species. We compared its accuracy with the seven most used and reliable prediction tools, using the largest reference variation datasets including more than 140,000 annotated variations. This system consistently demonstrated a better accuracy, specificity, Matthews correlation coefficient, diagnostic odds ratio, speed, and provided the shortest list of candidate mutations for WES. Webservices allow its implementation in any bioinformatics pipeline for next‐generation sequencing analysis. It could benefit to a wide range of users and applications varying from gene discovery to clinical diagnosis.
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Affiliation(s)
- David Salgado
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Jean-Pierre Desvignes
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Ghadi Rai
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Arnaud Blanchard
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Morgane Miltgen
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Amélie Pinard
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Nicolas Lévy
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France.,APHM, Hôpital TIMONE Enfants, Laboratoire de Génétique Moléculaire, Marseille 13385, France
| | - Gwenaëlle Collod-Béroud
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France
| | - Christophe Béroud
- Aix-Marseille Université, GMGF, Marseille 13385, France.,Inserm, UMR_S 910, Marseille 13385, France.,APHM, Hôpital TIMONE Enfants, Laboratoire de Génétique Moléculaire, Marseille 13385, France
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225
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Chen T, Jia Y, Dong C, Gao J, Mak PI, Martins RP. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device. LAB ON A CHIP 2016; 16:743-752. [PMID: 26781669 DOI: 10.1039/c5lc01533b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis.
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Affiliation(s)
- Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
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Wajnberg G, Passetti F. Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery. Expert Opin Drug Discov 2016; 11:257-68. [PMID: 26787005 DOI: 10.1517/17460441.2016.1143813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION A cancer cell is a mosaic of genomic and epigenomic alterations. Distinct cancer molecular signatures can be observed depending on tumor type or patient genetic background. One type of genomic alteration is the insertion and/or deletion (INDEL) of nucleotides in the DNA sequence, which may vary in length, and may change the encoded protein or modify protein domains. INDELs are associated to a large number of diseases and their detection is done based on low-throughput techniques. However, high-throughput sequencing has also started to be used for detection of novel disease-causing INDELs. This search may identify novel drug targets. AREAS COVERED This review presents examples of using high-throughput sequencing (DNA-Seq and RNA-Seq) to investigate the incidence of INDELs in coding regions of human genes. Some of these examples successfully utilized RNA-Seq to identify INDELs associated to diseases. In addition, other studies have described small INDELs related to chemo-resistance or poor outcome of patients, while structural variants were associated with a better clinical outcome. EXPERT OPINION On average, there is twice as much RNA-Seq data available at the most used repositories for such data compared to DNA-Seq. Therefore, using RNA-Seq data is a promising strategy for studying cancer samples with unknown mechanisms of drug resistance, aiming at the discovery of proteins with potential as novel drug targets.
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Affiliation(s)
- Gabriel Wajnberg
- a Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , RJ , Brazil
| | - Fabio Passetti
- a Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , RJ , Brazil
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Growing Embossed Nanostructures of Polymer Brushes on Wet-Etched Silicon Templated via Block Copolymers. Sci Rep 2016; 6:20291. [PMID: 26841692 PMCID: PMC4740862 DOI: 10.1038/srep20291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/30/2015] [Indexed: 01/10/2023] Open
Abstract
Block copolymer nanolithography has attracted enormous interest in chip technologies, such as integrated silicon chips and biochips, due to its large-scale and mass production of uniform patterns. We further modified this technology to grow embossed nanodots, nanorods, and nanofingerprints of polymer brushes on silicon from their corresponding wet-etched nanostructures covered with pendent SiHx (X = 1–3) species. Atomic force microscopy (AFM) was used to image the topomorphologies, and multiple transmission-reflection infrared spectroscopy (MTR-IR) was used to monitor the surface molecular films in each step for the sequential stepwise reactions. In addition, two layers of polymethacrylic acid (PMAA) brush nanodots were observed, which were attributed to the circumferential convergence growth and the diffusion-limited growth of the polymer brushes. The pH response of PMAA nanodots in the same region was investigated by AFM from pH 3.0 to 9.0.
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228
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Di Ventra M, Taniguchi M. Decoding DNA, RNA and peptides with quantum tunnelling. NATURE NANOTECHNOLOGY 2016; 11:117-26. [PMID: 26839257 DOI: 10.1038/nnano.2015.320] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/07/2015] [Indexed: 05/25/2023]
Abstract
Drugs and treatments could be precisely tailored to an individual patient by extracting their cellular- and molecular-level information. For this approach to be feasible on a global scale, however, information on complete genomes (DNA), transcriptomes (RNA) and proteomes (all proteins) needs to be obtained quickly and at low cost. Quantum mechanical phenomena could potentially be of value here, because the biological information needs to be decoded at an atomic level and quantum tunnelling has recently been shown to be able to differentiate single nucleobases and amino acids in short sequences. Here, we review the different approaches to using quantum tunnelling for sequencing, highlighting the theoretical background to the method and the experimental capabilities demonstrated to date. We also explore the potential advantages of the approach and the technical challenges that must be addressed to deliver practical quantum sequencing devices.
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Affiliation(s)
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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229
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Marian AJ. Clinical applications of molecular genetic discoveries. Transl Res 2016; 168:6-14. [PMID: 26548329 PMCID: PMC4718781 DOI: 10.1016/j.trsl.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 01/08/2023]
Abstract
Genome-wide association studies of complex traits have mapped >15,000 common single nucleotide variants (SNVs). Likewise, applications of massively parallel nucleic acid sequencing technologies often referred to as next-generation sequencing to molecular genetic studies of complex traits have catalogued a large number of rare variants (population frequency of <0.01) in cases with complex traits. Moreover, high-throughput nucleic acid sequencing, variant burden analysis, and linkage studies are illuminating the presence of large number of SNVs in cases and families with single-gene disorders. The plethora of the genetic variants has exposed the formidable challenge of identifying the causal and pathogenic variants from the enormous number of innocuous common and rare variants that exist in the population and in an individual genome. The arduous task of identifying the causal and pathogenic variants is further compounded by the pleiotropic effects of the variants, complexity of cis and trans interactions in the genome, variability in phenotypic expression of the disease, as well as phenotypic plasticity, and the multifarious determinants of the phenotype. Population genetic studies offer the initial roadmaps and have the potential to elucidate novel pathways involved in the pathogenesis of the disease. However, the genome of an individual is unique, rendering unambiguous identification of the causal or pathogenic variant in a single individual exceedingly challenging. Yet, the focus of the practice of medicine is on the individual, as Sir William Osler elegantly expressed in his insightful quotation: "The good physician treats the disease; the great physician treats the patient who has the disease." The daunting task facing physicians, patients, and researchers alike is to apply the modern genetic discoveries to care of the individual with or at risk of the disease.
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Affiliation(s)
- Ali J Marian
- Center for Cardiovascular Genetics, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Tex; Center for Cardiovascular Genetics, Texas Heart Institute, Houston, Tex.
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230
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Abstract
ABSTRACT
The three main species of the
Bacillus cereus sensu lato
,
B. cereus
,
B. thuringiensis
, and
B. anthracis
, were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits.
B. thuringiensis
isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen.
B. anthracis
, the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and
B. cereus
, a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species:
B. mycoides
,
B. weihenstephanensis
, and
B. pseudomycoides
. All of these “species” combined comprise the
Bacillus cereus sensu lato
group. Despite these apparently clear phenotypic definitions, early molecular approaches to separate the first three by various DNA hybridization and 16S/23S ribosomal sequence analyses led to some “confusion” because there were limited differences to differentiate between these species. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of
B. anthracis
and the biopesticide applications of
B. thuringiensis
appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained.
B. cereus sensu lato
represents a classic example of a now common bacterial species taxonomic quandary.
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231
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Lin E, Lane HY. Genome-wide association studies in pharmacogenomics of antidepressants. Pharmacogenomics 2016; 16:555-66. [PMID: 25916525 DOI: 10.2217/pgs.15.5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Major depressive disorder (MDD) is one of the most common psychiatric disorders worldwide. Doctors must prescribe antidepressants based on educated guesses due to the fact that it is unmanageable to predict the effectiveness of any particular antidepressant in an individual patient. With the recent advent of scientific research, the genome-wide association study (GWAS) is extensively employed to analyze hundreds of thousands of single nucleotide polymorphisms by high-throughput genotyping technologies. In addition to the candidate-gene approach, the GWAS approach has recently been utilized to investigate the determinants of antidepressant response to therapy. In this study, we reviewed GWAS studies, their limitations and future directions with respect to the pharmacogenomics of antidepressants in MDD.
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Affiliation(s)
- Eugene Lin
- Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
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232
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Park SJ, Saito-Adachi M, Komiyama Y, Nakai K. Advances, practice, and clinical perspectives in high-throughput sequencing. Oral Dis 2016; 22:353-64. [DOI: 10.1111/odi.12403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023]
Affiliation(s)
- S-J Park
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
| | - M Saito-Adachi
- Division of Cancer Genomics; National Cancer Center Research Institute; Tokyo Japan
| | - Y Komiyama
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
| | - K Nakai
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
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233
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Abstract
Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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234
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Vartia S, Villanueva-Cañas JL, Finarelli J, Farrell ED, Collins PC, Hughes GM, Carlsson JEL, Gauthier DT, McGinnity P, Cross TF, FitzGerald RD, Mirimin L, Crispie F, Cotter PD, Carlsson J. A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150565. [PMID: 26909185 PMCID: PMC4736940 DOI: 10.1098/rsos.150565] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 05/14/2023]
Abstract
This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
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Affiliation(s)
- Salla Vartia
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Republic of Ireland
| | - José L. Villanueva-Cañas
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - John Finarelli
- School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Edward D. Farrell
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Patrick C. Collins
- School of Biological Sciences, Queen’s University Belfast, Medical Biology Centre, Lisburn Road, Belfast, UK
| | - Graham M. Hughes
- School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Jeanette E. L. Carlsson
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - David T. Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Philip McGinnity
- Beaufort Fish Genetics Programme, School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland
| | - Thomas F. Cross
- Beaufort Fish Genetics Programme, School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland
| | - Richard D. FitzGerald
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Republic of Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Republic of Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland
- Alimentary Pharmabiotic Centre, Cork, Republic of Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland
- Alimentary Pharmabiotic Centre, Cork, Republic of Ireland
| | - Jens Carlsson
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
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235
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Tanisawa K, Tanaka M, Higuchi M. Gene-exercise interactions in the development of cardiometabolic diseases. THE JOURNAL OF PHYSICAL FITNESS AND SPORTS MEDICINE 2016. [DOI: 10.7600/jpfsm.5.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kumpei Tanisawa
- Faculty of Sport Sciences, Waseda University
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology
- Japan Society for the Promotion of Science
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology
| | - Mitsuru Higuchi
- Faculty of Sport Sciences, Waseda University
- Institute of Advanced Active Aging Research, Waseda University
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236
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Sharma M, Kumar A, Ahluwalia PK. Optical fingerprints and electron transport properties of DNA bases adsorbed on monolayer MoS2. RSC Adv 2016. [DOI: 10.1039/c6ra10008b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Electronic, optical and transport properties of DNA nucleobase adsorbed on monolayer MoS2 has been investigated using density functional theory.
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Affiliation(s)
- Munish Sharma
- Department of Physics
- Himachal Pradesh University
- Shimla 171005
- India
| | - Ashok Kumar
- Centre for Physical Sciences
- School of Basic and Applied Sciences
- Central University of Punjab
- Bathinda
- India
| | - P. K. Ahluwalia
- Department of Physics
- Himachal Pradesh University
- Shimla 171005
- India
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237
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Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics 2016; 107:1-8. [PMID: 26554401 PMCID: PMC4727787 DOI: 10.1016/j.ygeno.2015.11.003] [Citation(s) in RCA: 490] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/01/2015] [Accepted: 11/06/2015] [Indexed: 02/06/2023]
Abstract
Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.
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Affiliation(s)
- James M Heather
- Division of Infection & Immunity, UCL Cruciform Building, Gower Street, London, United Kingdom.
| | - Benjamin Chain
- Division of Infection & Immunity, UCL Cruciform Building, Gower Street, London, United Kingdom
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238
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Abstract
Genetic heterogeneity explains variation in predisposition for cancer. Whole-genome analysis allows risk to be quantified, giving better targeted screening and quantification of the personalized risk posed by environmental factors. Array-based approaches to whole-genome analysis are rapidly being overtaken by next-generation sequencing (NGS). In this review the different platforms currently available for NGS are compared and the opportunities and risks of this approach are discussed: including the informatics packages required and the ethical issues. Methods applicable to the personal genome machine (PGM) are given as an example of workflows.
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Affiliation(s)
- Victoria Shaw
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - Katie Bullock
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - William Greenhalf
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK.
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239
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Big Data and Cancer Research. BIG DATA ANALYTICS 2016. [DOI: 10.1007/978-81-322-3628-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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240
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RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. Genetics 2015; 202:389-400. [PMID: 26715661 DOI: 10.1534/genetics.115.183665] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/17/2015] [Indexed: 12/19/2022] Open
Abstract
Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture ( R: AD c APTURE: ). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.
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241
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Prasongkit J, Feliciano GT, Rocha AR, He Y, Osotchan T, Ahuja R, Scheicher RH. Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene. Sci Rep 2015; 5:17560. [PMID: 26634811 PMCID: PMC4669446 DOI: 10.1038/srep17560] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023] Open
Abstract
Fast, cost effective, single-shot DNA sequencing could be the prelude of a new era in genetics. As DNA encodes the information for the production of proteins in all known living beings on Earth, determining the nucleobase sequences is the first and necessary step in that direction. Graphene-based nanopore devices hold great promise for next-generation DNA sequencing. In this work, we develop a novel approach for sequencing DNA using bilayer graphene to read the interlayer conductance through the layers in the presence of target nucleobases. Classical molecular dynamics simulations of DNA translocation through the pore were performed to trace the nucleobase trajectories and evaluate the interaction between the nucleobases and the nanopore. This interaction stabilizes the bases in different orientations, resulting in smaller fluctuations of the nucleobases inside the pore. We assessed the performance of a bilayer graphene nanopore setup for the purpose of DNA sequencing by employing density functional theory and non-equilibrium Green’s function method to investigate the interlayer conductance of nucleobases coupling simultaneously to the top and bottom graphene layers. The obtained conductance is significantly affected by the presence of DNA in the bilayer graphene nanopore, allowing us to analyze DNA sequences.
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Affiliation(s)
- Jariyanee Prasongkit
- Division of Physics, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand.,Nanotec-KKU Center of Excellence on Advanced Nanomaterials for Energy Production and Storage, Khon Kaen 40002, Thailand
| | - Gustavo T Feliciano
- Institute of Chemistry, Physical Chemistry Department, Universidade Estadual Paulista (UNESP), Araraquara, SP, Brazil
| | - Alexandre R Rocha
- Instituto de Física Téorica, Universidade Estadual Paulista (UNESP), São Paulo, SP, Brazil
| | - Yuhui He
- School of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Tanakorn Osotchan
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rajeev Ahuja
- Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.,Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ralph H Scheicher
- Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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242
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Cheng R, Leung RKK, Chen Y, Pan Y, Tong Y, Li Z, Ning L, Ling XB, He J. Virtual Pharmacist: A Platform for Pharmacogenomics. PLoS One 2015; 10:e0141105. [PMID: 26496198 PMCID: PMC4619711 DOI: 10.1371/journal.pone.0141105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/03/2015] [Indexed: 01/15/2023] Open
Abstract
We present Virtual Pharmacist, a web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity at one glance. Batch submission facilitates multivariate analysis or data mining of targeted groups. Individual analysis consists of a report that is readily comprehensible to patients and practioners who have basic knowledge in pharmacology, a table that summarizes variants and potential affected drug response according to the US Food and Drug Administration pharmacogenomic biomarker labeled drug list and PharmGKB, and visualization of a gene-drug-target network. Group analysis provides the distribution of the variants and potential affected drug response of a target group, a sample-gene variant count table, and a sample-drug count table. Our analysis of genomes from the 1000 Genome Project underlines the potentially differential drug responses among different human populations. Even within the same population, the findings from Watson's genome highlight the importance of personalized medicine. Virtual Pharmacist can be accessed freely at http://www.sustc-genome.org.cn/vp or installed as a local web server. The codes and documentation are available at the GitHub repository (https://github.com/VirtualPharmacist/vp). Administrators can download the source codes to customize access settings for further development.
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Affiliation(s)
- Ronghai Cheng
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Ross Ka-Kit Leung
- Division of Genomics and Bioinformatics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yao Chen
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Yidan Pan
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Yin Tong
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Zhoufang Li
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Luwen Ning
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Xuefeng B. Ling
- Departments of Surgery, Stanford University, Stanford, California, United States of America
| | - Jiankui He
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
- * E-mail:
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243
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Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Brief Bioinform 2015; 17:841-62. [PMID: 26494363 DOI: 10.1093/bib/bbv084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 12/20/2022] Open
Abstract
Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.
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244
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Kasianowicz JJ, Balijepalli AK, Ettedgui J, Forstater JH, Wang H, Zhang H, Robertson JWF. Analytical applications for pore-forming proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:593-606. [PMID: 26431785 DOI: 10.1016/j.bbamem.2015.09.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/28/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023]
Abstract
Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- John J Kasianowicz
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States.
| | | | - Jessica Ettedgui
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Jacob H Forstater
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Haiyan Wang
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Dept. of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
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245
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Richter I, Fidler AE. Tunicate pregnane X receptor (PXR) orthologs: Transcript characterization and natural variation. Mar Genomics 2015; 23:99-108. [DOI: 10.1016/j.margen.2015.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 12/12/2022]
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246
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Sokolenko AP, Suspitsin EN, Kuligina ES, Bizin IV, Frishman D, Imyanitov EN. Identification of novel hereditary cancer genes by whole exome sequencing. Cancer Lett 2015; 369:274-88. [PMID: 26427841 DOI: 10.1016/j.canlet.2015.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 02/09/2023]
Abstract
Whole exome sequencing (WES) provides a powerful tool for medical genetic research. Several dozens of WES studies involving patients with hereditary cancer syndromes have already been reported. WES led to breakthrough in understanding of the genetic basis of some exceptionally rare syndromes; for example, identification of germ-line SMARCA4 mutations in patients with ovarian hypercalcemic small cell carcinomas indeed explains a noticeable share of familial aggregation of this disease. However, studies on common cancer types turned out to be more difficult. In particular, there is almost a dozen of reports describing WES analysis of breast cancer patients, but none of them yet succeeded to reveal a gene responsible for the significant share of missing heritability. Virtually all components of WES studies require substantial improvement, e.g. technical performance of WES, interpretation of WES results, mode of patient selection, etc. Most of contemporary investigations focus on genes with autosomal dominant mechanism of inheritance; however, recessive and oligogenic models of transmission of cancer susceptibility also need to be considered. It is expected that the list of medically relevant tumor-predisposing genes will be rapidly expanding in the next few years.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Ilya V Bizin
- Laboratory of Bioinformatics, RASA Research Center, St.-Petersburg State Polytechnical University, St.-Petersburg 195251, Russia
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen, Freising 85354, Germany; Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg 85764, Germany
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia; Department of Oncology, St.-Petersburg State University, St.-Petersburg 199034, Russia.
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Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) 2015; 7:1925-58. [PMID: 26404381 PMCID: PMC4586802 DOI: 10.3390/cancers7030869] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies and data have revolutionized cancer research and are increasingly being deployed to guide clinicians in treatment decision-making. NGS technologies have allowed us to take an “omics” approach to cancer in order to reveal genomic, transcriptomic, and epigenomic landscapes of individual malignancies. Integrative multi-platform analyses are increasingly used in large-scale projects that aim to fully characterize individual tumours as well as general cancer types and subtypes. In this review, we examine how NGS technologies in particular have contributed to “omics” approaches in cancer research, allowing for large-scale integrative analyses that consider hundreds of tumour samples. These types of studies have provided us with an unprecedented wealth of information, providing the background knowledge needed to make small-scale (including “N of 1”) studies informative and relevant. We also take a look at emerging opportunities provided by NGS and state-of-the-art third-generation sequencing technologies, particularly in the context of translational research. Cancer research and care are currently poised to experience significant progress catalyzed by accessible sequencing technologies that will benefit both clinical- and research-based efforts.
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248
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Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2015; 36:998-1009. [PMID: 26381035 DOI: 10.3109/07388551.2015.1083939] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.
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Affiliation(s)
- Salvatore Montella
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Antonella Amore
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
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249
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MacConnell AB, McEnaney PJ, Cavett VJ, Paegel BM. DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis. ACS COMBINATORIAL SCIENCE 2015; 17:518-34. [PMID: 26290177 PMCID: PMC4571006 DOI: 10.1021/acscombsci.5b00106] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The
promise of exploiting combinatorial synthesis for small molecule
discovery remains unfulfilled due primarily to the “structure
elucidation problem”: the back-end mass spectrometric analysis
that significantly restricts one-bead-one-compound (OBOC) library
complexity. The very molecular features that confer binding potency
and specificity, such as stereochemistry, regiochemistry, and scaffold
rigidity, are conspicuously absent from most libraries because isomerism
introduces mass redundancy and diverse scaffolds yield uninterpretable
MS fragmentation. Here we present DNA-encoded solid-phase synthesis
(DESPS), comprising parallel compound synthesis in organic solvent
and aqueous enzymatic ligation of unprotected encoding dsDNA oligonucleotides.
Computational encoding language design yielded 148 thermodynamically
optimized sequences with Hamming string distance ≥ 3 and total
read length <100 bases for facile sequencing. Ligation is efficient
(70% yield), specific, and directional over 6 encoding positions.
A series of isomers served as a testbed for DESPS’s utility
in split-and-pool diversification. Single-bead quantitative PCR detected
9 × 104 molecules/bead and sequencing allowed for
elucidation of each compound’s synthetic history. We applied
DESPS to the combinatorial synthesis of a 75 645-member OBOC
library containing scaffold, stereochemical and regiochemical diversity
using mixed-scale resin (160-μm quality control beads and 10-μm
screening beads). Tandem DNA sequencing/MALDI-TOF MS analysis of 19
quality control beads showed excellent agreement (<1 ppt) between
DNA sequence-predicted mass and the observed mass. DESPS synergistically
unites the advantages of solid-phase synthesis and DNA encoding, enabling
single-bead structural elucidation of complex compounds and synthesis
using reactions normally considered incompatible with unprotected
DNA. The widespread availability of inexpensive oligonucleotide synthesis,
enzymes, DNA sequencing, and PCR make implementation of DESPS straightforward,
and may prompt the chemistry community to revisit the synthesis of
more complex and diverse libraries.
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Affiliation(s)
- Andrew B. MacConnell
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Patrick J. McEnaney
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Valerie J. Cavett
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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250
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Orechia J, Pathak A, Shi Y, Nawani A, Belozerov A, Fontes C, Lakhiani C, Jawale C, Patel C, Quinn D, Botvinnik D, Mei E, Cotter E, Byleckie J, Ullman-Cullere M, Chhetri P, Chalasani P, Karnam P, Beaudoin R, Sahu S, Belozerova Y, Mathew JP. OncDRS: An integrative clinical and genomic data platform for enabling translational research and precision medicine. Appl Transl Genom 2015; 6:18-25. [PMID: 27054074 PMCID: PMC4803771 DOI: 10.1016/j.atg.2015.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/05/2015] [Indexed: 02/01/2023]
Abstract
We live in the genomic era of medicine, where a patient's genomic/molecular data is becoming increasingly important for disease diagnosis, identification of targeted therapy, and risk assessment for adverse reactions. However, decoding the genomic test results and integrating it with clinical data for retrospective studies and cohort identification for prospective clinical trials is still a challenging task. In order to overcome these barriers, we developed an overarching enterprise informatics framework for translational research and personalized medicine called Synergistic Patient and Research Knowledge Systems (SPARKS) and a suite of tools called Oncology Data Retrieval Systems (OncDRS). OncDRS enables seamless data integration, secure and self-navigated query and extraction of clinical and genomic data from heterogeneous sources. Within a year of release, the system has facilitated more than 1500 research queries and has delivered data for more than 50 research studies.
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Affiliation(s)
- John Orechia
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Ameet Pathak
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Yunling Shi
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Aniket Nawani
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Andrey Belozerov
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Caitlin Fontes
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Camille Lakhiani
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Chetan Jawale
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Chetansharan Patel
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Daniel Quinn
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Dmitry Botvinnik
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Eddie Mei
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Elizabeth Cotter
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - James Byleckie
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | | | - Padam Chhetri
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Poornima Chalasani
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Purushotham Karnam
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Ronald Beaudoin
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Sandeep Sahu
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Yelena Belozerova
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
| | - Jomol P Mathew
- Dana-Faber Cancer Institute, 450 Brookline Ave., Boston, MA-02215, United States
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