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Lee J. Seeking answers in a genetic code. Some hospitals plunge into genome sequencing despite concerns about evolving knowledge, clinical benefit and costs. MODERN HEALTHCARE 2013; 43:11-1. [PMID: 24422374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Some hospitals have begun offering genome sequencing to help patients assess genetic risks. But with the technology still in its early stages, it's unclear how whole genome sequencing will affect the majority of patients and the care they receive.
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Reinke T. Next-generation sequencing problematic, if promising. MANAGED CARE (LANGHORNE, PA.) 2013; 22:38-41. [PMID: 24555264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Abstract
The sequencing of the human genome offered a glimpse of future medical practices, where information retrieved from the genome could be harnessed to inform treatment decisions. However, making DNA sequencing accessible enough for widespread use poses a number of challenges. This perspective article traces the progress made in the field so far and looks at how close we may be already to real-life applications.
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Bakkali M. A bird's-eye view on the modern genetics workflow and its potential applicability to the locust problem. C R Biol 2013; 336:375-83. [PMID: 24018194 DOI: 10.1016/j.crvi.2013.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 01/16/2023]
Abstract
Genetics is an immense science and the current developments in its methods and techniques as well as the fast emerging tools make it one of the most powerful biological sciences. Indeed, from taxonomy and ecology to physiology and molecular biology, every biological science makes use of genetics techniques and methods at one time or another. In fact, development in genetics is such that it is now possible to characterize and analyze the expression of the whole set of genes of virtually every living organism, even if it is a non-model one. Locusts are notorious for the damage they cause to the ecosystems and economies of the areas affected by their recurrent population outbreaks. To prevent and deal with these outbreaks, we now count on both biological as well as chemical agents that are proving to be successful in reducing the damage that otherwise locust population outbreaks might cause. However, a better, efficient and environmentally friendly solution is still a hoped-for target. In my opinion, the ideal future pesticide should be both environmentally friendly, risk free and species-specific. To reach the knowledge needed for the development of such species-specific anti-locust agent, deep and accurate knowledge of the locusts' genetics and molecular biology is a must. Since genes and their expression levels lie at the bottom of every biological phenomenon, any species-specific solution to the locust problem requires a good knowledge of these organisms' genes as well as the quantitative and spatio-temporal dynamics of their expression. To reach such knowledge, collaborative work is needed as well as a clear workflow that, given the fast development in the genetics tools, is not always clear to all research groups. For this reason, here I describe a genetics workflow that should allow taking advantage of the most recent genetics tools and techniques to answer question relating to locust biology. My hope is that the adoption of this and other work strategies by different research groups, especially when the work is a collaborative one, would provide precious information on the biology and the biological phenomena that these economically important organisms exhibit.
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Blons H, Rouleau E, Charrier N, Chatellier G, Côté JF, Pages JC, de Fraipont F, Boyer JC, Merlio JP, Morel A, Gorisse MC, de Cremoux P, Leroy K, Milano G, Ouafik L, Merlin JL, Le Corre D, Aucouturier P, Sabourin JC, Nowak F, Frebourg T, Emile JF, Durand-Zaleski I, Laurent-Puig P. Performance and cost efficiency of KRAS mutation testing for metastatic colorectal cancer in routine diagnosis: the MOKAECM study, a nationwide experience. PLoS One 2013; 8:e68945. [PMID: 23935912 PMCID: PMC3723748 DOI: 10.1371/journal.pone.0068945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022] Open
Abstract
Purpose Rapid advances in the understanding of cancer biology have transformed drug development thus leading to the approval of targeted therapies and to the development of molecular tests to select patients that will respond to treatments. KRAS status has emerged as a negative predictor of clinical benefit from anti-EGFR antibodies in colorectal cancer, and anti-EGFR antibodies use was limited to KRAS wild type tumors. In order to ensure wide access to tumor molecular profiling, the French National Cancer Institute (INCa) has set up a national network of 28 regional molecular genetics centers. Concurrently, a nationwide external quality assessment for KRAS testing (MOKAECM) was granted to analyze reproducibility and costs. Methods 96 cell-line DNAs and 24 DNA samples from paraffin embedded tumor tissues were sent to 40 French laboratories. A total of 5448 KRAS results were collected and analyzed and a micro-costing study was performed on sites for 5 common methods by an independent team of health economists. Results This work provided a baseline picture of the accuracy and reliability of KRAS analysis in routine testing conditions at a nationwide level. Inter-laboratory Kappa values were >0.8 for KRAS results despite differences detection methods and the use of in-house technologies. Specificity was excellent with only one false positive in 1128 FFPE data, and sensitivity was higher for targeted techniques as compared to Sanger sequencing based methods that were dependent upon local expertise. Estimated reagent costs per patient ranged from €5.5 to €19.0. Conclusion The INCa has set-up a network of public laboratories dedicated to molecular oncology tests. Our results showed almost perfect agreements in KRAS testing at a nationwide level despite different testing methods ensuring a cost-effective equal access to personalized colorectal cancer treatment.
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Feero WG, Wicklund C, Veenstra DL. The economics of genomic medicine: insights from the IOM Roundtable on Translating Genomic-Based Research for Health. JAMA 2013; 309:1235-6. [PMID: 23532238 DOI: 10.1001/jama.2013.113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Chen F, Dong M, Ge M, Zhu L, Ren L, Liu G, Mu R. The history and advances of reversible terminators used in new generations of sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:34-40. [PMID: 23414612 PMCID: PMC4357665 DOI: 10.1016/j.gpb.2013.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/06/2013] [Accepted: 01/10/2013] [Indexed: 02/06/2023]
Abstract
DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of development, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerases to accommodate the reversible terminators as substrates during polymerization; particularly, we introduced the "REAP" method developed by us. At the end of this review, we discussed current limitations of this approach and provided potential solutions to extend its application.
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Piotrowski M, McGilvary GA, Sloan TM, Mewissen M, Lloyd AD, Forster T, Mitchell L, Ghazal P, Hill J. Exploiting parallel R in the cloud with SPRINT. Methods Inf Med 2012; 52:80-90. [PMID: 23223611 PMCID: PMC3547073 DOI: 10.3414/me11-02-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 05/03/2012] [Indexed: 11/09/2022]
Abstract
BACKGROUND Advances in DNA Microarray devices and next-generation massively parallel DNA sequencing platforms have led to an exponential growth in data availability but the arising opportunities require adequate computing resources. High Performance Computing (HPC) in the Cloud offers an affordable way of meeting this need. OBJECTIVES Bioconductor, a popular tool for high-throughput genomic data analysis, is distributed as add-on modules for the R statistical programming language but R has no native capabilities for exploiting multi-processor architectures. SPRINT is an R package that enables easy access to HPC for genomics researchers. This paper investigates: setting up and running SPRINT-enabled genomic analyses on Amazon's Elastic Compute Cloud (EC2), the advantages of submitting applications to EC2 from different parts of the world and, if resource underutilization can improve application performance. METHODS The SPRINT parallel implementations of correlation, permutation testing, partitioning around medoids and the multi-purpose papply have been benchmarked on data sets of various size on Amazon EC2. Jobs have been submitted from both the UK and Thailand to investigate monetary differences. RESULTS It is possible to obtain good, scalable performance but the level of improvement is dependent upon the nature of the algorithm. Resource underutilization can further improve the time to result. End-user's location impacts on costs due to factors such as local taxation. CONCLUSIONS Although not designed to satisfy HPC requirements, Amazon EC2 and cloud computing in general provides an interesting alternative and provides new possibilities for smaller organisations with limited funds.
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Devarakonda S, Govindan R, Hammerman PS. Cancer gene sequencing: ethical challenges and promises. THE VIRTUAL MENTOR : VM 2012; 14:868-872. [PMID: 23351899 DOI: 10.1001/virtualmentor.2012.14.11.stas1-1211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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At $1,000, is genomic sequencing clinically useful in newborns?: many key questions remain unanswered. Am J Med Genet A 2012; 158A:xi. [PMID: 22605524 DOI: 10.1002/ajmg.a.35460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Wales N, Romero-Navarro JA, Cappellini E, Gilbert MTP. Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing. PLoS One 2012; 7:e45644. [PMID: 23029156 PMCID: PMC3447772 DOI: 10.1371/journal.pone.0045644] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/20/2012] [Indexed: 01/01/2023] Open
Abstract
DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.
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Shute N. Personalized medicine. Sci Am 2012; 306:44. [PMID: 22550921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Puritz JB, Addison JA, Toonen RJ. Next-generation phylogeography: a targeted approach for multilocus sequencing of non-model organisms. PLoS One 2012; 7:e34241. [PMID: 22470543 PMCID: PMC3314618 DOI: 10.1371/journal.pone.0034241] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 02/24/2012] [Indexed: 11/18/2022] Open
Abstract
The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA) sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especially in non-model organisms. Here, we present a method utilizing the 454 GS-FLX Titanium pyrosequencing platform with the capacity to simultaneously sequence two species of sea star (Meridiastra calcar and Parvulastra exigua) at five different nDNA loci across 16 different populations of 20 individuals each per species. We compare results from 3 populations with traditional Sanger sequencing based methods, and demonstrate that this next-generation sequencing platform is more time and cost effective and more sensitive to rare variants than Sanger based sequencing. A crucial advantage is that the high coverage of clonally amplified sequences simplifies haplotype determination, even in highly polymorphic species. This targeted next-generation approach can greatly increase the use of nDNA sequence loci in phylogeographic and population genetic studies by mitigating many of the time, cost, and analytical issues associated with highly polymorphic, diploid sequence markers.
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Luan B, Stolovitzky G, Martyna G. Slowing and controlling the translocation of DNA in a solid-state nanopore. NANOSCALE 2012; 4:1068-77. [PMID: 22081018 PMCID: PMC3543692 DOI: 10.1039/c1nr11201e] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the solution to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using electric signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concentration or temperature. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielectric layers has been proposed as a solution. Molecular dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.
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Ong FS, Grody WW, Deignan JL. Privacy and data management in the era of massively parallel next-generation sequencing. Expert Rev Mol Diagn 2012; 11:457-9. [PMID: 21707452 DOI: 10.1586/erm.11.34] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Good JM. Reduced representation methods for subgenomic enrichment and next-generation sequencing. Methods Mol Biol 2012; 772:85-103. [PMID: 22065433 DOI: 10.1007/978-1-61779-228-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Several methods have been developed to enrich DNA for subsets of the genome prior to next-generation sequencing. These front-end enrichment strategies provide powerful and cost-effective tools for researchers interested in collecting large-scale genomic sequence data. In this review, I provide an overview of both general and targeted reduced representation enrichment strategies that are commonly used in tandem with next-generation sequencing. I focus on several key issues that are likely to be important when deciding which enrichment strategy is most appropriate for a given experiment. Overall, these techniques can enable the collection of large-scale genomic data in diverse species, providing a powerful tool for the study of evolutionary biology.
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Darmanis S, Nong RY, Vänelid J, Siegbahn A, Ericsson O, Fredriksson S, Bäcklin C, Gut M, Heath S, Gut IG, Wallentin L, Gustafsson MG, Kamali-Moghaddam M, Landegren U. ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing. PLoS One 2011; 6:e25583. [PMID: 21980495 PMCID: PMC3183061 DOI: 10.1371/journal.pone.0025583] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 09/06/2011] [Indexed: 11/23/2022] Open
Abstract
Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.
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Rodríguez F, Cai D, Teng Y, Spooner D. Asymmetric single-strand conformation polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. AMERICAN JOURNAL OF BOTANY 2011; 98:1061-1067. [PMID: 21730333 DOI: 10.3732/ajb.1000251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY An efficient alternative strategy to conventional cloning was needed to generate high-quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies. This method would facilitate studies and minimize technical problems typically encountered in cloning methodologies. METHODS We tested a variety of single-strand conformation polymorphism (SSCP) protocols including purified and unpurified symmetric and asymmetric PCR, loading buffers, and electrophoresis conditions (buffers, matrix, running time, temperature). Results obtained from direct SSCP band sequencing were compared to those obtained from cloning. KEY RESULTS Our optimized protocol uses asymmetric PCR, with the majority of the samples run in polyacrylamide gel electrophoresis (PAGE). It consistently separated PCR products from 450 to 1200 bp. CONCLUSIONS Asymmetric PCR single-strand conformation polymorphism is an efficient alternative technique for isolating allelic variants of highly heterozygous individuals, with its greatest applications in sequencing allopolyploids. It eliminates two common problems encountered in cloning: PCR recombination and heteroduplex fixation. In addition, our protocol greatly lowers costs and time associated with procedures.
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Bansal V, Tewhey R, LeProust EM, Schork NJ. Efficient and cost effective population resequencing by pooling and in-solution hybridization. PLoS One 2011; 6:e18353. [PMID: 21479135 PMCID: PMC3068187 DOI: 10.1371/journal.pone.0018353] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 02/26/2011] [Indexed: 12/24/2022] Open
Abstract
High-throughput sequencing of targeted genomic loci in large populations is an effective approach for evaluating the contribution of rare variants to disease risk. We evaluated the feasibility of using in-solution hybridization-based target capture on pooled DNA samples to enable cost-efficient population sequencing studies. For this, we performed pooled sequencing of 100 HapMap samples across ∼ 600 kb of DNA sequence using the Illumina GAIIx. Using our accurate variant calling method for pooled sequence data, we were able to not only identify single nucleotide variants with a low false discovery rate (<1%) but also accurately detect short insertion/deletion variants. In addition, with sufficient coverage per individual in each pool (30-fold) we detected 97.2% of the total variants and 93.6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient > = 0.995).
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Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, Peckham HE, Schroth GP, Kim RW, Kingsmore SF. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011; 3:65ra4. [PMID: 21228398 PMCID: PMC3740116 DOI: 10.1126/scitranslmed.3001756] [Citation(s) in RCA: 479] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~10% of pediatric hospitalizations. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening to most severe disease genes has hitherto been impractical. Here, we report a preconception carrier screen for 448 severe recessive childhood diseases. Rather than costly, complete sequencing of the human genome, 7717 regions from 437 target genes were enriched by hybrid capture or microdroplet polymerase chain reaction, sequenced by next-generation sequencing (NGS) to a depth of up to 2.7 gigabases, and assessed with stringent bioinformatic filters. At a resultant 160x average target coverage, 93% of nucleotides had at least 20x coverage, and mutation detection/genotyping had ~95% sensitivity and ~100% specificity for substitution, insertion/deletion, splicing, and gross deletion mutations and single-nucleotide polymorphisms. In 104 unrelated DNA samples, the average genomic carrier burden for severe pediatric recessive mutations was 2.8 and ranged from 0 to 7. The distribution of mutations among sequenced samples appeared random. Twenty-seven percent of mutations cited in the literature were found to be common polymorphisms or misannotated, underscoring the need for better mutation databases as part of a comprehensive carrier testing strategy. Given the magnitude of carrier burden and the lower cost of testing compared to treating these conditions, carrier screening by NGS made available to the general population may be an economical way to reduce the incidence of and ameliorate suffering associated with severe recessive childhood disorders.
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Buonaccorsi VP, Boyle MD, Grove D, Praul C, Sakk E, Stuart A, Tobin T, Hosler J, Carney SL, Engle MJ, Overton BE, Newman JD, Pizzorno M, Powell JR, Trun N. GCAT-SEEKquence: genome consortium for active teaching of undergraduates through increased faculty access to next-generation sequencing data. CBE LIFE SCIENCES EDUCATION 2011; 10:342-5. [PMID: 22135368 PMCID: PMC3228652 DOI: 10.1187/cbe.11-08-0065] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
To transform undergraduate biology education, faculty need to provide opportunities for students to engage in the process of science. The rise of research approaches using next-generation (NextGen) sequencing has been impressive, but incorporation of such approaches into the undergraduate curriculum remains a major challenge. In this paper, we report proceedings of a National Science Foundation-funded workshop held July 11-14, 2011, at Juniata College. The purpose of the workshop was to develop a regional research coordination network for undergraduate biology education (RCN/UBE). The network is collaborating with a genome-sequencing core facility located at Pennsylvania State University (University Park) to enable undergraduate students and faculty at small colleges to access state-of-the-art sequencing technology. We aim to create a database of references, protocols, and raw data related to NextGen sequencing, and to find innovative ways to reduce costs related to sequencing and bioinformatics analysis. It was agreed that our regional network for NextGen sequencing could operate more effectively if it were partnered with the Genome Consortium for Active Teaching (GCAT) as a new arm of that consortium, entitled GCAT-SEEK(quence). This step would also permit the approach to be replicated elsewhere.
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Di Ventra M. Nanobiotechnology: sequencing at the end of the tunnel. NATURE NANOTECHNOLOGY 2010; 5:828-829. [PMID: 21076403 DOI: 10.1038/nnano.2010.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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Kuroshu RM, Watanabe, J, Sugano S, Morishita S, Suzuki Y, Kasahara M. Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PLoS One 2010; 5:e10517. [PMID: 20479877 PMCID: PMC2866332 DOI: 10.1371/journal.pone.0010517] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 03/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. METHODOLOGY We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. CONCLUSIONS The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.
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Abstract
With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.
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Akil H, Brenner S, Kandel E, Kendler KS, King MC, Scolnick E, Watson JD, Zoghbi HY. Medicine. The future of psychiatric research: genomes and neural circuits. Science 2010; 327:1580-1. [PMID: 20339051 PMCID: PMC3091000 DOI: 10.1126/science.1188654] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Integrating the tools of genomics and neural science is needed to reveal causes of neuropsychiatric illnesses and to suggest new strategies for treatment and prevention.
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Abstract
The bold ambitions of one institute could make China the world leader in genome sequencing. David Cyranoski asks if its science will survive the industrial ramp-up.
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de Jong A, Teeuw M, Janssens ACJW. [Whole genome sequencing--new opportunities for health care practice?]. NEDERLANDS TIJDSCHRIFT VOOR GENEESKUNDE 2010; 154:A2753. [PMID: 21029487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In the near future it will probably be possible to unravel the DNA code of the human genome for less than US $ 1,000 by means of 'whole genome sequencing' (WGS). However, its usefulness in clinical practice is questionable. Although WGS of an individual may become relatively inexpensive and easily available, knowledge of the complete DNA sequence in itself does not provide clinically useful information. DNA data need to be analyzed and interpreted, but there are still many gaps and uncertainties in our knowledge of DNA variations and their clinical consequences. WGS may be a useful supplementary testing technique for establishing the diagnosis of monogenic disorders and syndromes, but potentially undesirable or unclear findings may cause ethical and practical problems. Therefore, WGS should only be applied very cautiously and after thorough deliberation of its possible consequences.
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Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One 2009; 4:e7453. [PMID: 19834618 PMCID: PMC2759544 DOI: 10.1371/journal.pone.0007453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 08/15/2009] [Indexed: 11/24/2022] Open
Abstract
Many techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. The sensitivity of the method was demonstrated by accurate and consistent readouts from a controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotide analog ribavirin on a typical poliovirus population through two rounds of passage. Our results show that this economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomic diversity, our SBE-based technique provides a scalable and cost-effective complement to both traditional and next generation sequencing methodologies.
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Nau JY. [Your genome sequence for the price of a car]. REVUE MEDICALE SUISSE 2009; 5:1688. [PMID: 19772204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol 2009; 5:e1000432. [PMID: 19593373 PMCID: PMC2700963 DOI: 10.1371/journal.pcbi.1000432] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 06/04/2009] [Indexed: 12/02/2022] Open
Abstract
The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen), with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs). SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome.) To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost. In recent years, the development of high throughput sequencing and array technologies has enabled the accurate re-sequencing of individual genomes, especially in identifying and reconstructing the variants in an individual's genome compared to a “reference”. The costs and sensitivities of these technologies differ considerably from each other, and even more technologies are expected to appear in the near future. To both reduce the total cost of re-sequencing to an affordable point and be adaptive to these constantly evolving bio-technologies, we propose to build a computationally efficient simulation framework that can help us optimize the combination of different technologies to perform low cost comparative genome re-sequencing, especially in reconstructing large structural variants, which is considered in many respects the most challenging step in genome re-sequencing. Our simulation results quantitatively show how much improvement one can gain in reconstructing large structural variants by integrating different technologies in optimal ways. We envision that in the future, more experimental technologies will be incorporated into this simulation framework and its results can provide informative guidelines for the actual experimental design to achieve optimal genome re-sequencing output at low costs.
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Sanders D, Kmiecik T. Personalized medicine gets practical. HEALTHCARE INFORMATICS : THE BUSINESS MAGAZINE FOR INFORMATION AND COMMUNICATION SYSTEMS 2009; 26:50-51. [PMID: 19514241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Greenbaum D, Du J, Gerstein M. Genomic anonymity: have we already lost it? THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2008; 8:71-74. [PMID: 19003717 DOI: 10.1080/15265160802478560] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Abstract
A new type of company is offering to scan a person's genome and reveal the information it holds for as little as $1000. Are these services fun novelty items or do they provide valuable information that will help people take better care of their health?
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Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452:872-6. [PMID: 18421352 DOI: 10.1038/nature06884] [Citation(s) in RCA: 1151] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 03/04/2008] [Indexed: 12/13/2022]
Abstract
The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.
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