Emerging technologies in DNA sequencing

Metzker, Michael L.

doi:10.1101/gr.3770505

Cited by 410 publications

(279 citation statements)

References 111 publications

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“…PCR was used to amplify two products from the pol and env gene regions of the HIV-1 genome, as previously described (30,44). Approximately 20 molecular clones derived from these regions were sequenced using the automated Sanger method (45). HIV-1 sequences from each case sample were examined against those previously obtained from the Louisiana case (30) and the laboratory sequence pNL4-3 and did not reveal any evidence of laboratory contamination (SI Text).…”

Section: Methodsmentioning

confidence: 99%

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Scaduto

Brown

Haaland

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield , case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu , case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant.

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Section: Methodsmentioning

confidence: 99%

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Scaduto

Brown

Haaland

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…The NGS technology has enabled rapid sequencing of the genomes of individuals at a low cost and with maximum genome coverage 40. Before NGS, the gold standard for sequencing technology was automated Sanger sequencing 80. Sanger sequencing technology was developed in the late 1970s and later automated to increase throughput 81.…”

Section: Next Generation Sequencing Techniquesmentioning

confidence: 99%

Genetic Susceptibility to Rhodococcus equi

McQueen

Dindot

2015

Veterinary Internal Medicne

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Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).

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“…As a result of various improvements in the speed, scalability and price of sequencing technology [14,15], the volume of sequence data has increased exponentially in the past 10-20 years [16] and will continue to do so. Although a variety of other large-scale data augment our knowledge of protein function [3,4, Given this operational definition of function, here we will try to assess the completeness of protein function space using computational analysis of sequence data, scaling up from the model organism Escherichia coli via full genome sequences and complete environmental data sets.…”

Section: Introductionmentioning

confidence: 99%

Protein function space: viewing the limits or limited by our view?

Raes

Harrington

Singh

et al. 2007

Current Opinion in Structural Biology

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| Given that the number of protein functions on earth is finite, the rapid expansion of biological knowledge and the concomitant exponential increase in the number of protein sequences should, at some point, enable the estimation of the limits of protein function space. The functional coverage of protein sequences can be investigated using computational methods, especially given the massive amount of data being generated by large-scale environmental sequencing (metagenomics). In completely sequenced genomes, the fraction of proteins to which at least some functional features can be assigned has recently risen to as much as ~85%. Although this fraction is more uncertain in metagenomics surveys, because of environmental complexities and differences in analysis protocols, our global knowledge of protein functions still appears to be considerable. However, when we consider protein families, continued sequencing seems to yield an ever-increasing number of novel families. Until we reconcile these two views, the limits of protein space will remain obscured.

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Emerging technologies in DNA sequencing

Cited by 410 publications

References 111 publications

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Genetic Susceptibility to Rhodococcus equi

Protein function space: viewing the limits or limited by our view?

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