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DNA testing and privacy
\"Home DNA testing companies, such as 23 and Me and AncestryDNA, are at peak popularity, fulfilling our desires to know where we come from and what our future might look like. But questions have arisen about who owns test results and whether testing companies have the right to sell customers' data to pharmaceutical companies and other outlets. Yet home DNA tests have been credited with catching criminals, such as the Golden State Killer. Containing viewpoints from diverse voices in the field, this volume examines the controversies surrounding home DNA tests.\"-- Provided by publisher.
Book
Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq
Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long.
Size-selected and amplified circular DNA molecules are sequenced on the PacBio platform and processed with a custom pipeline, resulting in full-length annotated genomes of circular DNA viruses and sequences of extrachromosomal circular DNA at single-molecule resolution.
Journal Article
Neandertal and Denisovan DNA from Pleistocene sediments
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.
Journal Article
Origin : a genetic history of the Americas
\"From celebrated genetic anthropologist Jennifer Raff comes the untold story-and fascinating mystery-of how humans migrated to the Americas\"-- Provided by publisher.
Book
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
Background
The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse
et al.
in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments.
Results
We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables.
Conclusions
The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.
Journal Article
DNA sequencing at 40: past, present and future
This review commemorates the 40th anniversary of DNA sequencing, a period in which we have already witnessed multiple technological revolutions and a growth in scale from a few kilobases to the first human genome, and now to millions of human and a myriad of other genomes. DNA sequencing has been extensively and creatively repurposed, including as a ‘counter’ for a vast range of molecular phenomena. We predict that in the long view of history, the impact of DNA sequencing will be on a par with that of the microscope.
The history and future potential of DNA sequencing, including the development of the underlying technologies and the expansion of its areas of application, are reviewed.
DNA sequencing at 40
This year marks the 40th anniversary of the Sanger method for DNA sequencing, the most widely used sequencing method, pioneered by Fred Sanger and his team in 1977. Jay Shendure and colleagues review the evolution of sequencing technologies since their inception, highlighting the major milestones in the development, analyses and applications of genome sequencing over the past 40 years. Despite multiple technological revolutions and growth in scale, the authors see DNA sequencing as a relatively nascent technology in the grand scheme of scientific history. They review current emerging applications and discuss the continued evolution and future of DNA sequencing from population-scale resequencing to networks of portable sensors used for real-time monitoring in environmental settings.
Journal Article
Who we are and how we got here : the ancient DNA revolution and the new science of the human past
\"Technological innovations now allow scientists to extract and analyze ancient DNA as never before, and it has become clear--in part from David Reich's own contributions to the field--that genomics is as important a means of understanding the human past as archeology, linguistics, and the written word. Now, in [this book], Reich describes ... just how the human genome provides not only all the information that a fertilized human egg needs to develop but also contains within it the history of our species\"-- Provided by publisher.
Book
Sequencing technologies — the next generation
Key Points
The major advance offered by next-generation sequencing (NGS) technologies is the ability to produce, in some cases, in excess of one billion short reads per instrument run, which makes them useful for many biological applications.
The variety of NGS features makes it likely that multiple platforms will coexist in the marketplace, with some having clear advantages for particular applications over others.
The leading NGS platforms use clonally amplified templates, which are not affected by the arbitrary losses of genomic sequences that are inherent in bacterial cloning methods.
An important advantage of single-molecule template platforms is that PCR is not required. PCR can create mutations that masquerade as sequence variants and amplification bias that underrepresents AT-rich and GC-rich regions in target sequences.
There are four primary NGS chemistry methods: cyclic reversible termination, sequencing by ligation, pyrosequencing and real-time sequencing, which are described in this Review.
To call sequence variants in genomes, NGS reads are aligned to a reference sequence using various bioinformatics mapping tools.
Whole-genome sequencing using current NGS platforms is still expensive, but targeting regions of interest may provide an interim solution to analysing hundreds, if not thousands, of samples.
To date, the sequences of twelve human genomes have been published using a number of NGS platforms, marking the beginning of personalized genomics.
NGS costs will continue to drop in the foreseeable future, although the cost reduction should be weighed against the quality of the produced genome sequence.
There is an increasing demand for next-generation sequencing technologies that rapidly deliver high volumes of accurate genome information at a low cost. This Review provides a guide to the features of the different platforms, and describes the recent advances in this fast-moving area.
Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.
Journal Article