Erratum: Corrigendum: Performance comparison of benchtop high-throughput sequencing platforms

Abstract

In the version of the article originally published, the ExoInTouch product being used by Pfizer in its virtual trial for overactive bladder (OAB) is eDiary, not Recruit, which allows patients to report through mobile phone or internet portals. The Recruit technology is being used in other studies. The text references to Recruit have been replaced with an explanation of eDiary. Instead of "new technology to recruit patients faster and in a more standardized fashion, " the text now reads, "new technology to allow home-based clinical trial data reporting. " Instead of "'Recruit' text messaging technology in a pilot study" for Detrol, the text now reads, "'eDiary' tool in a Phase 4 trial, called Research on Electronic Monitoring of OAB Treatment Experience. " Additional explanation has been added, including "Patients can respond to simple questionnaires (Fig. 3) via their mobile phones or home computers. If they delay in responding, a reminder can be sent. " And for space reasons, other text relating to Recruit, "The tool is integrated with Pfizer's volunteer database and allows immediate text message-based communication and assessment of a subject's suitability within 5-10 min" and "It can also be used to send protocol-specific messages to patients already enrolled in trials" was deleted. In addition, it should have been noted that Eric Westin, who was interviewed while senior director of Lilly Oncology, had left the company. The errors have been corrected in the HTML and PDF versions of the article. In the version of this article initially published, BASF's Amflora, a genetically modified potato for industrial use, was mistakenly said to be blight resistant when it is not. The error has been corrected in the HTML and PDF versions of the article. In the version of this article initially published, the accession code to obtain raw sequence data was given as SRA045736.2; the correct code is SRA045736. The error has been corrected in the HTML and PDF versions of the article. In the version of this article initially published online, in the Online Methods "Ion Torrent Sequencing" section, the sentence beginning with "Ten milligrams of this DNA was fragmented with a Bioruptor instrument…. " should have read "Ten micrograms…. " and in the "454 GS Junior sequencing" section, "(500 total)" should have read "(500 ng total). " The errors have been corrected in the PDF and HTML versions of this article.e r r ata a N D C O r r I G e N D a npg

Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

“…The individualized ctDNA fingerprint panels are designed to probe mainly somatic SNVs because they rely on multiplex PCR, which is prone to homopolymer-associated indel errors [ 22 , 23 ]. First, clonal clusters were measured using SciClone tools [ 24 ] with the following parameters: tumor purity as determined by pathologists, and tumor copy number alterations (CNA), loss of heterozygosity (LOH) ratio in somatic mutation regions, and somatic variant allele frequency (VAF).…”

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study withSalmonella

“…Unsurprisingly however, differences in the chemistry and engineering of different platforms mean they do not agree exactly, but have different error rates and error structure. For example, studies of “benchtop” NGS platforms have repeatedly found that the MiSeq has the lowest single-base error rate followed by Roche’s 454 GS Junior followed by the Ion Torrent PGM ( Junemann et al, 2013 ; Loman et al, 2012 ; Quail et al, 2012 ); unlike the MiSeq, homopolymer-associated indel errors were an artifact of the latter two platforms ( Loman et al, 2012 ). SOLiD, with much smaller read lengths than the other platforms investigated, had the lowest sequencing accuracy, lowest coverage rate, and highest false-positive rate when compared to Roche 454 and Illumina GA data ( Harismendy et al, 2009 ).…”

“…Three factors that may differ within or among studies are (1) the NGS platform on which the sequences were generated, (2) the method used to detect variant sites and create a SNP matrix, and (3) the phylogenetic inference method used to cluster samples. With regards to NGS platform, it is well documented that performance (e.g., error rates and error structure) differs among them ( Harismendy et al, 2009 ; Loman et al, 2012 ; Mardis, 2013 ; Shendure & Ji, 2008 ). Although some may argue this is not a significant issue as certain platforms are no longer maintained or less likely to be used in the future (e.g., SOLiD and Roche 454), the fact that large amounts of data have been produced under such platforms means that NGS platform artifacts will need to be accounted for within analyses that incorporate historical data.…”

Emerging technologies for hybridization based single nucleotide polymorphism detection

“…For human genetic screening the preferable method is sequencing because it can capture the complete spectrum of genetic variation in an individual. 13 Although in recent years sequencing technologies have experienced a dramatic drop in price and time to acquire results, 14,15 some hurdles still severely limit their direct application, in routine diagnostics: 13 (1) reliable sequencing results depend in the rst place on careful construction of a sequence library and sample preparation 16 and (2) the amount of data generated by sequencing and the complexity of their processing are not compatible with routine applications. 17,18 In microbiological applications, the preferred method for pathogen detection and evaluation of antibiotic resistance still relies on actual selective bacterial growth, limiting the speed of these assays to 48 h. 19 Molecular diagnostics such as PCR are able to improve the sample throughput, time to detection and sensitivity for non-cultivable bacteria but introduce new problems such as sample preparation, expertise and facility requirements.…”