2019
DOI: 10.1101/679423
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Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

Abstract: BackgroundHighly accurate next-generation sequencing (NGS) of genetic variants is key to many areas of science and medicine, such as cataloguing population genetic variation and diagnosing patients with genetic diseases. Certain genomic loci and

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Cited by 2 publications
(3 citation statements)
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“…Even though such a motif is not seen in HIV gp41, it is observed near the MPER region in g-retroviral glycoproteins and has been suggested as a possible conserved mechanism to drive oligomerization (Salamango and Johnson, 2015). (Of note, we had originally identified the S943P as a mutation of interest because it had met our threshold critia, and it was also located in the fusion core, but a closer examination of this mutation revealed that it was the result of a sequencing processing error (Freeman et al, 2020) (see Fig. S8, and methods for details).)…”
Section: Additional Sites Of Interest In Spike With Accruing But Rarementioning
confidence: 99%
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“…Even though such a motif is not seen in HIV gp41, it is observed near the MPER region in g-retroviral glycoproteins and has been suggested as a possible conserved mechanism to drive oligomerization (Salamango and Johnson, 2015). (Of note, we had originally identified the S943P as a mutation of interest because it had met our threshold critia, and it was also located in the fusion core, but a closer examination of this mutation revealed that it was the result of a sequencing processing error (Freeman et al, 2020) (see Fig. S8, and methods for details).)…”
Section: Additional Sites Of Interest In Spike With Accruing But Rarementioning
confidence: 99%
“…We identified the issue with this site as part of another study using a method to detect systematic sequencing errors (Freeman et al, 2020); we are interrogating the quality of available sequencing data and these positions were highlighted as suspect. We interrogated these positions in the raw sequencing data from Sheffield, and although these two variants are not present in the final consensus sequence from any of the Sheffield isolates, the raw, untrimmed bam files show their presence in only one of the amplicons covering the site (Fig.…”
Section: Sequence Quality Control Identification Of a Sequencing Errormentioning
confidence: 99%
“…Taking a conservative approach, many researchers remove mutations that are observed only once during the evolution of the virus when constructing a phylogenetic tree, as these may be more likely to be errors [21,22] , or non-transmitted mutations. However, systematic errors, where the same error from a common source is introduced many times in otherwise distinct viral genome sequences, are not removed by that approach [23,24] . These are more problematic, as they can appear as if they are genuine transmitted mutations (Figure 1).…”
Section: Figure 1: Effect Of Recurrent Sequencing Mutations On Phylogmentioning
confidence: 99%