A large genome centre’s improvements to the Illumina sequencing system

By M. Quail, I. Kozarewa, Frances Smith, Aylwyn Scally, P. Stephens, Richard Durbin, H. Swerdlow, D. Turner. Nature Methods, 2008

765 citations recorded by the source corpus.

The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/86ef3de0413649e11f0307864663a6886cc25745

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Citations in the corpus

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. (2009, methodology): “After 45 min, fragments corresponding to an insert size of 250–350 bp were excised, and DNA was extracted from the gel slice without heating (Quail et al. 2008).”
Target-enrichment strategies for next-generation sequencing (2010, neutral): “These are paramagnetic beads to which nucleic acids can bind reversibly, and captured DNA can be eluted in water 45 ( Supplementary Protocol 3 ).”
Genome-wide genetic marker discovery and genotyping using next-generation sequencing (2011, neutral): “Some protocols for genome and transcriptome sequencing avoid PCR altogethe”
High Resolution Mapping of Protein Sequence–Function Relationships (2010, background): “Under optimal conditions, short-read Illumina sequencing has an error rate of slightly less than 1”
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts (2011, background): “Some of the reported fusions may in fact be chimeric sequences due to ligation of cDNA fragments [26], which would make the false Table 2 Seventy-six candidate fusions reported by TopHat-Fusion in four breast cancer cell lines (Continued)”
Summarizing and correcting the GC content bias in high-throughput sequencing (2012, background): “Sequence-related biases in the priming (9), size selection (3), PCR (10) and probability of sequencing errors (11–13) have all been found.”
Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities (2011, background): “However, given the rapid ongoing progression of sequencing technologies (Quail et al., 2008; Schwartz and Waterman, 2010), as well as the increase in our understanding of how microbial communities are structured and how they differ across habitats and times (Arumugam et al., 2011; Caporaso et al.,…”
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species (2012, neutral): “We surveyed several combinations of REs, seeking a pair that would yield between 1e(4) and 5e(4) fragments (targeting the 3e(4) calculation above) when subjected to size selection appropriate for Illumina library preparation: a mean fragment size between 200 bp and 400 bp and the size-selection wind”
CNV-seq, a new method to detect copy number variation using high-throughput sequencing (2009, background): “Solexa sequencing reads are recently reported to be GC-biased dependent on a library preparation procedure [28].”
Distinct factors control histone variant H3.3 localization at specific genomic regions (2010, methodology): “We did not use gel purification to isolate our library, as standard methods of gel purification have been shown to decrease the representation of A+T-rich sequences (Quail et al., 2008), and we have also found decreased DNA yield following gel purification (data not shown).”