Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

By N. Rohland, David Reich. Genome Research, 2012

1,084 citations recorded by the source corpus.

Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about $15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5a7873240eeb760a134186702c081c2dbb561655

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Citations in the corpus

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext) (2019, background): “Our approach builds upon many of the previous approaches introduced by Illumina, MK-2010, F-2011, Rohland & Reich (2012) , and others to develop library preparation methods for genomic DNA that overcome many of these limitations.”
Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “Because I observed adapter-dimer peaks following initial quality control, I cleaned libraries one to two additional times using 1:1 SPRI-substitute.”
A general framework for estimating the relative pathogenicity of human genetic variants (2014, background): “We therefore examined the distribution of C-scores in the genomes of 11 individuals representing diverse populations 39,40 , and find that CADD highly ranks known disease-causal variants (ClinVar pathogenic) within the complete spectrum of variation in personal genomes (Fig.”
Neotropical Plant Evolution: Assembling the Big Picture (2013, background): “…decreasing sequencing costs, options for targeted enrichment sequence capture (Cronn et al., 2012; Grover et al., 2012) and deep multiplexing (Rohland & Reich, 2012), and the potential of these methods to use partially degraded DNA (Mason et al., 2011; Straub et al., 2012; Särkinen et al.,…”
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes (2015, methodology): “In lieu of the significantly more expensive Illumina-recommended AmPure XP beads, we use the simple magnetic bead solution with the “MagNA” bead-extraction protocol from [11,16] and Thermo Sera-Mag SpeedBeads.”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, methodology): ““Home-brew” methods for sequencing library preparation [55,56] have reduced persample cost and prices of commercial kits have followed a”