title: Comparison of sequencing platforms for single nucleotide variant calls in a human sample.
abstract: Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required.
authors: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA.
authors: Aakrosh
authors: A
authors: Ratan
authors: Webb
authors: W
authors: Miller
authors: Joseph
authors: J
authors: Guillory
authors: Jeremy
authors: J
authors: Stinson
authors: Somasekar
authors: S
authors: Seshagiri
authors: Stephan C
authors: SC
authors: Schuster
mesh_terms: D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
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