title: Accurate and comprehensive sequencing of personal genomes.
abstract: As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126×). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide" for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.
authors.affiliation: Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Subramanian S
authors.initials: SS
authors.lastname: Ajay
authors.forename: Stephen C J
authors.initials: SC
authors.lastname: Parker
authors.forename: Hatice Ozel
authors.initials: HO
authors.lastname: Abaan
authors.forename: Karin V Fuentes
authors.initials: KV
authors.lastname: Fajardo
authors.forename: Elliott H
authors.initials: EH
authors.lastname: Margulies
mesh_terms: D015894:Genome, Human; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA