title: Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting.
abstract: BACKGROUND
  Targeted capture, combined with massively-parallel sequencing, is a powerful technique that allows investigation of specific portions of the genome for less cost than whole genome sequencing. Several methods have been developed, and improvements have resulted in commercial products targeting the human or mouse exonic regions (the exome). In some cases it is desirable to custom-target other regions of the genome, either to reduce the amount of sequence that is targeted or to capture regions that are not targeted by commercial kits. It is important to understand the advantages, limitations, and complexity of a given capture method before embarking on a targeted sequencing experiment.
  
  
  RESULTS
  We compared two custom targeted capture methods suitable for single chromosome analysis: Solution Hybrid Selection (SHS) and Flow Sorting (FS) of single chromosomes. Both methods can capture targeted material and result in high percentages of genotype identifications across these regions: 59-92% for SHS and 70-79% for FS. FS is amenable to current structural variation detection methods, and variants were detected. Structural variation was also assessed for SHS samples with paired end sequencing, resulting in variant identification.
  
  
  CONCLUSIONS
  While both methods can effectively target genomic regions for genotype determination, several considerations make each method appropriate in different circumstances. SHS is well suited for experiments targeting smaller regions in a larger number of samples. FS is well suited when regions of interest cover large regions of a single chromosome. Although whole genome sequencing is becoming less expensive, the sequencing, data storage, and analysis costs make targeted sequencing using SHS or FS a compelling option.
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Jamie.Teer@moffitt.org
authors.forename: Jamie K
authors.initials: JK
authors.lastname: Teer
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Johnston
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Anzick
authors.forename: Marbin
authors.initials: M
authors.lastname: Pineda
authors.forename: Gary
authors.initials: G
authors.lastname: Stone
authors.forename: Paul S
authors.initials: PS
authors.lastname: Meltzer
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.forename: Leslie G
authors.initials: LG
authors.lastname: Biesecker
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics*; D005434:Flow Cytometry / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*