title: Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies.
abstract: OBJECTIVE
  This review discusses the strengths and challenges of using whole genome sequencing (WGS)/whole exome sequencing (WES) for identifying novel genetic causes of primary immunodeficiencies.
  
  
  RESULTS
  WGS permits comprehensive sequencing of introns and exons, whereas WES allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS/WES.
  
  
  CONCLUSIONS
  WGS/WES is a powerful screening tool with great potential to identify genetic causes of primary immunodeficiencies for research and clinical applications. To use WGS/WES effectively, it is necessary to understand how to filter the sequencing data and to realize its limitations as well as its strengths.
authors.affiliation: Division of Immunology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Chou
authors.forename: Toshiro K
authors.initials: TK
authors.lastname: Ohsumi
authors.forename: Raif S
authors.initials: RS
authors.lastname: Geha
mesh_terms: D000818:Animals; D001483:Base Sequence; D059472:Exome; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods