title: Diagnostic whole genome sequencing and split-read mapping for nucleotide resolution breakpoint identification in CNTNAP2 deficiency syndrome.
abstract: Whole genome sequencing (WGS) has the potential to report on all types of genetic abnormality, thus converging diagnostic testing on a single methodology. Although WGS at sufficient depth for robust detection of point mutations is still some way from being affordable for diagnostic purposes, low-coverage WGS is already an excellent method for detecting copy number variants ("CNVseq"). We report on a family in which individuals presented with a presumed autosomal recessive syndrome of severe intellectual disability and epilepsy. Array comparative genomic hybridization (CGH) analysis had revealed a homozygous deletion apparently lying within intron 3 of CNTNAP2. Since this was too small for confirmation by FISH, CNVseq was used, refining the extent of this mutation to approximately 76.8 kb, encompassing CNTNAP2 exon 3 (an out-of-frame deletion). To characterize the precise breakpoints and provide a rapid molecular diagnostic test, we resequenced the CNVseq library at medium coverage and performed split read mapping. This yielded information for a multiplex polymerase chain reaction (PCR) assay, used for cascade screening and/or prenatal diagnosis in this family. This example demonstrates a rapid, low-cost approach to converting molecular cytogenetic findings into robust PCR-based tests.
authors.affiliation: Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; School of Medicine, University of Leeds, St. James's University Hospital, Leeds, United Kingdom.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Watson
authors.forename: Laura A
authors.initials: LA
authors.lastname: Crinnion
authors.forename: Antigoni
authors.initials: A
authors.lastname: Tzika
authors.forename: Alison
authors.initials: A
authors.lastname: Mills
authors.forename: Andrea
authors.initials: A
authors.lastname: Coates
authors.forename: Maria
authors.initials: M
authors.lastname: Pendlebury
authors.forename: Sarah
authors.initials: S
authors.lastname: Hewitt
authors.forename: Sally M
authors.initials: SM
authors.lastname: Harrison
authors.forename: Catherine
authors.initials: C
authors.lastname: Daly
authors.forename: Paul
authors.initials: P
authors.lastname: Roberts
authors.forename: Ian M
authors.initials: IM
authors.lastname: Carr
authors.forename: Eamonn G
authors.initials: EG
authors.lastname: Sheridan
authors.forename: David T
authors.initials: DT
authors.lastname: Bonthron
mesh_terms: D000293:Adolescent; D056915:DNA Copy Number Variations / Q000235:genetics; D005091:Exons / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000172:deficiency* / Q000235:genetics*; D025202:Molecular Diagnostic Techniques / Q000379:methods; D009154:Mutation / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000172:deficiency* / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics*; D010375:Pedigree; D017422:Sequence Analysis, DNA / Q000379:methods; D017384:Sequence Deletion / Q000235:genetics*
chemical_list: C403049:CNTNAP2 protein, human; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; D009711:Nucleotides
keywords: CNTNAP2; split read mapping; whole genome sequencing