title: Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis.
abstract: Velo-cardio-facial syndrome/DiGeorge syndrome/22q11.2 deletion syndrome (22q11.2DS) is caused by meiotic non-allelic homologous recombination events between flanking low copy repeats termed LCR22A and LCR22D, resulting in a 3 million base pair (Mb) deletion. Due to their complex structure, large size and high sequence identity, genetic variation within LCR22s among different individuals has not been well characterized. In this study, we sequenced 13 BAC clones derived from LCR22A/D and aligned them with 15 previously available BAC sequences to create a new genetic variation map. The thousands of variants identified by this analysis were not uniformly distributed in the two LCR22s. Moreover, shared single nucleotide variants between LCR22A and LCR22D were enriched in the Breakpoint Cluster Region pseudogene (BCRP) block, suggesting the existence of a possible recombination hotspot there. Interestingly, breakpoints for atypical 22q11.2 rearrangements have previously been located to BCRPs To further explore this finding, we carried out in-depth analyses of whole genome sequence (WGS) data from two unrelated probands harbouring a de novo 3Mb 22q11.2 deletion and their normal parents. By focusing primarily on WGS reads uniquely mapped to LCR22A, using the variation map from our BAC analysis to help resolve allele ambiguity, and by performing PCR analysis, we infer that the deletion breakpoints were most likely located near or within the BCRP module. In summary, we found a high degree of sequence variation in LCR22A and LCR22D and a potential recombination breakpoint near or within the BCRP block, providing a starting point for future breakpoint mapping using additional trios.
authors.affiliation: Department of Neurology.
authors.forename: Xingyi
authors.initials: X
authors.lastname: Guo
authors.affiliation: Department of Genetics.
authors.forename: Maria
authors.initials: M
authors.lastname: Delio
authors.affiliation: Department of Genetics.
authors.forename: Nousin
authors.initials: N
authors.lastname: Haque
authors.affiliation: Department of Genetics.
authors.forename: Raquel
authors.initials: R
authors.lastname: Castellanos
authors.affiliation: Department of Human Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Hestand
authors.affiliation: Department of Human Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Joris R
authors.initials: JR
authors.lastname: Vermeesch
authors.affiliation: Department of Genetics deyou.zheng@einstein.yu.edu bernice.morrow@einstein.yu.edu.|Departments of Ob/Gyn and Pediatrics.
authors.forename: Bernice E
authors.initials: BE
authors.lastname: Morrow
authors.affiliation: Department of Neurology deyou.zheng@einstein.yu.edu bernice.morrow@einstein.yu.edu.|Department of Genetics.|Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
authors.forename: Deyou
authors.initials: D
authors.lastname: Zheng
mesh_terms: D000070997:ATP Binding Cassette Transporter, Subfamily G, Member 2 / Q000235:genetics; D056905:Chromosome Breakpoints; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D004062:DiGeorge Syndrome / Q000235:genetics*; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion
chemical_list: C116614:ABCG2 protein, human; D000070997:ATP Binding Cassette Transporter, Subfamily G, Member 2; D009363:Neoplasm Proteins