title: Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research.
abstract: The contribution of balanced chromosomal rearrangements to complex disorders remains unclear because they are not detected routinely by genome-wide microarrays and clinical localization is imprecise. Failure to consider these events bypasses a potentially powerful complement to single nucleotide polymorphism and copy-number association approaches to complex disorders, where much of the heritability remains unexplained. To capitalize on this genetic resource, we have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequencing. For rearrangements already mapped regionally by karyotyping and fluorescence in situ hybridization, a targeted approach enabled capture and sequencing of multiple breakpoints simultaneously. Importantly, this strategy permitted capture and unique alignment of up to 97% of repeat-masked sequences in the targeted regions. Genome-wide analyses estimate that only 3.7% of bases should be routinely omitted from genomic DNA capture experiments. Illustrating the power of these approaches, the rearrangement breakpoints were rapidly defined to base pair resolution and revealed unexpected sequence complexity, such as co-occurrence of inversion and translocation as an underlying feature of karyotypically balanced alterations. These findings have implications ranging from genome annotation to de novo assemblies and could enable sequencing screens for structural variations at a cost comparable to that of microarrays in standard clinical practice.
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Talkowski
authors.forename: Carl
authors.initials: C
authors.lastname: Ernst
authors.forename: Adrian
authors.initials: A
authors.lastname: Heilbut
authors.forename: Colby
authors.initials: C
authors.lastname: Chiang
authors.forename: Carrie
authors.initials: C
authors.lastname: Hanscom
authors.forename: Amelia
authors.initials: A
authors.lastname: Lindgren
authors.forename: Andrew
authors.initials: A
authors.lastname: Kirby
authors.forename: Shangtao
authors.initials: S
authors.lastname: Liu
authors.forename: Bhavana
authors.initials: B
authors.lastname: Muddukrishna
authors.forename: Toshiro K
authors.initials: TK
authors.lastname: Ohsumi
authors.forename: Yiping
authors.initials: Y
authors.lastname: Shen
authors.forename: Mark
authors.initials: M
authors.lastname: Borowsky
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
authors.forename: Cynthia C
authors.initials: CC
authors.lastname: Morton
authors.forename: James F
authors.initials: JF
authors.lastname: Gusella
mesh_terms: D007446:Chromosome Inversion; D002877:Chromosomes, Human / Q000235:genetics*; D019295:Computational Biology; D058893:DNA Barcoding, Taxonomic; D053960:DNA Breaks; D005260:Female; D015723:Gene Library; D015321:Gene Rearrangement; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D020071:Interspersed Repetitive Sequences; D007621:Karyotyping; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA / Q000379:methods*; D014178:Translocation, Genetic