Article

Next-Generation Sequencing Strategies Enable Routine Detection of Balanced Chromosome Rearrangements for Clinical Diagnostics and Genetic Research

Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
The American Journal of Human Genetics (Impact Factor: 10.93). 04/2011; 88(4):469-81. DOI: 10.1016/j.ajhg.2011.03.013
Source: PubMed

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.

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Available from: Toshiro K. Ohsumi
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    • "Furthermore, DNA-Seq does not require a priori knowledge of the genome being sequenced and thus, can be used for de novo genome assembly of multiple species (Hurd and Nelson 2009). Lastly, NGS also allows for the analysis of repetitive DNA sequences (Gisselsson et al. 2001), balanced chromosomal rearrangements, and an initial map of insertion and deletion (INDEL) variation in the genome (Talkowski et al. 2011). Until bioinformatics pipelines and NGS analysis software are developed and simplified for use in IVF clinics, however, microarray-based technologies are likely to continue to dominate the PGS field (Van der Aa et al. 2013). "
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    • "These data were calculated by using the cost shown in Talkowski et al. (2011). Since the cost of 76-cycle paired-end multiplex sequencing on Hiseq 2000 platform is $3,280 per lane, the cost of PE50 and PE25 are simply calculated as $ "

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