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Fig. 3.1 Target enrichment methods. ( a ) In molecular inversion probes (MIPs), probes composed
of a universal spacer region fl anked by target-specifi c sequences are designed for each amplicon.
The gap is fi lled by a DNA polymerase and a ligase following probe annealing to the target region.
The target DNA is PCR-amplifi ed after genomic digestion and sequenced. ( b ) In a typical PCR, a
single amplicon is generated by one reaction. By RDT, up to 4,000 primer pairs are used simulta-
neously in a single reaction. ( c ) By hybridization-based captures, genomic DNA libraries contain-
ing adaptors are hybridized to target-specifi c probes either on a microarray surface or in solution.
The target DNA is eluted and sequenced after removal of background DNA by washing (adapted
from Mamanova et al. 2010 )
Porreca et al. 2007 ). Capture probes can be immobilized on a solid surface (Roche
NimbleGen, Agilent Technologies, and Febit) or used in solution (Agilent). Another
enrichment approach that relies on the use of molecular inversion probes (MIPs)
was initially developed for multiplex target detection and SNP genotyping (Ding
et al. 2008 ; Kim et al. 2008 ). In principle, single-stranded oligonucleotides, consist-
ing of a common linker fl anked by target-specifi c sequences, anneal to their target
sequence and become circularized by a ligase (Hodges et al. 2007 ). In an alternative
enrichment approach, developed by RainDance Technologies (RDT), individual
pairs of PCR primers for the genomic regions of interest are segregated in water in
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