Dual Indexing for NimbleGen SeqCap

geertvandeweyer

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Join Date: Jan 2011

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Dual Indexing for NimbleGen SeqCap

04-20-2015, 04:26 AM

Hi all,

For all here performing dual indexed panel resequencing: We just published an adaptation of the seqCap protocol to allow dual indexing and 96 sample multiplexing.

For details, see:

A Robust Protocol to Increase NimbleGen SeqCap EZ Multiplexing Capacity to 96 Samples

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123872

Contemporary genetic studies frequently involve sequencing of a targeted gene panel, for instance consisting of a set of genes associated with a specific disease. The NimbleGen SeqCap EZ Choice kit is commonly used for the targeted enrichment of sequencing libraries comprising a target size up to 7 Mb. A major drawback of this commercially available method is the exclusive use of single-indexing, meaning that at most 24 samples can be multiplexed in a single reaction. In case of relatively small target sizes, this will lead to excessive amounts of data per sample. We present an extended version of the NimbleGen SeqCap EZ protocol which allows to robustly multiplex up to 96 samples. We achieved this by incorporating Illumina dual-indexing based custom adapters into the original protocol. To further extend the optimization of cost-efficient sequencing of custom target panels, we studied the effect of higher pre-enrichment pooling factors and show that pre-enrichment pooling of up to 12 samples does not affect the quality of the data. To facilitate evaluation of capture efficiency in custom design panels, we also provide a detailed reporting tool.

Best,

Geert
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liangpingping1985

Junior Member

Join Date: Mar 2017

Posts: 1
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05-22-2017, 01:54 PM

Hi, can I ask why adapter and blocking oligo are HPLC and PAGE purification respectively?
Thanks!
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