Dual Indexing for NimbleGen SeqCap

geertvandeweyer

Member

Join Date: Jan 2011

Posts: 14
Share

Post
#1

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
Tags: None
liangpingping1985

Junior Member

Join Date: Mar 2017

Posts: 1
Share

Post
#2

05-22-2017, 01:54 PM

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

Previous template Next

Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t

by SEQadmin2

Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...
- Channel: Articles
10-14-2026, 09:55 AM
New Genomics Technologies Take Aim at Long-Standing Limits

by SEQadmin2

Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
- Channel: Articles
09-28-2026, 10:25 AM

Topics	Statistics	Last Post
Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2 Started by SEQadmin2, 10-22-2026, 11:13 AM	0 responses 26 views 0 reactions	Last Post by SEQadmin2 10-22-2026, 11:13 AM
Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2 Started by SEQadmin2, 10-22-2026, 10:48 AM	0 responses 20 views 0 reactions	Last Post by SEQadmin2 10-22-2026, 10:48 AM
Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2 Started by SEQadmin2, 10-15-2026, 10:52 AM	0 responses 36 views 0 reactions	Last Post by SEQadmin2 10-15-2026, 10:52 AM
Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2 Started by SEQadmin2, 10-14-2026, 05:39 AM	0 responses 43 views 0 reactions	Last Post by SEQadmin2 10-14-2026, 05:39 AM

Unconfigured Ad

Dual Indexing for NimbleGen SeqCap

Comment

Latest Articles

ad_right_rmr

News