ArticlePloS one2015
A robust protocol to increase NimbleGen SeqCap EZ multiplexing capacity to 96 samples.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients.Scientific reports · 2024Article
- Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value.Disease markers · 2024Review
- System analysis of the sequencing quality of human whole exome samples on BGI NGS platform.Scientific reports · 2022Article
- Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo).BMC genomics · 2020Article
- Targeted exome sequencing of unselected heavy-ion beam-irradiated populations reveals less-biased mutation characteristics in the rice genome.The Plant journal : for cell and molecular biology · 2019Article
- Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Transfer of a starch phenotype from wild wheat to bread wheat by deletion of a locus controlling B-type starch granule content.Journal of experimental botany · 2017Article
- Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2.Journal of human genetics · 2017Article
- Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome.Molecular genetics and metabolismArticle
Corrections and comments
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Authors and funding
3 authors.
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Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.