ArticleBMC genomics2012
Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- System analysis of the sequencing quality of human whole exome samples on BGI NGS platform.Scientific reports · 2022Article
- Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing.BMC bioinformatics · 2021Article
- Highly Efficient and Comprehensive Identification of Ethyl Methanesulfonate-Induced Mutations inFrontiers in plant science · 2021Article
- Review
- Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes.Antimicrobial agents and chemotherapy · 2019Article
- Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion.Plant biotechnology journal · 2019Article
- 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
- Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing.Mutation research · 2018Article
- Massively Parallel Sequencing of Genes Implicated in Heritable Cardiac Disorders: A Strategy for a Small Diagnostic Laboratory.Medical sciences (Basel, Switzerland) · 2017Article
- Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus).Scientific reports · 2017Article
- Article
- Multiplexed direct genomic selection (MDiGS): a pooled BAC capture approach for highly accurate CNV and SNP/INDEL detection.Nucleic acids research · 2014Article
- Advancing genetic testing for deafness with genomic technology.Journal of medical genetics · 2013Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundTargeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection.
resultsWe adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification.
conclusionsPre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.
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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.