Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

Abstract

We present a simple molecular indexing method for quantitative targeted RNA sequencing, in which mRNAs of interest are selectively captured from complex cDNA libraries and sequenced to determine their absolute concentrations. cDNA fragments are individually labeled so that each molecule can be tracked from the original sample through the library preparation and sequencing process. Multiple copies of cDNA fragments of identical sequence become distinct through labeling, and replicate clones created during PCR amplification steps can be identified and assigned to their distinct parent molecules. Selective capture enables efficient use of sequencing for deep sampling and for the absolute quantitation of rare or transient transcripts that would otherwise escape detection by standard sequencing methods. We have also constructed a set of synthetic barcoded RNA molecules, which can be introduced as controls into the sample preparation mix and used to monitor the efficiency of library construction. The quantitative targeted sequencing revealed extremely low efficiency in standard library preparations, which were further confirmed by using synthetic barcoded RNA molecules. This finding shows that standard library preparation methods result in the loss of rare transcripts and highlights the need for monitoring library efficiency and for developing more efficient sample preparation methods.cDNA library | molecular barcoding | RNA-seq R NA sequencing (RNA-Seq) is a powerful method for the measurement of global gene expression (1, 2). As a discovery tool, the method has dramatically increased our knowledge of the transcriptome, providing new insights into transcript diversity, including the discovery of new structural variants such as alternative splicing, gene fusions or rearrangements, and lowexpressed molecules. As a profiling tool, the method is primarily challenged by the large dynamic range of expression levels of mRNAs in a library. Sequencing of millions to tens of millions of copies of high-abundance transcripts is required to detect rare transcripts of interest (3, 4). To compensate, increased numbers of reads are often used, despite the low efficiency of this strategy. Reports estimate that ∼40 million reads may be required for the reliable measurement of gene expression for transcripts of high and moderate abundance, and as many as 500 million reads may be required to cover the full sequence diversity of a complex transcript library (1,5,6). In routine use, sparse coverage is further compromised by the practice of multiplexing samples in a single RNA-Seq run, primarily driven by cost constraints when designing studies involving large numbers of samples, such as those required in clinical applications.To efficiently sample the rare or low-abundance isoforms of transcripts, capture methods have recently been used (7,8). These promising methods use a targeted strategy whereby genomic regions of interest are enriched through hybridization capture and amplification before sequence sampling. When applied to generate th...

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