Target-enrichment strategies for next-generation sequencing

Mamanova, Lira; Coffey, Alison J.; Scott, Carol; Kozarewa, Iwanka; Turner, Emily H.; Kumar, Akash; Howard, Eleanor; Shendure, Jay; Turner, Daniel J.

doi:10.1038/nmeth.1419

Cited by 1,059 publications

(893 citation statements)

References 45 publications

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“…[20][21][22][23][24] Because whole genome sequencing is still limited in throughput and too costly to be applied as the main tool for disease gene discovery, different capturing approaches have been developed to enrich the exome before NGS. 25 The advantage of this enrichment is that many more exomes than genomes can be sequenced per NGS system per run, and despite the additional enrichment, costs are lower by a factor of 5-10. A single run on the latest generation of such NGS systems can generate enough sequence data to simultaneously study up to 100 exomes in parallel.…”

Section: Next Generation Sequencing (Ngs) Technologymentioning

confidence: 99%

Disease gene identification strategies for exome sequencing

et al. 2012

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Section: Next Generation Sequencing (Ngs) Technologymentioning

confidence: 99%

Disease gene identification strategies for exome sequencing

et al. 2012

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“…The basic principle is that large panels of target molecules can be selected and circularised in a single reaction using specially designed probes containing universal sequences. The reaction is then subjected to Mamanova et al (2010) exonuclease digestion which degrades all the unwanted DNA but leaves the targets untouched since, being circles, they have no ends. The target sequences can then be amplified using the universal sequences to generate suitable target material for sequencing.…”

Section: Targeting Methodsmentioning

confidence: 99%

“…The method of choice is dependent on application; in particular target size, type of target and sample number, required performance, ease of use and costs (Albert et al 2007;Mamanova et al 2010). Ideally the targeting method should allow enrichment of multiple different loci independent of their size, sequence composition or spatial distribution, and should be amenable to automation so that it can match the sequencing capacity.…”

Section: Targeting Methodsmentioning

confidence: 99%

Review of massively parallel DNA sequencing technologies

Moorthie

Mattocks

Wright

2011

HUGO J

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Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.

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“…Target‐enrichment strategy is the method, in which genomic regions of particular interest are selectively captured before sequencing 14, 15. This approach has proved to be a cost‐effective solution for studying MHC region,16 particularly facilitating the population‐based research.…”

Section: Introductionmentioning

confidence: 99%

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

et al. 2018

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The major histocompatibility complex (MHC) is most closely associated with nasopharyngeal carcinoma (NPC), but the complexity of its genome structure has proven challenging for the discovery of causal MHC loci or genes. We conducted a targeted MHC sequencing in 40 Cantonese NPC patients followed by a two‐stage replication in 1065 NPC cases and 2137 controls of Southern Chinese descendent. Quantitative RT‐PCR analysis (qRT‐PCR) was used to detect gene expression status in 108 NPC and 43 noncancerous nasopharyngeal (NP) samples. Luciferase reporter assay and chromatin immunoprecipitation (ChIP) were used to assess the transcription factor binding site. We discovered that a novel SNP rs117565607_A at TRIM26 displayed the strongest association (OR = 1.909, Pcombined = 2.750 × 10−19). We also observed that TRIM26 was significantly downregulated in NPC tissue samples with genotype AA/AT than TT. Immunohistochemistry (IHC) test also found the TRIM26 protein expression in NPC tissue samples with the genotype AA/AT was lower than TT. According to computational prediction, rs117565607 locus was a binding site for the transcription factor Yin Yang 1 (YY1). We observed that the luciferase activity of YY1 which is binding to the A allele of rs117565607 was suppressed. ChIP data showed that YY1 was binding with T not A allele. Significance analysis of microarray suggested that TRIM26 downregulation was related to low immune response in NPC. We have identified a novel gene TRIM26 and a novel SNP rs117565607_A associated with NPC risk by regulating transcriptional process and established a new functional link between TRIM26 downregulation and low immune response in NPC.

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Target-enrichment strategies for next-generation sequencing

Cited by 1,059 publications

References 45 publications

Disease gene identification strategies for exome sequencing

Disease gene identification strategies for exome sequencing

Review of massively parallel DNA sequencing technologies

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

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