Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

Gabrieli, Tslil; Sharim, Hila; Fridman, Dena; Arbib, Nissim; Michaeli, Yael; Ebenstein, Yuval

doi:10.1093/nar/gky411

Cited by 105 publications

(99 citation statements)

References 29 publications

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“…To analyze the modification of target regions without performing whole-genome sequencing, native DNA must be enriched without PCR. Methods involving Cas9-mediated enrichment have been developed to enrich a target region [52,53]. Gilpatrick et al developed nCATS (nanopore Cas9targeted sequencing), which is a simple target enrichment method [52].…”

Section: Genome Sequencingmentioning

confidence: 99%

Recent advances in the detection of base modifications using the Nanopore sequencer

Seki

2019

J Hum Genet

116

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DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.

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Section: Genome Sequencingmentioning

confidence: 99%

Recent advances in the detection of base modifications using the Nanopore sequencer

Seki

2019

J Hum Genet

116

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“…; Bennett‐Baker & Mueller ; Gabrieli et al. ; Slesarev et al. ), repetitive or high complexity genomic regions (Bennett‐Baker & Mueller ; Shin et al.…”

Section: Crispr Targeted Sequencing and Genotypingmentioning

confidence: 99%

Transforming ecology and conservation biology through genome editing

Phelps

Seeb

2019

Conservation Biology

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As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.

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“…Of course, both technologies have their pros and cons, but with fast turn-around times and lower start-up costs, and despite higher error rates of >10%, ONT WGS has already been used to resolve SVs in clinical cases 28,29 . Within cancer research specifically, low coverage ONT (Nanopore) WGS has been used for same-day diagnosis of brain tumours 30 , while targeted approaches SHORT VS LONG-READ GENOME SEQUENCING FOR SOMATIC VARIANT DETECTION 4 have been developed for detecting BCR-ABL1 fusion transcripts 31 , analysing prognostically relevant genes in chronic lymphocytic leukaemia 32,33 , and sequencing the entirety of BRCA1 34 .…”

Section: Introductionmentioning

confidence: 99%

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

Roberts

Lopopolo

Pagnamenta

et al. 2020

Preprint

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Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies (ONT) PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables genome-wide detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from the long-read data achieved good specificity and sensitivity.However, results of somatic SNV calling highlight the need for the development of specialized joint calling algorithms. We find the comparative performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.

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Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

Cited by 105 publications

References 29 publications

Recent advances in the detection of base modifications using the Nanopore sequencer

Recent advances in the detection of base modifications using the Nanopore sequencer

Transforming ecology and conservation biology through genome editing

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

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