Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology

Minervini, Crescenzio Francesco; Cumbo, Cosimo; Orsini, Paola; Anelli, Luisa; Zagaria, Antonella; Impera, Luciana; Coccaro, Nicoletta; Brunetti, Claudia; Minervini, Angela; Casieri, Paola; Tota, Giuseppina; Rossi, Antonella Russo; Specchia, Giorgina; Albano, Francesco

doi:10.1016/j.yexmp.2017.06.007

Cited by 39 publications

(46 citation statements)

References 15 publications

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“…Other emergent techniques, such as Oxford Nanopore Technologies, appears to offer tremendous promise 16 ; unfortunately, this technique is currently limited by an inability to be applied toward conventional Using the TruSight RNA Fusion panel, we found 100% concordance between the test platform and cases previously molecularly confirmed by FISH and/or and RT-PCR. 22 Others have reported a FIGURE 1 Representative example of an informative RNA-Seq result obtained from suboptimal RNA.…”

Section: 31 | Selection Of An Assaymentioning

confidence: 91%

“…Some robust techniques, including the NanoString nCounter Analysis System (NanoString, Seattle, WA), have been successfully applied in fusion gene detection in sarcoma; however, this technology is limited by an inability to detect novel fusion partners. Other emergent techniques, such as Oxford Nanopore Technologies, appears to offer tremendous promise; unfortunately, this technique is currently limited by an inability to be applied toward conventional FFPE specimens, and low read accuracy …”

Section: Introductionmentioning

confidence: 99%

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Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

Dickson

Swanson

2018

Genes Chromosomes & Cancer

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The past decade has witnessed remarkable progress in delineating the molecular pathogenesis of many mesenchymal neoplasms. This, in large part, is attributable to the application of next‐generation sequencing. As these techniques decrease in cost, and increasingly support the use of routine clinical specimens—such as formalin‐fixed paraffin‐embedded tissue and cytology samples—they are beginning to be routinely implemented in diagnostic pathology laboratories. The breadth of testing possible by next‐generation sequencing makes this a useful adjunct for pathologists, particularly with the emergence of targeted therapies. The intent of this article is to share our experience, over 2 years, as an early adopter of targeted RNA sequencing as an ancillary diagnostic technique for fusion gene detection in bone and soft tissue neoplasms.

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Section: 31 | Selection Of An Assaymentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

Dickson

Swanson

2018

Genes Chromosomes & Cancer

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“…Grâce à des algorithmes fondés sur le maximum de vraisemblance, elle a aussi révélé des isoformes de récepteurs dans des lymphocytes B [28]. Des variants structuraux et des mutations dans le cancer du pancréas et dans la leucémie [29,30] ont pu aussi être détectés dans des études dans lesquelles la méthode s'est montrée complémentaire de celles existantes. Elle a également été testée avec succès pour la détection prénatale d'aneuploïdies dans le sang maternel [31].…”

Section: Séquençage De L'adn Par Nanopores Résultats Et Perspectivesunclassified

Séquençage de l’ADN par nanopores

Montel

2018

Med Sci (Paris)

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Après des années de développement, l’utilisation du nanopore comme sonde pour séquencer les molécules d’ADN est maintenant une possibilité viable et prometteuse. La détection d’une seule paire de bases lors du transport de l’ADN permet d’enregistrer de très longs fragments de polynucléotides, avec une parallélisation et des vitesses élevées. Dans cette revue, les méthodologies actuelles fondées sur la détection électrique et les nanopores biologiques seront présentées de même que les nouvelles méthodes utilisant des nanopores à l’état solide, ou la détection optique.

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“…It has been used for applications ranging from pathogen sequencing in the field (Quick et al, ) to sequencing a whole human genome (Jain et al, ). It is still not routinely used in human disease diagnostics, but has been successfully used for SNV detection in CYP2D6 , HLA‐A, and HLA‐B (Sović et al, ); TP53 in cancer (Crescenzio Francesco Minervini et al, ); and BCR‐ABL1 in leukemia (Crescenzio F. Minervini et al, ). SNPs were successfully typed in chromosome 20 in a recent whole genome sequencing study of the NA12878 genome (Jain et al, ).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

Leija‐Salazar

Sedlazeck

Toffoli

et al. 2019

Molec Gen & Gen Med

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Background Mutations in GBA cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing GBA using long reads. Methods We sequenced GBA on the Oxford Nanopore MinION as an 8.9 kb amplicon from 102 individuals, including patients with Parkinson's and Gaucher diseases. We used NanoOK for quality metrics, NGMLR to align data (after comparing with GraphMap), Nanopolish and Sniffles to call variants, and WhatsHap for phasing. Results We detected all known missense mutations in these samples, including the common p.N409S (N370S) and p.L483P (L444P) in multiple samples, and nine rarer ones, as well as a splicing and a truncating mutation, and intronic SNPs. We demonstrated the ability to phase mutations, confirm compound heterozygosity, and assign haplotypes. We also detected two known risk variants in some Parkinson's patients. Rare false positives were easily identified and filtered, with the Nanopolish quality score adjusted for the number of reads a very robust discriminator. In two individuals carrying a recombinant allele, we were able to detect and fully define it in one carrier, where it included a 55‐base pair deletion, but not in another one, suggesting a limitation of the PCR enrichment method. Missense mutations were detected at the correct zygosity, except for the case where the RecNciI one was missed. Conclusion The Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantages of phasing and intronic analysis. It can be used as an efficient research tool, but additional work is required to exclude all recombinants.

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Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology

Cited by 39 publications

References 15 publications

Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

Séquençage de l’ADN par nanopores

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

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