ArticleEuropean journal of human genetics : EJHG2014
Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model.
Article in European journal of human genetics : EJHG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 59 citations in OpenAlex.
- Prevalence of BRCA homopolymeric indels in an ION Torrent-based tumour-to-germline testing workflow in high-grade ovarian carcinoma.Scientific reports · 2023Article
- Next Generation Sequencing in Newborn Screening in the United Kingdom National Health Service.International journal of neonatal screening · 2019Article
- Dissection of major cancer gene variants in subsets of circulating tumor cells in advanced breast cancer.Scientific reports · 2019Article
- Rare single-nucleotide variants in oculo-auriculo-vertebral spectrum (OAVS).Molecular genetics & genomic medicine · 2019Article
- Identification of novelPeerJ · 2019Article
- Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants inCancer research and treatment · 2018Article
- Identification of a novel hypertrophic cardiomyopathy-associated mutation using targeted next-generation sequencing.International journal of molecular medicine · 2017Article
- Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.Oncotarget · 2017Article
- Statistical method to compare massive parallel sequencing pipelines.BMC bioinformatics · 2017Article
- Mosaicism and prenatal diagnosis options: insights from retinoblastoma.European journal of human genetics : EJHG · 2017Article
- Next-generation sequencing of the human TRPV1 gene and the regulating co-players LTB4R and LTB4R2 based on a custom AmpliSeq™ panel.PloS one · 2017Article
- Next-generation sequencing of human opioid receptor genes based on a custom AmpliSeq™ library and ion torrent personal genome machine.Clinica chimica acta; international journal of clinical chemistry · 2016Article
- Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples.Oncotarget · 2016Article
- New challenges for BRCA testing: a view from the diagnostic laboratory.European journal of human genetics : EJHG · 2016Review
- Identification of novel mutations including a double mutation in patients with inherited cardiomyopathy by a targeted sequencing approach using the Ion Torrent PGM system.International journal of molecular medicine · 2016Article
- Mutational analysis of single circulating tumor cells by next generation sequencing in metastatic breast cancer.Oncotarget · 2016Article
- Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.Orphanet journal of rare diseases · 2016Article
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- Next-generation sequencing: advances and applications in cancer diagnosis.OncoTargets and therapy · 2016Review
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To meet challenges in terms of throughput and turnaround time, many diagnostic laboratories are shifting from Sanger sequencing to higher throughput next-generation sequencing (NGS) platforms. Bearing in mind that the performance and quality criteria expected from NGS in diagnostic or research settings are strikingly different, we have developed an Ion Torrent's PGM-based routine diagnostic procedure for BRCA1/2 sequencing. The procedure was first tested on a training set of 62 control samples, and then blindly validated on 77 samples in parallel with our routine technique. The training set was composed of difficult cases, for example, insertions and/or deletions of various sizes, large-scale rearrangements and, obviously, mutations occurring in homopolymer regions. We also compared two bioinformatic solutions in this diagnostic context, an in-house academic pipeline and the commercially available NextGene software (Softgenetics). NextGene analysis provided higher sensitivity, as four previously undetected single-nucleotide variations were found. Regarding specificity, an average of 1.5 confirmatory Sanger sequencings per patient was needed for complete BRCA1/2 screening. Large-scale rearrangements were identified by two distinct analyses, that is, bioinformatics and fragment analysis with electrophoresis profile comparison. Turnaround time was enhanced, as a series of 30 patients were sequenced by one technician, making the results available for the clinician in 10 working days following blood sampling. BRCA1/2 genes are a good model, representative of the difficulties commonly encountered in diagnostic settings, which is why we believe our findings are of interest for the whole community, and the pipeline described can be adapted by any user of PGM for diagnostic purposes.
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Registered trials
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.