ArticleHuman genetics2016
Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.
Article in Human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Association between HMGCR, CRP, and CETP gene polymorphisms and metabolic/inflammatory serum profile in healthy adolescents.Journal of translational medicine · 2023Article
- APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma.Lung cancer (Amsterdam, Netherlands) · 2022Article
- Individual Oligogenic Background in p.D91A-Genes · 2021Article
- Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI).Diagnostic pathology · 2020Article
- Bleeding risks for uncharacterized platelet function disorders.Research and practice in thrombosis and haemostasis · 2020Article
- Clinical utility of 24-h rapid trio-exome sequencing for critically ill infants.NPJ genomic medicine · 2020Article
- A novel knowledge-derived data potentizing method revealed unique liver cancer-associated genetic variants.Human genomics · 2019Article
- Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues.Frontiers in molecular biosciences · 2019Article
- Whole-Exome Sequencing Identifies Somatic Mutations Associated With Mortality in Metastatic Clear Cell Kidney Carcinoma.Frontiers in genetics · 2019Article
- Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton.Frontiers in genetics · 2019Article
- Whole exome sequencing for the identification of CYP3A7 variants associated with tacrolimus concentrations in kidney transplant patients.Scientific reports · 2018Article
- HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay.Genome research · 2018Article
- Single nucleotide variant sequencing errors in whole exome sequencing using the Ion Proton System.Biomedical reports · 2017Article
- Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.PloS one · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.
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