ArticleEuropean journal of human genetics : EJHG2018
Optimization of the diagnosis of inherited colorectal cancer using NGS and capture of exonic and intronic sequences of panel genes.
Article in European journal of human genetics : EJHG, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genomic mosaicism in colorectal cancer and polyposis syndromes: a systematic review and meta-analysis.International journal of colorectal disease · 2024Pooled it
- Lynch syndrome caused by a pathogenic SINE-VNTR-Alu (SVA) insertion in MSH2 gene identified by long-read DNA sequencing.Familial cancer · 2026Article
- Detecting likely germline variants during tumor-based molecular profiling.The Journal of clinical investigation · 2025Review
- Article
- New RPS20 gene variant in colorectal cancer diagnosis: insight from a large series of patients.Familial cancer · 2025Article
- Exploring the Role of Non-synonymous and Deleterious Variants Identified in Colorectal Cancer: A Multi-dimensional Computational Scrutiny of Exomes.Current genomics · 2024Article
- Research progress on the biological basis of Traditional Chinese Medicine syndromes of gastrointestinal cancers.Heliyon · 2023Review
- Detection of a pathogenic Alu element insertion in PALB2 gene from targeted NGS diagnostic data.European journal of human genetics : EJHG · 2022Article
- Detecting inversions in routine molecular diagnosis in MMR genes.Familial cancer · 2022Article
- Familial Lynch syndrome with early age of onset and confirmed splice site mutation in MSH2: A case report.Biomedical reports · 2022Article
- Novel method for the genomic analysis ofFrontiers in cell and developmental biology · 2022Article
- Identification and Characterization of NewGenes · 2021Article
- Copy Number Variation and Rearrangements Assessment in Cancer: Comparison of Droplet Digital PCR with the Current Approaches.International journal of molecular sciences · 2021Review
- Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation.European journal of human genetics : EJHG · 2021Article
- Feedback of extended panel sequencing in 1530 patients referred for suspicion of hereditary predisposition to adult cancers.Clinical genetics · 2021Article
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22 authors.
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Abstract
We have developed and validated for the diagnosis of inherited colorectal cancer (CRC) a massive parallel sequencing strategy based on: (i) fast capture of exonic and intronic sequences from ten genes involved in Mendelian forms of CRC (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, STK11, SMAD4, BMPR1A and PTEN); (ii) sequencing on MiSeq and NextSeq 500 Illumina platforms; (iii) a bioinformatic pipeline that includes BWA-Picard-GATK (Broad Institute) and CASAVA (Illumina) in parallel for mapping and variant calling, Alamut Batch (Interactive BioSoftware) for annotation, CANOES for CNV detection and finally, chimeric reads analysis for the detection of other types of structural variants (SVs). Analysis of 1644 new index cases allowed the identification of 323 patients with class 4 or 5 variants, corresponding to a 20% disease-causing variant detection rate. This rate reached 37% in patients with Lynch syndrome, suspected on the basis of tumour analyses. Thanks to this strategy, we detected overlapping phenotypes (e.g., MUTYH biallelic mutations mimicking Lynch syndrome), mosaic alterations and complex SVs such as a genomic deletion involving the last BMPR1A exons and PTEN, an Alu insertion within MSH2 exon 8 and a mosaic deletion of STK11 exons 3-10. This strategy allows, in a single step, detection of all types of CRC gene alterations including SVs and provides a high disease-causing variant detection rate, thus optimizing the diagnosis of inherited CRC.
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