ArticleScientific reports2018
Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 42 citations in OpenAlex.
- Genome-wide interaction study with major depression identifies novel variants associated with cognitive function.Molecular psychiatry · 2022Pooled it
- Whole Exome Sequencing IdentifiesInternational journal of molecular sciences · 2021Trial
- RUNX1-Driven CPXM1 Transcription Promotes Malignant Phenotypes and EMT in Gastric Cancer Cells.Cancer science · 2026Article
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Transformative Applications and Innovations in Next-Generation Sequencing Data Analysis.Journal of applied genetics · 2026Review
- Familial colorectal cancer: search for novel predisposition genes.Human genomics · 2025Article
- Introduction to Integrated Proteogenomic Pipeline for Dealing with Pathogenic Missense SNPs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Breast cancer genomic analyses reveal genes, mutations, and signaling networks.Functional & integrative genomics · 2024Article
- Variant ranking pipeline for complex familial disorders.Scientific reports · 2024Article
- Article
- Chromosomal localization of mutated genes in non-syndromic familial thyroid cancer.Frontiers in oncology · 2024Review
- The complementary roles of genome-wide approaches in identifying genes linked to an inherited risk of colorectal cancer.Hereditary cancer in clinical practice · 2023Review
- Article
- Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer.Molecular genetics and genomics : MGG · 2022Article
- Cpxm2 as a novel candidate for cardiac hypertrophy and failure in hypertension.Hypertension research : official journal of the Japanese Society of Hypertension · 2022Article
- Germline Variants ofCancers · 2022Article
- Whole-Exome Sequencing Identifies a Novel Germline Variant inInternational journal of molecular sciences · 2022Article
- Review
- A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer.Journal of personalized medicine · 2021Article
- Whole Genome Sequencing PrioritizesFrontiers in endocrinology · 2021Article
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Authors and funding
10 authors at 2 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing methods in familial cancer are useful to unravel rare clinically important cancer predisposing variants. Here, we present improvements in our pedigree-based familial cancer variant prioritization pipeline referred as FCVPPv2, including 12 tools for evaluating deleteriousness and 5 intolerance scores for missense variants. This pipeline is also capable of assessing non-coding regions by combining FANTOM5 data with sets of tools like Bedtools, ChromHMM, Miranda, SNPnexus and Targetscan. We tested this pipeline in a family with history of a papillary thyroid cancer. Only one variant causing an amino acid change G573R (dbSNP ID rs145736623, NM_019609.4:exon11:c.G1717A:p.G573R) in the carboxypeptidase gene CPXM1 survived our pipeline. This variant is located in a highly conserved region across vertebrates in the peptidase_M14 domain (Pfam ID PF00246). The CPXM1 gene may be involved in adipogenesis and extracellular matrix remodelling and it has been suggested to be a tumour suppressor in breast cancer. However, the presence of the variant in the ExAC database suggests it to be a rare polymorphism or a low-penetrance risk allele. Overall, our pipeline is a comprehensive approach for prediction of predisposing variants for high-risk cancer families, for which a functional characterization is a crucial step to confirm their role in cancer predisposition.
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