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Familial Cancer Var...
Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family
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- Kumar, Abhishek (author)
- German Cancer Research Centre
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- Bandapalli, Obul Reddy (author)
- German Cancer Research Centre
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- Paramasivam, Nagarajan (author)
- German Cancer Research Centre,Heidelberg University
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- Giangiobbe, Sara (author)
- German Cancer Research Centre
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- Diquigiovanni, Chiara (author)
- St. Orsola-Malpighi University Hospital
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- Bonora, Elena (author)
- St. Orsola-Malpighi University Hospital
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- Eils, Roland (author)
- German Cancer Research Centre,Heidelberg University
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- Schlesner, Matthias (author)
- German Cancer Research Centre
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- Hemminki, Kari (author)
- Lund University,Lunds universitet,Allmänmedicin och klinisk epidemiologi,Forskargrupper vid Lunds universitet,Family Medicine and Clinical Epidemiology,Lund University Research Groups,Center for Primary Health Care Research,German Cancer Research Centre
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- Försti, Asta (author)
- Lund University,Lunds universitet,Allmänmedicin och klinisk epidemiologi,Forskargrupper vid Lunds universitet,Family Medicine and Clinical Epidemiology,Lund University Research Groups,Center for Primary Health Care Research,German Cancer Research Centre
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(creator_code:org_t)
- 2018-08-02
- 2018
- English.
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Abstract
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- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
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- By the author/editor
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Kumar, Abhishek
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Bandapalli, Obul ...
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Paramasivam, Nag ...
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Giangiobbe, Sara
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Diquigiovanni, C ...
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Bonora, Elena
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show more...
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Eils, Roland
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Schlesner, Matth ...
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Hemminki, Kari
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Försti, Asta
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
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Scientific Repor ...
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Lund University