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Pedigree based DNA ...
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Försti, AstaGerman Cancer Research Centre,Center for Primary Health Care Research
(författare)
Pedigree based DNA sequencing pipeline for germline genomes of cancer families
- Artikel/kapitelEngelska2016
Förlag, utgivningsår, omfång ...
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2016-08-09
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Springer Science and Business Media LLC,2016
Nummerbeteckningar
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LIBRIS-ID:oai:lup.lub.lu.se:d5d1a49a-dc3c-48c2-afd2-a08559ebcbf6
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https://lup.lub.lu.se/record/d5d1a49a-dc3c-48c2-afd2-a08559ebcbf6URI
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https://doi.org/10.1186/s13053-016-0058-1DOI
Kompletterande språkuppgifter
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Språk:engelska
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Sammanfattning på:engelska
Ingår i deldatabas
Klassifikation
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Ämneskategori:art swepub-publicationtype
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Ämneskategori:ref swepub-contenttype
Anmärkningar
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Background: In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP). Results: The variant calling step distinguishes two types of genomic variants: single nucleotide variants (SNVs) and indels, which undergo technical quality control. Mendelian types of variants are assumed to be rare and variants with frequencies higher that 0.1 % are screened out using human 1000 Genomes (Phase 3) and non-TCGA ExAC population data. Segregation in the pedigree allows variants to be present in affected family members and not in old, unaffected ones. The effectiveness of variant segregation depends on the number and relatedness of the family members: if over 5 third-degree (or more distant) relatives are available, the experience has shown that the number of likely variants is reduced from many hundreds to a few tens. These are then subjected to bioinformatics analysis, starting with the combined annotation dependent depletion (CADD) tool, which predicts the likelihood of the variant being deleterious. Different sets of individual tools are used for further evaluation of the deleteriousness of coding variants, 5' and 3' untranslated regions (UTRs), and intergenic variants. Conlusions: The likelihood of success of the present genomic pipeline in finding novel high- or medium-penetrant genes depends on many steps but first and foremost, the pedigree needs to be reasonably large and the assignments and diagnoses among the members need to be correct.
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Kumar, AbhishekGerman Cancer Research Centre
(författare)
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Paramasivam, NagarajanHeidelberg University,German Cancer Research Centre
(författare)
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Schlesner, MatthiasGerman Cancer Research Centre
(författare)
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Catalano, CalogerinaGerman Cancer Research Centre
(författare)
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Dymerska, DagmaraPomeranian Medical University
(författare)
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Lubinski, JanPomeranian Medical University
(författare)
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Eils, RolandGerman Cancer Research Centre
(författare)
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Hemminki, KariLund 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(Swepub:lu)med-khk
(författare)
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German Cancer Research CentreCenter for Primary Health Care Research
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Hereditary Cancer in Clinical Practice: Springer Science and Business Media LLC14:11731-23021897-4287
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