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Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants : Application of a points-based ACMG/AMP approach

Thomassen, Mads (author)
Odense University Hospital
Mesman, Romy L.S. (author)
Leiden University Medical Centre
Hansen, Thomas V.O. (author)
Copenhagen University Hospital
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Menendez, Mireia (author)
Catalan Institute of Oncology
Rossing, Maria (author)
Copenhagen University Hospital
Esteban-Sánchez, Ada (author)
Hospital Clinico San Carlos de Madrid
Tudini, Emma (author)
QIMR Berghofer Medical Research Institute
Törngren, Therese (author)
Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
Parsons, Michael T. (author)
QIMR Berghofer Medical Research Institute
Pedersen, Inge S. (author)
Aalborg University,Aalborg University Hospital
Teo, Soo H. (author)
University of Malaya,Cancer Research Initiatives Foundation
Kruse, Torben A. (author)
Odense University Hospital
Møller, Pål (author)
Norwegian Radium Hospital
Borg, Åke (author)
Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
Jensen, Uffe B. (author)
Aarhus University Hospital
Christensen, Lise L. (author)
Aarhus University Hospital
Singer, Christian F. (author)
Medical University of Vienna
Muhr, Daniela (author)
Medical University of Vienna
Santamarina, Marta (author)
Complejo Hospitalario Universitario de Santiago,Biomedical Network on Rare Diseases (CIBERER)
Brandao, Rita (author)
Yukioka Hospital
Andresen, Brage S. (author)
University of Southern Denmark
Feng, Bing Jian (author)
Huntsman Cancer Institute
Canson, Daffodil (author)
QIMR Berghofer Medical Research Institute
Richardson, Marcy E. (author)
Ambry Genetics Corporation
Karam, Rachid (author)
Ambry Genetics Corporation
Pesaran, Tina (author)
Ambry Genetics Corporation
LaDuca, Holly (author)
Ambry Genetics Corporation
Conner, Blair R. (author)
Ambry Genetics Corporation
Abualkheir, Nelly (author)
Ambry Genetics Corporation
Hoang, Lily (author)
Ambry Genetics Corporation
Calléja, Fabienne M.G.R. (author)
Leiden University Medical Centre
Andrews, Lesley (author)
James, Paul A. (author)
Peter MacCallum Cancer Centre,University of Melbourne
Bunyan, Dave (author)
University of Southampton
Hamblett, Amanda (author)
Radice, Paolo (author)
Istituto Nazionale dei Tumori
Goldgar, David E. (author)
Huntsman Cancer Institute
Walker, Logan C. (author)
Engel, Christoph (author)
Leipzig University
Claes, Kathleen B.M. (author)
Ghent University Hospital
Macháčková, Eva (author)
Masaryk Memorial Cancer Institute
Baralle, Diana (author)
University of Southampton
Viel, Alessandra (author)
CRO (Centro di Riferimento Oncologico) Aviano National Cancer Institute
Wappenschmidt, Barbara (author)
University Hospital of Cologne
Lazaro, Conxi (author)
Catalan Institute of Oncology
Vega, Ana (author)
Biomedical Network on Rare Diseases (CIBERER),Complejo Hospitalario Universitario de Santiago
Vreeswijk, Maaike P.G. (author)
Leiden University Medical Centre
de la Hoya, Miguel (author)
Hospital Clinico San Carlos de Madrid
Spurdle, Amanda B. (author)
QIMR Berghofer Medical Research Institute
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 (creator_code:org_t)
 
2022-10-23
2022
English 24 s.
In: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 43:12, s. 1921-1944
Related links:
http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
https://doi.org/10.1...
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  • Journal article (peer-reviewed)
Abstract Subject headings
Close  
  • Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

Keyword

ACMG/AMP classification
BRCA2
dPCR
functional analysis
quantitation
splicing

Publication and Content Type

art (subject category)
ref (subject category)

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