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Your search keyword '"de Vree, Paula J P"' showing total 4 results
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4 results on '"de Vree, Paula J P"'

1. Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing

Author

Allahyar, Amin, Pieterse, Mark, Swennenhuis, Joost, Los-de Vries, G. Tjitske, Yilmaz, Mehmet, Leguit, Roos, Meijers, Ruud W. J., van der Geize, Robert, Vermaat, Joost, Cleven, Arjen, van Wezel, Tom, Diepstra, Arjan, van Kempen, Léon C., Hijmering, Nathalie J., Stathi, Phylicia, Sharma, Milan, Melquiond, Adrien S. J., de Vree, Paula J. P., Verstegen, Marjon J. A. M., Krijger, Peter H. L., Hajo, Karima, Simonis, Marieke, Rakszewska, Agata, van Min, Max, de Jong, Daphne, Ylstra, Bauke, Feitsma, Harma, Splinter, Erik, and de Laat, Wouter

Published
2021
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2. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Author

de Vree, Paula J P, de Wit, Elzo, Yilmaz, Mehmet, van de Heijning, Monique, Klous, Petra, Verstegen, Marjon J A M, Wan, Yi, Teunissen, Hans, Krijger, Peter H L, Geeven, Geert, Eijk, Paul P, Sie, Daoud, Ylstra, Bauke, Hulsman, Lorette O M, van Dooren, Marieke F, van Zutven, Laura J C M, van den Ouweland, Ans, Verbeek, Sjef, van Dijk, Ko Willems, Cornelissen, Marion, Das, Atze T, Berkhout, Ben, Sikkema-Raddatz, Birgit, van den Berg, Eva, van der Vlies, Pieter, Weening, Desiree, den Dunnen, Johan T, Matusiak, Magdalena, Lamkanfi, Mohamed, Ligtenberg, Marjolijn J L, ter Brugge, Petra, Jonkers, Jos, Foekens, John A, Martens, John W, van der Luijt, Rob, van Amstel, Hans Kristian Ploos, van Min, Max, Splinter, Erik, de Laat, Wouter, de Vree, Paula J P, de Wit, Elzo, Yilmaz, Mehmet, van de Heijning, Monique, Klous, Petra, Verstegen, Marjon J A M, Wan, Yi, Teunissen, Hans, Krijger, Peter H L, Geeven, Geert, Eijk, Paul P, Sie, Daoud, Ylstra, Bauke, Hulsman, Lorette O M, van Dooren, Marieke F, van Zutven, Laura J C M, van den Ouweland, Ans, Verbeek, Sjef, van Dijk, Ko Willems, Cornelissen, Marion, Das, Atze T, Berkhout, Ben, Sikkema-Raddatz, Birgit, van den Berg, Eva, van der Vlies, Pieter, Weening, Desiree, den Dunnen, Johan T, Matusiak, Magdalena, Lamkanfi, Mohamed, Ligtenberg, Marjolijn J L, ter Brugge, Petra, Jonkers, Jos, Foekens, John A, Martens, John W, van der Luijt, Rob, van Amstel, Hans Kristian Ploos, van Min, Max, Splinter, Erik, and de Laat, Wouter

Abstract

Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. We show that, unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. This enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, including BRCA1 and BRCA2, and enables haplotyping. We show that TLA can also be used to uncover insertion sites and sequences of integrated transgenes and viruses. TLA therefore promises to be a useful method in genetic research and diagnostics when comprehensive or allele-specific genetic information is needed.

Published
2014

3. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Author

de Vree, Paula J P, primary, de Wit, Elzo, additional, Yilmaz, Mehmet, additional, van de Heijning, Monique, additional, Klous, Petra, additional, Verstegen, Marjon J A M, additional, Wan, Yi, additional, Teunissen, Hans, additional, Krijger, Peter H L, additional, Geeven, Geert, additional, Eijk, Paul P, additional, Sie, Daoud, additional, Ylstra, Bauke, additional, Hulsman, Lorette O M, additional, van Dooren, Marieke F, additional, van Zutven, Laura J C M, additional, van den Ouweland, Ans, additional, Verbeek, Sjef, additional, van Dijk, Ko Willems, additional, Cornelissen, Marion, additional, Das, Atze T, additional, Berkhout, Ben, additional, Sikkema-Raddatz, Birgit, additional, van den Berg, Eva, additional, van der Vlies, Pieter, additional, Weening, Desiree, additional, den Dunnen, Johan T, additional, Matusiak, Magdalena, additional, Lamkanfi, Mohamed, additional, Ligtenberg, Marjolijn J L, additional, ter Brugge, Petra, additional, Jonkers, Jos, additional, Foekens, John A, additional, Martens, John W, additional, van der Luijt, Rob, additional, van Amstel, Hans Kristian Ploos, additional, van Min, Max, additional, Splinter, Erik, additional, and de Laat, Wouter, additional

Published
2014
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4. 4C technology: protocols and data analysis.

Author

van de Werken HJ, de Vree PJ, Splinter E, Holwerda SJ, Klous P, de Wit E, and de Laat W

Subjects
Chromatin Assembly and Disassembly, Cross-Linking Reagents, DNA genetics, DNA Restriction Enzymes chemistry, Formaldehyde chemistry, High-Throughput Nucleotide Sequencing methods, Nucleic Acid Conformation, Polymerase Chain Reaction methods, beta-Globins chemistry, beta-Globins genetics, Chromatin chemistry, Chromosome Mapping methods, DNA chemistry, Sequence Analysis, DNA methods, Statistics as Topic methods
Abstract

Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Published
2012
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