Barbara Hrdlickova

Publications (2)43.89 Total impact

• Source

  Available from: Isaäc J Nijman

  Article: Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing.

  Magdalena Harakalova, Michal Mokry, Barbara Hrdlickova, Ivo Renkens, Karen Duran, Henk van Roekel, Nico Lansu, Mark van Roosmalen, Ewart de Bruijn, Isaac J Nijman, Wigard P Kloosterman, Edwin Cuppen
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  ABSTRACT: The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has become a rate-limiting and costly step in high-throughput genetic analysis. Here we present an efficient protocol for parallel library preparation and targeted enrichment of pooled multiplexed bar-coded samples. The procedure is compatible with microarray-based and solution-based capture approaches. The high flexibility of this method allows multiplexing of 3-5 samples for whole-exome experiments, 20 samples for targeted footprints of 5 Mb and 96 samples for targeted footprints of 0.4 Mb. From library preparation to post-enrichment amplification, including hybridization time, the protocol takes 5-6 d for array-based enrichment and 3-4 d for solution-based enrichment. Our method provides a cost-effective approach for a broad range of applications, including targeted resequencing of large sample collections (e.g., follow-up genome-wide association studies), and whole-exome or custom mini-genome sequencing projects. This protocol gives details for a single-tube procedure, but scaling to a manual or automated 96-well plate format is possible and discussed.
  Nature Protocol 12/2011; 6(12):1870-86. · 8.36 Impact Factor
• Source

  Available from: Sabyasachi Senapati

  Article: Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.

  Gosia Trynka, Karen A Hunt, Nicholas A Bockett, Jihane Romanos, Vanisha Mistry, Agata Szperl, Sjoerd F Bakker, Maria Teresa Bardella, Leena Bhaw-Rosun, Gemma Castillejo, [......], Bozena Cukrowska, Elena Urcelay, Jose Ramon Bilbao, M Luisa Mearin, Donatella Barisani, Jeffrey C Barrett, Vincent Plagnol, Panos Deloukas, Cisca Wijmenga, David A van Heel
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  ABSTRACT: Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.
  Nature Genetics 11/2011; 43(12):1193-201. · 35.53 Impact Factor