HotTopics: Detecting variations in the human genome using NGS

HotTopicsPepper

April 16, 2012, SURF Utrecht

The new sequencing technologies are transforming the study of genomic variation. Detection of base-pair level and structural variants (SVs) and their association to human disease is a challenging and although various computational methods have been described for the detection of variations, no algorithm is fully capable of discovering all types of variants reliably.

During this HotTopics meeting we will elaborate on the use of different experimental and computation approaches to call all types of variants across different size ranges. The comprehensive discovery, characterization and understanding the origins of genomic variants have important implications for studying human evolution and disease.

The aim is to identify advances, issues and challenges of these methods in the context of recent developments in genomics, proteomics and metabolomics. In an open discussion we want to learn how to make the best out of these computational techniques for a better understanding of biology.

Keywords: variation detection, SVs, high-throughput data, NGS, human genome

Programme April 16th

12:30 – 12:35 Welcome – Marc van Driel
12:35 – 13:10 Lunch
13:10 – 14:00 GATK (SNP, short indel and VQSR): mismatch, gap alignment
and filtering
Laurent Francioli, UMC Utrecht
14:00 – 14:50 Pindel: Split-read method for detecting indels and structural variants
Eric-Wubbo Lameijer, LUMC
14:50 – 15:00 Tea break
15:00 – 15:50 123SV and DWAC-Seq: read-pair and read-depth
Victor Guryev, Hubrecht Institute
15:50 – 16:40 CLEVER: Clique-Enumerating Variant Finder
Alexander Schönhuth, CWI
16:50 – 17:10 General discussion
17:10 – 17:15 Closing

Location

SURFfoundation, Hojel City Center, gebouw D (5e verdieping), Graadt van Roggenweg 340, 3531 AH Utrecht, (max. 25 participants) – Website/route

About HotTopics

NBIC HotTopics are a new series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

Four scientists will give a 20 minute lecture followed by 40 minutes of discussion on the important computational concepts:

  • What does a method try to accomplish?
  • What assumptions were made?
  • How does this method compare to similar ones?
  • What are the strengths, weaknesses and pitfalls?
  • Can we apply it in other areas?
  • What are the limitations and challenges for new applications and developments?

Flip over, beamer and laptop are available.

Organising committee