Pre-Conference Short Courses* 

Monday, 8 October

Short Course 1 REGISTRATION 8:30 - 9:00

Short Course 1 • 9:00 - 12:00

Considerations for Analyzing Targeted Next-Generation Sequencing Data 

Introduction to the Challenges of Targeted Sequencing Analysis

Attila Berces, Ph.D., CEO, Omixon Biocomputing

There is a myriad of mapping, alignment and variant calling algorithms most of which have been developed for whole genome sequencing and to some extent population genetic studies. In contrast, NGS based diagnostics deals particular genes or mutations of an individual. In the introduction, I will show some examples of different diagnostic targets and related specific challenges. The audience will learn analysis issues related to
• Target specific differences (GC content, repetitive structures, rate of polymorphism)
• Sequencing technology specific differences (homopolymer error vs snp error, etc)
• Targeting technology based differences (PCR vs hybridization assay)
• Pseudogenes and segmental duplication and alternative haplotype structures

Targeted Sequencing Analysis of Human Leukocyte Antigen Mutations

Tim Hague, Msc, Chief Technology Officer, Omixon

Human leukocyte antigens represent gene-specific analysis challenges regardless the sequencing technology. One of the challenges relate to the high rate of polymorphism which can be as high as hundred times the average mutation rate of the human genome. This problem is made even more severe by the high level of segmental duplications. The duplicated segments can be more similar than the genes of the sequenced individual are similar to the  corresponding gene in the reference genome. For these reasons, often it is impossible to decide between alternative mappings. HLA a prototypical example of many other genes of high pharmacological significance, for example GPCRs and Ion Channels. The audience will learn what tools are available to deal with these issues. In addition, HLA will be used as an example to show how to resolve the two alleles since HLA shows a high degree of heterozygosity.

Targeted Sequencing Analysis of Some Cancer-Susceptibility Genes

Tim Hague, Msc, Chief Technology Officer, Omixon

Finding deleterious mutations in BRCA1 and 2 are breast/ovarian cancer susceptibility genes represent some specific challenge due to the nature of the genomic variants. While the mutation rate in BRCA1 and 2 is low, the number of known mutations is over hundred thousand and there is a high chance of finding novel deleterious mutations in screening samples. A disproportionately high proportion of the mutations are insertions and deletions and the size varies from small missing large segments. In some populations one third of inherited breast cancer is related to fairly large deletions. For these reasons, some of the common analysis techniques that is based on known mutation database such as aligning reads around known indels will unlikely lead to correct identification many important variants. The audience will learn how to overcome these challenges.


13:00 - 13:30 Short Course 2 REGISTRATION


Short Course 2 • 13:30 - 16:30

Software Considerations for Processing, Analyzing and Interpreting Sequence Data 

There is a growing gap between the generation of massively parallel sequencing output and the ability to process, analyze and interpret the resulting data. New users to the sequencing era are left to navigate a bewildering maze of base calling, alignment, assembly and analysis tools, limiting the utility of data for clinical applications. This course will show the comparison results of selected tools and provide a practical guide to choosing and using software to derive variant-phenotype information for researchers, as well as those providing clinically relevant information for physicians.



13:30 Chairperson’s Opening Remarks
Kip Harry, Associate Producer, Conferences, Cambridge Healthtech Institute

13:45 Next Generation Sequencing: An Overview of Technologies, Applications and Analysis Strategies                                                Sponsored by:  Genomatix Software

Matthias Scherf, Ph.D., CTO, Genomatix
The massive amounts of short sequence reads generated by modern next generation sequencing (NGS) technologies can provide detailed insight, if you combine the sequencing results with existing biological knowledge. The talk will introduce some NGS technologies and describe the challenges of downstream data analysis. It will cover the complete path from a brief overview of mapping techniques to some downstream analysis pipelines for typical NGS applications and association with existing knowledge.

14:20 Detecting Single-Nucleotide Variations in Small ncRNAs Using Next-Generation Sequencing

Mario Fasold, Co-Founder and CTO, ecSeq GbR

Next-generation sequencing technologies offer the possibilty to not only capture DNA variations that constitute genetic markers for disease, but also to capture post-transcriptionaly introduced variations on the RNA level. RNA editing has been correlated with several human disease phenotypes. Transcriptome sequencing data in principle can provide information about both SNPs and RNA editing sites. In practice, however, substantial bioinformatic challenges are presented with the analysis of these data.

14:55 Networking Coffee Break

15:10 Analysing Exome Sequencing: How to Choose Your Pipeline and Why

Francesco Lescai, Ph.D., Senior Research Associate, Genome Analysis, University College London

A short overview of different opportunities to analyse exomes data in a human medical context will be given. The presentation will cover the essential criteria in choosing your analysis tools, depending on your level of expertise. Practical examples will be given to help participants understand the main challenges of data analysis and how to deal with them.

Podcasts15:45 Summary of Efforts to Achieve and Evaluate High-Quality Exomes and Genomes - Download Podcast

Gholson J. Lyon, M.D., Ph.D., Assistant Professor, Human Genetics, Cold Spring Harbor Laboratory; Research Scientist, Utah Foundation for Biomedical Research; Adjunct Assistant Professor, Psychiatry, New York University Child Study Center

I will summarize our efforts to optimize variant-calling for single nucleotide variants and indels, using exome and whole genome sequencing datasets obtained using the Illumina and Complete Genomics platforms. I will also discuss the many variant prioritization software programs, along with emphasizing the need to study variants within the immediate family members, so as to best control for genetic background and environmental effects.

16:20 Short Course Wrap-Up

16:30 End of Short Course Two


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