Next-Generation Sequencing 101:  Clinical Exome & Target Region Sequencing Workshop

In collaboration with Ramathibodi, Medical Genomic Center, Mahidol University, Thailand Center of Excellence for Life Sciences (TCELS), European Research Institute for the Biology of Ageing, University Medical Center Groningen,
The Netherlands, and Life Technologies, we are proud to present the
Next-Generation Sequencing 101:
Clinical Exome & Target Region Sequencing Workshop

40 participants

Day 1
Lectures & Demonstrations
NGS wet lab demonstration for Exome, Whole human genome, & Target Region Sequencing.
NGS data handling and analysis in Excel and in-house DNA and RNA mapping pipelines.
Point-and-Click NGS data analysis tools.
Installing software to participants’ PC for Day 2 & 3 training

Day 2-3
Lecture & Practical sessions.
Exome sequencing data analysis.
Participants are required to bring their personal notebook with window 7, XP, or vista, but not window 8. Computer should equipped with WiFi receiver.

Day One

8:00-8:45 Registration
8:45-15:00 Participants bring their PC to organizer for installing software to use on Day 2 & 3
(Dr. Ekawat and his staff).
8:45- 9:00 Opening ceremony
Dean of Faculty of Medicine, Ramathibodi Hospital, Mahidol University
9:00-12:00 Lecture1
Ramathibodi Medical Genomic center; the completion from small pathogen genomes to whole human genome sequencing in less than 3 hours.
Speakers: Wasun Chantratita, Objoon Trachu , Kristian Ridley, Ekawat Pasomsub
9:00-9:30 Ramathibodi Medical Genomic Center (Wasun)
Reporting of incidental findings in clinical exome and genome sequencing (Wasun)
9:30-10:30 Mutation discovery in rare monogenic disorders.
Using amplicon & exome sequencing in clinical practice.
From Preimplantation genetic diagnosis to newborn and adult screening based on next-generation sequencing (Objoon)
10:30-11:30 Using NGS for Preimplantation aneuploidy detection
Using NGS for Target region sequencing. Inherited Disease and Cancer Panels
Using NGS for Microbial sequencing, panels for metagenomics (Kris)
11:30-12:15 NGS data handling and analysis using Excel & in-house NGS software tools (Ekawat)

Gr.1 Demonstration 1: 13:00-14:00, Demonstration 2: 14:10-15:10, Demonstration 3: 15:20-16:20
Gr.2 Demonstration 3: 13:00-14:00, Demonstration 1: 14:10-15:10, Demonstration 2: 15:20-16:20
Gr.3 Demonstration 2: 13:00-14:00, Demonstration 3: 14:10-15:10, Demonstration 1: 15:20-16:20

Demonstration 1
NGS wet lab based on SOLID XL 5500, Ion PGM, & Ion Proton
Trainers: Chutatip Srichunrusami, Pareena Janchompoo, Suthee Benjaphokee, and Jeerawat Nakkuntod

  • Whole human genome sequencing
  • Rapid exome, transcriptome, targeted amplicon sequencing using semiconductor sequencing technology
  • Primer design tool to create custom, ultrahigh-multiplex primer pools for next generation sequencing.
  • Next generation sequencing comprehensive inherited disease gene panels.
  • Next generation sequencing comprehensive cancer gene panels.
  • Next generation sequencing for metagenomics.
  • HIV-1, HBV, and HCV deep sequencing

Demonstration 2
Point-and-Click software programs for NGS data analysis tools (part1).
Trainers: Chuphong Thongnak, Nipaporn Sankuntaw , Nareenart Iemwimangsa

  • DNASTAR VS Golden Helix VS Enlis Genomics: Server based NGS genome analysis software suites.
  • Ion reporter: Cloud based-automated variant analysis and driver mutation identification for clinical research.
  • HIV-1, HBV, and HCV deep sequencing data analysis & interpretation (DeepChek)

Demonstration 3
Point-and-Click software programs for NGS data analysis tools(part2).
Trainers: Partek specialists

  • Partek Genomics Suite: Server based RNA-Seq, ChIP-Seq, and Methyl-Seq and DNA-Seq.

Day Two

9:00-12:00 Lecture 3
Finding genes for Mendelian disorders. Past and present
Speaker: Marianna Bevova
  • Mendelian disorders. Definition. Short repetition of the main terms
  • Overview of the past methods and approaches. Examples of it successes and limitations. Need for new methods to resolve the remaining cases
  • NGS technology as one of the main breakthrough in medical genetics of the past decade
  • Exome capture technology. New method in finding genes for Mendelian disorders.
Lecture 4
Exome sequence. Overview of the workflow: from samples to data analysis
Speaker: Marianna Bevova
  • How to choose which samples to sequence?
  • DNA isolation and exome capture
  • NGS technique overview (Illumina technology as an example)
  • Data analysis
    1. QC of the data
    2. Alignment of the reads
    3. Variant calling
    4. Variant filtering
    5. Data interpretation
Lecture 5
Initial QC of the data. Alignment. Variant calling
Speaker: Victor Guryev
  • Importance of QC in next generation sequencing data
  • Main parameters to take into account
  • FastQC program for data quality check
  • Mapping sequence reads
  • Quality control of aligned data
  • Mapping files formats
  • Tools for calling SNPs and structural variants
  • Visualizing of the data. IGV software and USCS genome browser
12:00-13:00 Break
13:00-16:00 Practical session
Trainers: Victor Guryev, Marianna Bevova

1. FastQC software - quality of the sequence data
2. Mapping the sequence reads
3. Variant calling
4. Data visualization (IGV, UCSC genome browser)

Day Three

9:00-11:00 Lecture 6
Structural variant calling in whole exome sequence
Speaker: Victor Guryev

Lecture 7
Annotation, filtering and prioritization of variants
Speaker: Marianna Bevova
  • Databases to annotate the variants
    1. Identification of variants (nomenclature, standard databases)
    2. Frequencies (population frequency, control dataset)
  • Algorithms and softwares for functional predictions. Overview. Limitations
    1. Functional modification of the proteins
    2. Species conservation
  • Other annotations
    1. Literature, knowledge
    2. Transcription/posttranscriptional effects
  • Filtering strategies to find the causal variant. Examples of the different scenarios.
11:00-12: 00 Practical session
Finding the causal variant in the whole exome sequence data
Speakers: Marianna Bevova, Victor Guryev
12:00-13:00 Break
13:00-14:00 Practical session (continuation)
14:15-16.30 Lecture 8
Variant found- what next? Main steps to prove causality of the variant. Integration exome data with other genomic data
Speaker: Marianna Bevova

Lecture 9
Exome & Target region sequencing of inherited diseases and familial cancers.
Speaker: Victor Guryev

Lecture 10
Ethical issues. Incidental and secondary findings in exome data. Going back to the family
Speaker: Marianna Bevova

Lecture 11
Exome & Target region sequencing as a strategy to find gene for Mendelian disorders and cancer Advantages and limitations. From research to diagnostics. Conclusions.
Speaker: Marianna Bevova

Q and A