Miguel and Youssef

Thank you to all participant of the 4th Annual X-Gen Congress & Expo held this past March San Diego, California.

The excitement and vibe at this year's event is parallel to the technical advances and innovation applications leading the field of diagnostic discovery. X-Gen Congress is a unique event delivering multiple topic focused conferences, short courses and workshops presented by a renowned line-up of speakers representing industry and academia. As in years past the focused short courses provided valuable learning and networking opportunity. And new this year, we proudly welcomed NIST to present an update on the efforts of Genome in a Bottle Consortium, which developed widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing.

Posters featured some of the most current research and data. Congratulations to our poster winners:

"Eliminating Sample Preparation Kits: A Validated Cost-Effective Strategy for NGS Application into the Clinical Diagnosis Routine"
Miguel Mitne-Neto, Fleury S. A. 

"The Use of KRAS Deep Sequencing as a Method to Evaluate Tumour Cellularity in Pancreatic Adenocarcinoma Ductal Samples"
Ami Panchal, Ontario Institute for Cancer Research (OICR) 

"The CARTaGENE Genomics Project: Systems Genetics of Cardiometabolic Phenotypes"
Youssef Idaghdour, University of Montreal 

If you would like to share your feedback, or give input for next year’s event, please contact Mary Ann Brown at mabrown@healthtech.com.

Next-Generation Sequencing (NGS) has enabled faster and cheaper mapping of DNA/RNA, allowing genomic comparisons and accelerating genomic discoveries. Cambridge Healthtech Institute is proud to host the Fourth Annual X-Gen Congress and Expo, which is uniquely designed to cover these technological advances and discover advancing applications. With the focus now on clinical utility, find out why data analysis is the driving force that enables discovery, and is sequencing’s strategic step.

Plenary Keynote Session

Plenary Keynote Session 

2:00 Chairperson’s Opening Remarks

Abizar lakdawalla, Ph.D., Associate Director, New Sequencing Technologies, Illumina

2:15 Profiling Dynamic Regulation of the Epigenome Defines Linkages between Metabolism and Breast Cancer

Kevin GardnerKevin Gardner, M.D., Ph.D., Senior Investigator and Head, Transcription Regulation Section, Center for Cancer Research, NCI, NIH, DHHS
New findings linking epigenetic regulation to cellular processes that drive important hallmarks of cancer will be discussed. The broader impact of these findings on defining molecular and genomic mechanisms that uncover important connections between race, obesity and breast cancer will be reviewed.

3:00 Landscape of Somatic Retrotransposition in Human Cancers

Peter ParkPeter J. Park, Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School; Informatics Program, Children’s Hospital Boston
Transposable elements (TEs) comprise close to half of the human genome, and some TE families are still able to copy and insert their sequences into other genomic loci through an RNA-mediated mechanism. We will describe our analysis of somatic retrotransposition events in cancer and their potential role in tumorigenesis, using a computational method called Tea (Transposable Element Analyzer) we developed for detecting TE integration sites at single-nucleotide resolution from paired-end whole-genome sequencing data. We have identified nearly 200 high-confidence somatic TE insertions in the cancer genomes of 43 patients across multiple tumor types, and our integrative analyses with other data types have indicated their potential impact in tumorigenesis. We will give an update on our efforts at characterizing TE activities in a more comprehensive panel of tumor types.

3:45 Afternoon Refreshment Break

4:00 Gene Regulation and Common Disease

John Stamatoyannopoulos, M.D. Associate Professor, Genome Sciences and Medicine, School of Medicine, University of Washington

5:00 Panel Discussion with Plenary Speakers

Moderator: Abizar lakdawalla, Ph.D., Associate Director, New Sequencing Technologies, Illumina

Thanks to the explosive power of NGS and extraordinary collaborative projects such as ENCODE and TCGA, researchers are gaining important new insights regarding genome function and architecture, including the role of non-coding RNAs and epigenetic modifications in health and disease. In this plenary panel discussion, our opening speakers will discuss the implications of current research and future directions and priorities.

Monday, March 18, 9:00 am – 12:00 pm

(SC1) NGS Sample Prep

(SC2) Functional Genomics

Tuesday, March 19, 5:30 pm – 8:30 pm

(SC3) Sequencing 101

(SC4) NGS Assembly and Alignment

Co-located Events

Genome in a BottleGenome in a Bottle Consortium

Thursday, March 21

7:30 am Consortium Registration

8:30 Genome in a Bottle Consortium

NIST has recently convened the Genome in a Bottle Consortium to develop the reference materials, reference methods, and reference data needed to support confidence in human whole genome variant calls. The work of this consortium will enable translation of sequencing to clinical applications through a community standards development effort.

The consortium will host a morning session to present its work plan, progress at NIST in developing whole-genome reference materials, and updates from each of four working groups: (1) Reference Material (RM) Selection and Design; (2) Measurements for Reference Material Characterization; (3) Bioinformatics, Data Integration and Data Representation; (4) Performance Metrics and Figures of Merit.

Presenters Include:

PodcastMarc Salit, Ph.D., Leader, Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory
Justin Zook, Ph.D., Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory

Justin Johnson, Director, Bioinformatics, EdgeBio
Andrew Grupe, Ph.D., Senior Director Pharmacogenomics, Celera/Quest Diagnostics
Stephen Sherry, Ph.D., Chief, Reference Collections Sections, Information Engineering, National Center for Biotechnology
Michael Eberle, Ph.D., Associate Director, Bioinformatics, Illumina

Click here for detailed agenda 

NISTAn open discussion with the working group  chairs  and consortium hosts from NIST will follow the presentations.

NGS for Drugs, Patients and Clinical Trials

March 22-23
Designed for drug developers to explore the unparalleled advantages of NGS technologies for translational research, while addressing common challenges.
Learn more at healthtech.com/ngs-drug-development 

Media Gallery 

NEW! Genome in a Bottle 

Marc Salit, Ph.D., Leader, Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory
Justin Zook, Ph.D., Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory

Leaders of NIST’s Genome in a Bottle Consortium discuss the importance of developing reference materials, methods, and data needed to support confidence in human whole genome variant calls. Challenges and initial progress stemming from the consortium’s efforts are also discussed.

Click here to download 

Knowing your NGS Upstream: Alignment and Variant Callers 

PodcastGuest: Gabe Rudy, Vice President, Product Development, Golden Helix

Gabe Rudy discusses the importance of choosing the correct alignment and calling tools for successful sequencing.

Click here to download 


Applying NGS and Data Analysis

Hear first-hand what thought leaders are saying about the use of NGS over the past two years, as well as their perspective on where NGS will take us in the future.



Detecting Sense-Antisense Transcripts Differentially Regulated by Androgens in Prostate Cancer Cells

Melanie LehmanMelanie Lehman, Ph.D., Research Scientist, Australian Prostate Cancer Research Centre, Queensland University of Technology

To view the poster, please click here.



2012 DVD 

Technologies and Tools for Life Sciences DVD CoverSequencing 101  
In less than five years next-generation sequencing has gone from radical to routine. Naturally, in a field moving so fast, newbies can feel overwhelmed. Sequencing 101 is designed to provide definitions in terminology, types of platforms, workflow strategies, and current applications, to what's next? Learn about the genomic data revolution from data generation to management to analysis and interpretation.
Click here for more informationOrder DVD    




Ending Diagnostic Odysseys”: A Bio-IT World Podcast

Guest: ELIZABETH WORTHEY PhD, Assistant Professor, Medical College of Wisconsin
Host: KEVIN DAVIES, Editor, Bio-IT World

Elizabeth WortheyA team led by Liz Worthey and Howard Jacob recently published a landmark case report in which genome sequencing of an individual patient, Nicholas Volker, produced a specific diagnosis and a meaningful therapy. Since October 2010, their team at the Medical College of Wisconsin has established a comprehensive review system to end the diagnostic odysseys of other young patients.
In this exclusive podcast, recorded at the Copenhagenomics conference in June 2011, Liz Worthey discusses with Bio-IT World editor Kevin Davies the highs and lows of the Volker case, the challenges of genome data analysis, and how that experience has provided the foundation for ongoing clinical genome sequencing efforts.

Click here to download 

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