=Identifying Genes for Mendelian Traits using Next Generation Sequence Data=
===September 18-22, 2017<br data-attributes="%20/">Max Delbrück Center (MDC) for Molecular Medicine<br data-attributes="%20/">Berlin, Germany===The second annual Identifying Genes for Mendelian Traits using Next Generation Sequence Data Course will be held at the [http://www.mdc-berlin.de/ MDC] in Berlin from September 18-22, 2017. The goal of the course is to teach the course participants both theory and application of methods to identify genes for Mendelian diseases/traits using filtering methods, homozygosity mapping and linkage analysis.
Emphasis in this course is on strategies for gene mapping and variant/gene identification for Mendelian Traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (e.g. Gemini, GeneHunter, GERP, Homozygosity Mapper, Integrative Genome Viewer, MERLIN, PhlyoP, Polyphen, SEQLinkage, Variant Mendelian Tools,) and with pencil and paper. TOPICS include: study design; linkage analysis and homozygosity mapping using genotype array and next generation sequence data (exome and whole genome), haplotype reconstruction, evaluating pedigree informativeness and power to detect linkage, vcf file annotation; generation of NGS data; identification of causal variants using filter approaches, variant annotation, evaluation of deleterious effects of variants and their functionality. The organizers and instructors for the course are [https://www.bcm.edu/research/labs/center-for-statistical-genetics/ Suzanne Leal] (Baylor College of Medicine) and [http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/ Michael Nothnagel] (University of Cologne).
The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels. The maximum number of participants is 40.
* Tel: +1 (713) 798-4011
* Fax: +1 (713) 798-4012
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=====[https://statgen.research.bcm.edu/files/2016/10/Schedule_NGS_Mendelian_2016.pdf Click here for course schedule]=====
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=====[http://statgen.us/files/2016/10/BerlinHotelTaxExemptionForm.pdf Link to Berlin hotel tax exemption form]=====
=====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]=====
=====Direction to the classroom=====
Location:
:: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map])
:: Room Axion 2
The building is red and stands across the street from the campus bus stop and the blue bear.
[[File:MDC_C.jpg|none|300x300px]]
===Course Instructors===
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
[[File:2017-NGCM-Instructors.jpg|none|300px]]
===Course Participants===
[[File:2017-NGCM-Participants.jpg|none|500px]]<br />[[File:2017-NGCM-All.jpg|none|500px]]
===Downloads for Course===
Alohomora ([http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32_linux.zip Linux] [http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32-win32.zip Windows])
::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
IGV ([https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar])
::* [https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files]
X11 support
::* [https://sourceforge.net/projects/xming/ Xming (for Windows)]
::* [https://www.xquartz.org/index.html XQuartz (for macOS)]
Gemini
::* [https://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
[https://statgen.research.bcm.edu/files/2017/09/img/Mendelian.tar.bz2 Virtualbox Image] of Course Computers (requires [https://www.virtualbox.org/ VirtualBox])
===Commands for Computer Exercises===
::* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Annovar - Functional Annotation]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Annovar - Variant Filtering]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/gemini.txt Gemini]
::* [https://statgen.research.bcm.edu/files/2016/10/commands/seqlinkage.txt SEQLinkage]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/vat.txt Variant Assocaition Tools]
::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools]
===Data Sets===
::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Alohomora]
::* [https://statgen.research.bcm.edu/files/2017/09/data/annovar.tar.gz Annovar]
::* [https://statgen.research.bcm.edu/files/2017/09/data/gemini.tar.gz Gemini]
::* [https://statgen.research.bcm.edu/files/2016/10/data/genehunter.tar.gz GeneHunter]
::* [https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip IGV BAM and VCF files]
::* [https://statgen.research.bcm.edu/files/2016/10/data/linkage.tar.gz Linkage]
::* [https://statgen.research.bcm.edu/files/2016/10/data/merlin.tar.gz Merlin]
::* [https://statgen.research.bcm.edu/files/2016/10/data/seqlinkage.tar.gz SEQLinkage]
::* [https://statgen.research.bcm.edu/files/2016/10/data/slink.tar.gz SLINK]
::* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
::* [https://statgen.research.bcm.edu/files/2016/10/data/vat.tar.gz Variant Association Tools]
::* [https://statgen.research.bcm.edu/files/2016/10/data/vmt.tar.gz Variant Mendelian Tools]
===Software Links===
::* [http://gmc.mdc-berlin.de/alohomora/ Alohomora]
::* [http://annovar.openbioinformatics.org/en/latest/user-guide/download/ ANNOVAR]
::* [http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html FASTLINK]
::* [https://gemini.readthedocs.org/ Gemini]
::* [http://www.broad.mit.edu/ftp/distribution/software/genehunter/ GeneHunter]
::* [http://www.homozygositymapper.org/ Homozygosity Mapper]
::* [https://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] [https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar [download jar]]
::* [http://www.jurgott.org/linkage/LinkagePC.html LINKAGE]
::* [http://csg.sph.umich.edu/abecasis/Merlin/ MERLIN]
::* [http://www.bioinformatics.org/seqlink/ SEQLinkage]
::* [http://www.jurgott.org/linkage/SLINK.htm SLINK/MSIM]
::* [http://bioinfo.cs.technion.ac.il/superlink-online/index-working2.shtml SUPERLINK]
::* [http://varianttools.sourceforge.net/Association/HomePage Variant Association Tools]
::* [http://statgen.research.bcm.edu/VMT Variant Mendelian Tools]
===Databases===
::* [http://exac.broadinstitute.org/ ExAC]
::* [http://gnomad.broadinstitute.org/ gnomAD]
===Bioinformatic Tools===
::* [http://cadd.gs.washington.edu/score CADD]
::* [http://fathmm.biocompute.org.uk/inherited.html FATHMM]
::* [http://mendel.stanford.edu/SidowLab/downloads/gerp/ GERP]
::* [http://www.genetics.wustl.edu/jflab/lrt_query.html LRT]
::* [http://www.mutationtaster.org/ChrPos.html Mutation Taster]
::* [http://genome.ucsc.edu/cgi-bin/hgGateway Nucleotide Conservation]
::* [http://compgen.bscb.cornell.edu/phast/ PhyloP]
::* [http://genetics.bwh.harvard.edu/pph2/bgi.shtml PolyPhen-2]
::* [http://provean.jcvi.org/genome_submit_2.php?species=human PROVEAN and SIFT]
::* [http://grch37.ensembl.org/Homo_sapiens/Tools/VEP VEP]
===Other Links===
::* [https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf ACMG Standards and Guidelines for the Interpretation of Sequence Variants]