HSLS MolBio Workshops

This is a two-part workshop. Part-1, the morning session provides a brief overview of human genetic variations with the introduction to various genetic variation databases (dbSNP, ClinVar, HGMD, COSMIC, TumorPortal, gnomAD, and RegulomeDb). 

Part-2, the afternoon session  covers variant identification using the HSLS-licensed software CLC Genomics Workbench, how to use bioinformatics tools for functional analysis of mutations, and open-access web tools such as Ensembl Variant Effect Predictor and wANNOVAR

Target Audience

Experimental biologists seeking to identify genetic variations from Whole Exome or Whole Genome Sequencing data. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Powerpoints

• Slides
• Practice Exercise

Data Download

• Genome in a Bottle: Garvan_NA12878_HG001_HiSeq_Exome - a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice and innovations in technologies. 
• Nextera Exome Target Regions
• Genome in a Bottle (.vcf) - mutations presented in a .vcf format
• Hu889433 (.vcf) - mutations presented in a .vcf format
• Personal Genome Project- Data - public genomic data

Software Registration

• HSLS Software Registration
• Register for CLC Genomics Workbench
• HGMD Professional 

Pre-analyzed Results

• VEP_giab_NIST7035_Exome_vcf : identified mutations
• wANNOVAR_gib_NIST7035_exome_Summary - annotated genetic mutations
• wANNOVAR_Hu889433_Exome - annotated genetic mutations
• PredictSNP2 Results- predictions of SNP effect

Video Tutorials

• How to import reads (FASTQ files) into CLCGW 

Documentations

• Knoweng - An interactive learning resource for next-generation sequencing (NGS) techniques

Databases

• Human Gene Mutation Database 
• dbSNP - contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
• 1000 Genomes - a catalogue of common human genetic variation,
• dbVAR - NCBI's database of human genomic Structural Variation
• EBI GWAS Catalog - Catalog of human genome-wide association studies
• Decipher - used by the clinical community to share and compare phenotypic and genotypic data.
• NCBI PheGenI - he Phenotype-Genotype Integrator (PheGenI), merges NHGRI genome-wide association study (GWAS) catalog data with several databases housed at the National Center for Biotechnology Information (NCBI), including Gene, dbGaP, OMIM, eQTL and dbSNP. 
• ClinVar - aggregates information about genomic variation and its relationship to human health.
• PharmGKB - Pharmacogenomics knowledge for personalized medicine
• Cosmic - the Catalogue Of Somatic Mutations In Cancer,
• Tumor Portal - provides Genes, Cancers, DNA Mutations & Annotations
• OMIM-a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily
• GnomAD Browser - genome aggregation database

Functional Analysis Tools

• Entrez SNP - search engine for dbSNP
• Entrez Protein  - search NCBI protein database
• TMHMM Server - Prediction of transmembrane helices in proteins
• ESE Finder
• Variant Effect Predictor- a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data
• wANNOVAR- a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data.
• PredictSNP2 - a platform for prediction of SNP effect

Key References

• Bao, R., Huang, L., Andrade, J., Tan, W., Kibbe, W. A., Jiang, H., & Feng, G. (2014). Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Informatics, 13(Suppl 2), 67–82. doi:10.41
• GATK Best Practices
• Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., … Alexander, N. (2016). Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data, 3, 160025. doi:10.1038/sdata.2016.25
• Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10(10):1556-1566. doi:10.1038/nprot.2015.105 

Publications citing HGMD from Pitt researchers

Attribution

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

[Software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.

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Support

• Contact Pitt- CRC
• HSLS-MBIS
• Qiagen Bioinformatics