Resources

CSER's research has generated an abundance of resources about CSER work and the use of genomic sequencing in medical care. Some of these resources are listed on this page, including information about CSER as a whole and the software and applications CSER sites have developed and made available for others to use.

Information about the CSER Consortium:

The CSER Consortium Information Slides, a slide deck of the basic information about CSER, ranging from the purpose & specific aims to a site map to the leadership of various aspects of the program: [downloadable file: .ppt] [downloadable file: .pdf]

The CSER Consortium Organizational Chart, a useful diagram of all different components of the CSER Program and their relationships to one another: [downloadable file: .pdf]

Software created by the CSER Consortium:

CSER Guide to Interpreting Genomic Reports, a just-in-time resource toolkit to aid physicians in interpreting genomic reports. Created by the CSER Practitioner Education working group: http://www.ashg.org/education/csertoolkit/index.html

MEGA (MEdicine Gene Annotation), the official CSER variant database. Created by NextMed: https://redcap.iths.org/

TARGET (Tumor Alterations releveant for GEnomic-drive Therapy), is a database of genes that, when somatically altered in cancer, are directly linked to a clinical action. Created by CanSeq: http://www.broadinstitute.org/cancer/cga/target

PHIAL (Precision Heuristics for Interpreting the Alteration Landscape), is a heuristic algorithm for clinical interpretation of cancer genome sequencing data. Created by CanSeq: http://www.broadinstitute.org/cancer/cga/phial

Cassandra combines annovar output with other public datasources to output annotated .vcf files. Created by BASIC3: https://www.hgsc.bcm.edu/software/cassandra

Atlas 2 is a next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data. Created by BASIC3: https://www.hgsc.bcm.edu/software/atlas-2

Proband is an app for taking family history pedigrees, designed exclusively for the iPad. Created by PediSeq: http://probandapp.com/

Preferences Instrument for Genomic Secondary Results (PIGSR) is tool to allow adults undergoing genomic testing to record their preferences about getting incidental or secondary results. http://www.pigsr.org/

Interactive Graphic | Genome and Exome Sequencing in Clinical Practice, a NEJM interactive graphic on clinical genome and exome sequencing. Created by ClinSeq and MedSeq: http://www.nejm.org/action/showMediaPlayer?doi=10.1056/NEJMra1312543&aid...

Genetic and genomic online CME courses

Dartmouth University's Interactive Media Laboratory provides an online "Mini-Fellowship" developed to help a general clinician learn about Clinical Genetics: https://www.genetics-cme.com/tour

The Jackson Laboratory offers online courses about using family history in the clinic: http://www.jaxge.org/content/course-offerings

National Coalition for Health Professional Education in Genetics offers online resources for improving health care through the use of genomics: http://www.nchpeg.org/index.php?option=com_content&view=article&id=26&It...

Harvard Medical School offers online CME courses in a wide range of different topics related to health care: http://hms.harvard.edu/education/continuing-education/online-cme-courses

Medscape offers diverse topics in its online CME library: http://www.medscape.org/resource/genomic-medicine/cme

Other genetic and genomic databases and information sources:

ClinVar, a freely accessible, public archive of reports of the relationships among human variations and phenotypes with supporting evidence: http://www.ncbi.nlm.nih.gov/clinvar/

The Exome Variant Server (EVS), a data browser for data from the Exome Sequencing Project (ESP): http://evs.gs.washington.edu/EVS/

dbGaP (Database of Genotypes and Phenotypes), a database developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype: http://www.ncbi.nlm.nih.gov/gap

The UCSC Genome Browser, containing the reference sequence and working draft assemblies for a large collection of genomes: http://genome.ucsc.edu/

OMIM (Online Mendelian Inheritance in Man), a comprehensive, authoritative compendium of human genes and genetic phenotypes: http://www.ncbi.nlm.nih.gov/omim

GeneReviews, expert-authored, peer-reviewed genetic disease descriptions with a clinical focus : http://www.genereviews.org

Genetics Home Reference, consumer-friendly information about the effects of genetic variations on human health: http://ghr.nlm.nih.gov

Center for Mendelian Genomics, will apply next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions.: http://mendelian.org/

The CSER ELSI literature archive, an ongoing collection of articles and other literature relevant to the ethical, legal, and social implications of genomic sequencing: [downloadable file: .doc]

Participant Consent Forms

Baylor College of Medicine

Brigham & Women's Hospital

Children's Hospital of Philadelphia

ClinSeq

Dana-Farber Cancer Institute

Kaiser Permanente

HudsonAlpha

University of Michigan

University of North Carolina

Univerisity of Washington

Participant Education Materials

Baylor College of Medicine

ClinSeq

Dana-Farber Cancer Institute

University of Michigan

University of North Carolina

University of Washington

Protocol and Research Resources

Baylor College of Medicine

Brigham & Women's Hospital

Dana-Farber Cancer Institute

University of Michigan

Results Report Template

Baylor College of Medicine

Brigham & Women's Hospital

Children's Hospital of Philadelphia

ClinSeq

Dana-Farber Cancer Institute

HudsonAlpha

Kaiser Permanente

University of Michigan

University of North Carolina

University of Washington

Description of Variant Analysis Pipeline

Baylor College of Medicine

Brigham & Women's Hospital

University of North Carolina

Framework for Primary and Secondary Results

Baylor College of Medicine

HudsonAlpha

Kaiser Permanente

University of Washington