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
- Patient Consent Form
- Patient Consent Form (Spanish Version)
- Physician Consent Form
- Parent Consent Form
- Parent Consent Form (Spanish Version)
- Age of Majority Consent Form
Brigham & Women's Hospital
- Cardiologist Consent Form
- Primary Care Physician Consent Form
- Patient Consent Form (Cardiology)
- Patient Consent Form (Primary Care Physician)
Children's Hospital of Philadelphia
ClinSeq
Dana-Farber Cancer Institute
Kaiser Permanente
HudsonAlpha
University of Michigan
University of North Carolina
- Parental Consent for Child Relatives of an study participant to test for a specific variant
- Assent Form: (Ages 7-14) Relatives of an study participant to test for a specific variant
- Assent Form: (Ages 15-17) Relatives of an study participant to test for a specific variant
- Consent for Adult Relatives of an study participant to test for a specific variant
Univerisity of Washington
Participant Education Materials
Baylor College of Medicine
- Study Brochure
- Study Borchure (Spanish Version)
- Genetic Information Nondiscrimination Act (GINA) Document
- GINA Document (Spanish Version)
- Tumor Mutation Explanation Card
- Tumor Mutation Explanation Card (Spanish Version)
- Inherited Mutation Explanation Card
- INherited Mutation Explanation Card (Spanish Version)
- X-Linked Explanation Card
- X-Linked Explanation Card (Spanish Version)
- Revised Carrier Status Explanation Card
- Revised Carrier Status Explanation (Spanish Version)
ClinSeq
Dana-Farber Cancer Institute
University of Michigan
University of North Carolina
University of Washington
Protocol and Research Resources
Baylor College of Medicine
- Germline Requisition Document
- Study Questionnaires for Primary or Secondary parent completing for themselves
- Study Questionnaires for Primary or Secondary parent completing for themselves (Spanish Version)
- Family history questionnaire for primary parent
- Family history questionnaire for primary parent (Spanish Version)
- Study questionnaire for primary parent completing for child
- Study questionnaire for primary completing comleting for child (Spanish Version)
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
- Negative Carrier Status Report Template
- Positive Carrier Status Report Template
- Negative Whole Genome Sequencing Incidental Findings Template
University of Michigan
University of North Carolina
University of Washington
- Report Template for Positive Incidental Finding result
- Report Template for Negative Diagnosis Result
- Report Template for Positive Diagnosis Result
Description of Variant Analysis Pipeline
Baylor College of Medicine
Brigham & Women's Hospital
University of North Carolina
- NCGenes Medical Workflow Engine Description
- NCGenes Variant Database Description
- NCGenes MapSeq Sequence Analysis Workflow Description
Framework for Primary and Secondary Results
Baylor College of Medicine
HudsonAlpha
Kaiser Permanente
- List of Genes/Conditions reported for Carrier Status
- List of Genes/Conditions reported for Incidental Findings
University of Washington