AnVIL Portal
CSERClinical Sequencing Evidence-Generating ResearchActive August, 2020 to July, 2023

  • About
  • News
  • Projects
  • Publications
  • Resources
  • Research Materials


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.

CSER Phase 2 Harmonized Measures
CSER1 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:

CSER1 Consortium Organizational Chart

A useful diagram of all different components of the CSER Program and their relationships to one another:

CSER1 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:

CSER Provider Toolkit PDF
MEGA (MEdicine Gene Annotation)

The official CSER1 variant database. Created by NextMed:
TARGET (Tumor Alterations releveant for GEnomic-drive Therapy)

A database of genes that, when somatically altered in cancer, are directly linked to a clinical action. Created by CanSeq:

PHIAL (Precision Heuristics for Interpreting the Alteration Landscape)

A heuristic algorithm for clinical interpretation of cancer genome sequencing data. Created by CanSeq:


Cassandra combines annovar output with other public datasources to output annotated .vcf files. Created by BASIC3:
Atlas 2

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:

Proband is an app for taking family history pedigrees, designed exclusively for the iPad. Created by PediSeq.

Preferences Instrument for Genomic Secondary Results (PIGSR)

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.
Interactive Graphic | Genome and Exome Sequencing in Clinical Practice

A NEJM interactive graphic on clinical genome and exome sequencing. Created by ClinSeq and MedSeq:

Dartmouth University's Interactive Media Laboratory

An online "Mini-Fellowship" developed to help a general clinician learn about Clinical Genetics:

The Jackson Laboratory

Online courses about using family history in the clinic:

Clinical Education at JAX
Harvard Medical School

Online CME courses in a wide range of different topics related to health care:


Medscape offers diverse topics in its online CME library:

A freely accessible, public archive of reports of the relationships among human variations and phenotypes with supporting evidence:
The Exome Variant Server (EVS)

The Exome Variant Server (EVS), a data browser for data from the Exome Sequencing Project (ESP):
dbGaP (Database of Genotypes and Phenotypes)

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:
The UCSC Genome Browser

The UCSC Genome Browser, containing the reference sequence and working draft assemblies for a large collection of genomes:
OMIM (Online Mendelian Inheritance in Man)

OMIM (Online Mendelian Inheritance in Man), a comprehensive, authoritative compendium of human genes and genetic phenotypes:

GeneReviews, expert-authored, peer-reviewed genetic disease descriptions with a clinical focus:
Genetics Home Reference

Genetics Home Reference, consumer-friendly information about the effects of genetic variations on human health:
Center for Mendelian Genomics

Center for Mendelian Genomics, will apply next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions:
The CSER1 ELSI Literature Archive

The CSER1 ELSI literature archive, an ongoing collection of articles and other literature relevant to the ethical, legal, and social implications of genomic sequencing:

Literature Archive