Resources

arisLIMS

arisLIMS is an in-house inventory management system designed for dealing with sample documentation and tracking.

Download arisLIMS from GitHub or DockerHub.

Structural Variant Truncator

Converts PennCNV structural variants from spanning multiple regions to one SV per region. Typically this is used for converting microarray called SVs to exome only SVs.

Download Structural Variant Truncator from GitHub.

liftOverCNV

Wrapper to use liftOver to convert CNVs between genome builds. The minimum match is reduced by 1% each time until a matching liftover can be found.

Download liftOverCNV from GitHub.

Curated Gene Lists

CPMG Gene Lists

We have custom curated gene lists based on many different disease types.

Download these lists here.

Curated list of known genomic disorders

This is a curated list from Verbitsky et al. J. Clin Invest 2015 (PMID 25893603) and Verbitsky et al. Nat. Genet 2019 (PMID: 30578417).

Download this list here.

List of Genes for Mendelian Kidney and Genitourinary Disorders

This is an expanded list of 625 Mendelian disorders that can involve the kidney and genitourinary tract developed by Hila Rasouly, Emily Groopman and Reuben Heyman-Kantor (7/31/18).

Download this list here.

Below is the version that is ATAV-compatible. It only has 620 genes because some genes cannot be found on ATAV.

Download this list here.

List of Nephropathy Genes

This is the list of 287 genes for Mendelian disorders of the kidney and genitourinary tract we used in our pilot study of exome sequencing for chronic kidney disease. (Lata et al. Ann Intern Med. 2018 Jan 16;168(2):100-109, PMID: 29204651)

Download this list here.

Diagnosticator

Diagnosticator is a web-based platform open to the broad audience of clinical researchers. It automatically implements American College of Medical Genetics (ACMG) guidelines and screens uploaded variants based on the specification of a few simple parameters, returning a prioritized list of variants for clinical evaluation. The systematic and standardized approach reduces discrepancies related to the human manual interpretation. Diagnosticator also stores and communicates user decisions, creating a community based open-source variant-disease association tool.

Diagnosticator publication is coming out very soon, we'll post it here as soon as it's published, in the meanwhile you can find all necessary documentation and instructions on the Diagnosticator website. We are looking forward to having you abroad and participating in our community development!