Copy number variant heterogeneity among cancer types reflects inconsistent concordance with diagnostic classifications

Paula Carrio Cordo and Michael Baudis

DNA copy number imbalances in primary cutaneous lymphomas (PCL)

Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2018)

bioRxiv, 2018-09-14. doi:10.1101/417766

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2019)

Enabling population assignment from cancer genomes with SNP2pop.

Huang Q and Baudis M. (2019)

bioRxiv, 2019-01-14. https://doi.org/10.1101/368647 (first version 2018-07-14)

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Bo Gao and Michael Baudis (2021)

Published at Frontiers in Genetics, 2021-05-13

Abstract

Copy number aberrations (CNA) are one of the most important classes of genomic mutations relatedto oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated bymolecular-cytogenetic and genome sequencing based methods. While this data has been instrumentalin the identification of cancer-related genes and promoted research into the relation between CNA andhisto-pathologically defined cancer types, the heterogeneity of source data and derived CNV profilespose great challenges for data integration and comparative analysis. Furthermore, a majority of exist-ing studies have been focused on the association of CNA to pre-selected ”driver” genes with limitedapplication to rare drivers and other genomic elements.

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Khalifa A, Krawitz PM, Koehler S, Laraway BJ, Lehvaeslaiho H, Lloyd KC, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Schofield PN, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN.

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation.

Alex H. Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L. Cameron, Melissa Cline, Malachi Griffith, Obi L. Griffith, Sarah E. Hunt, David Kreda, Jennifer M. Lee, Stephanie Li, Javier Lopez, Eric Moyer, Tristan Nelson, Ronak Y. Patel, Kevin Riehle, Peter N. Robinson, Shawn Rynearson, Helen Schuilenburg, Kirill Tsukanov, Brian Walsh, Melissa Konopko, Heidi L. Rehm, Andrew D. Yates, Robert R. Freimuth, Reece K. Hart

The Progenetix oncogenomic resource in 2021

Qingyao Huang, Paula Carrio Cordo, Bo Gao, Rahel Paloots, Michael Baudis

Database (Oxford). 2021 Jul 17;2021:baab043.

• doi: 10.1093/database/baab043.
• PMID: 34272855
• PMCID: PMC8285936.
• bioRxiv. doi: https://doi.org/10.1101/2021.02.15.428237

This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.