Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.

Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M.

Abstract BACKGROUND: Chromothripsis is a recently discovered phenomenon of genomic rearrangement, possibly arising during a single genome-shattering event. This could provide an alternative paradigm in cancer development, replacing the gradual accumulation of genomic changes with a “one-off” catastrophic event. However, the term has been used with varying operational definitions, with the minimal consensus being a large number of locally clustered copy number aberrations.

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2020)

Genomic Copy Number Signatures Based Classifiers for Subtype Identification in Cancer

Bo Gao and Michael Baudis (2020)

bioRxiv, 2020-12-18

Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data.

Baudis M.

Abstract BACKGROUND: Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. METHODS: Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed.

Geographic assessment of cancer genome profiling studies.

Paula Carrio Cordo, Elise Acheson, Qingyao Huang and Michael Baudis (2020)

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2019)

Online database and bioinformatics toolbox to support data mining in cancer cytogenetics.

Baudis M.

Enabling population assignment from cancer genomes with SNP2pop.

Huang Q and Baudis M. (2020)

Progenetix.net: an online repository for molecular cytogenetic aberration data.

Baudis M, Cleary ML.

Abstract Through sequencing projects and, more recently, array-based expression analysis experiments, a wealth of genetic data has become accessible via online resources. In contrast, few of the (molecular-) cytogenetic aberration data collected in the last decades are available in a format suitable for data mining procedures. www.progenetix.net is a new online repository for previously published chromosomal aberration data, allowing the addition of band-specific information about chromosomal imbalances to oncologic data analysis efforts.

Progenetix: 12 years of oncogenomic data curation.

Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M.

Abstract DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix project (http://www.progenetix.org) has provided a reference resource dedicated to provide the most comprehensive collection of genome-wide CNA profiles.

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Bo Gao and Michael Baudis (2021)

Accepted at Frontiers in Genetics, 2021-04-15

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 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.

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.

arrayMap 2014: an updated cancer genome resource.

Cai H, Gupta S, Rath P, Ai N, Baudis M.

Abstract Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support.