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

Paula Carrio Cordo and Michael Baudis

The Progenetix oncogenomic resource in 2021

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

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

Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith O, Hunt S, Kreda D, Lee J, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm H, Yates AD, Freimuth RR, Hart RK.

bioRxiv. 20212021.01.15.426843.

Genomic Copy Number Signatures Based Classifiers for Subtype Identification in Cancer

Bo Gao and Michael Baudis (2020)

bioRxiv, 2020-12-18

DNA Copy Number Changes in Diffuse Large B Cell Lymphomas (Review)

Luciano Cascione, Luca Aresu, Michael Baudis and Francesco Bertoni

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

Salgado D, Armean IM, Baudis M et al.

F1000Research 2020, 9 (ELIXIR):1229

The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency

Marco Gatti, Ralph Imhof, Qingyao Huang, Michael Baudis, Matthias Altmeyer

Oncology Informatics: Status Quo and Outlook.

Paul Martin Putora, Michael Baudis, Beth M. Beadle, Issam El Naqa, Frank A. Giordano and Nils H. Nicolay

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2020)

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Alex H. Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P. Duren, Jianjiong Gao, Julie McMurry, Sara Patterson, Catherine del Vecchio Fitz, Beth A. Pitel, Ozman U. Sezerman, Kyle Ellrott, Jeremy L. Warner, Damian T. Rieke, Tero Aittokallio, Ethan Cerami, Deborah I. Ritter, Lynn M. Schriml, Robert R. Freimuth, Melissa Haendel, Gordana Raca, Subha Madhavan, Michael Baudis, Jacques S. Beckmann, Rodrigo Dienstmann, Debyani Chakravarty, Xuan Shirley Li, Susan Mockus, Olivier Elemento, Nikolaus Schultz, Nuria Lopez-Bigas, Mark Lawler, Jeremy Goecks, Malachi Griffith, Obi L. Griffith, Adam A. Margolin & Variant Interpretation for Cancer Consortium

Nature Genetics volume 52, pages 448–457 (2020)

Geographic assessment of cancer genome profiling studies.

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

Enabling population assignment from cancer genomes with SNP2pop.

Huang Q and Baudis M. (2020)

Geographic assessment of cancer genome profiling studies.

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

Leveraging European infrastructures to access 1 million human genomes by 2022

Gary Saunders, Michael Baudis, Regina Becker, Sergi Beltran, Christophe Béroud, Ewan Birney, Cath Brooksbank, Søren Brunak, Marc Van den Bulcke, Rachel Drysdale, Salvador Capella-Gutierrez, Paul Flicek, Francesco Florindi, Peter Goodhand, Ivo Gut, Jaap Heringa, Petr Holub, Jef Hooyberghs, Nick Juty, Thomas M. Keane, Jan O. Korbel, Ilkka Lappalainen, Brane Leskosek, Gert Matthijs, Michaela Th. Mayrhofer, Andres Metspalu, Steven Newhouse, Tommi Nyrönen, Angela Page, Bengt Persson, Aarno Palotie, Helen Parkinson, Jordi Rambla, David Salgado, Erik Steinfelder, Morris A. Swertz, Susheel Varma, Niklas Blomberg, and Serena Scollen

Nature Reviews Genetics volume 20, pages693–701 (2019)

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2019)

Federated discovery and sharing of genomic data using Beacons

Miroslav Cupak , Stephen Keenan , Jordi Rambla , Sabela de la Torre , Stephanie Dyke , Anthony Brookes , Knox Carey , David Lloyd , Peter Goodhand , Maximilian Haeussler , Michael Baudis , Heinz Stockinger , Lena Dolman , Ilkka Lappalainen , Juha Törnroos , Mikael Linden , John Spalding , Saif Ur-Rehman , Angela Page , Paul Flicek , Susheel Varma , Gary Saunders , Serena Scollen , Stephen Sherry , David Haussler , Beacon Project Team

Nat Biotechnol (2019), accepted 2019-01-23

DNA copy number imbalances in primary cutaneous lymphomas (PCL)

Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2019)

JEADV, 2019-01-19. https://doi.org/10.1111/jdv.15442

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)

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

Registered access: authorizing data access

Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, and Flicek P

European Journal of Human Genetics (2018)

Mountains and Chasms - Surveying the Oncogenomic Publication Landscape

Carrio Cordo P and Baudis M. (2018)

Preprints 2018, 2018070618 (doi: 10.20944/preprints201807.0618.v1).

Oncology (2018; online Oct 26)

Population assignment from cancer genome profiling data.

Huang Q and Baudis M. (2018)

bioRxiv, 2018-07-14. doi:10.1101/368647

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu Pons J, Duren R, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Sezerman OU, Warner J, Rieke DT, Aittokallio T, Cerami E, Ritter D, Schriml LM, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus SM, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, and Margolin A

bioRxiv. doi:10.1101/366856

Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins.

Marrero-Rodríguez D, Taniguchi-Ponciano K, Subramaniam M, Hawse JR, Pitel KS, Arreola-De la Cruz H, Huerta-Padilla V, Ponce-Navarrete G, Figueroa-Corona MDP, Gomez-Virgilio L, Martinez-Cuevas TI, Mendoza-Rodriguez M, Rodriguez-Esquivel M, Romero-Morelos P, Ramirez-Salcedo J, Baudis M, Meraz-Rios M, Jimenez-Vega F, Salcedo M.

segment_liftover : a Python tool to convert segments between genome assemblies.

Gao B, Huang Q and Baudis M

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma.

Mackay A, Burford A, Carvalho D, Izquierdo E, Fazal-Salom J, Taylor KR, Bjerke L, Clarke M, Vinci M, Nandhabalan M, Temelso S, Popov S, Molinari V, Raman P, Waanders AJ, Han HJ, Gupta S, Marshall L, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Ng HK, Li X, Mu K, Trabelsi S, Brahim DH, Kisljakov AN, Konovalov DM, Moore AS, Carcaboso AM, Sunol M, de Torres C, Cruz O, Mora J, Shats LI, Stavale JN, Bidinotto LT, Reis RM, Entz-Werle N, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Monje M, Debily MA, Castel D, Grill J, Hawkins C, Nikbakht H, Jabado N, Baker SJ, Pfister SM, Jones DTW, Fouladi M, von Bueren AO, Baudis M, Resnick A, Jones C.

CNARA: reliability assessment for genomic copy number profiles.

Ai N, Cai H, Solovan C, Baudis M.

PKCα and HMGB1 antagonistically control hydrogen peroxide-induced poly-ADP-ribose formation.

Andersson A, Bluwstein A, Kumar N, Teloni F, Traenkle J, Baudis M, Altmeyer M, Hottiger MO.

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members.

A Biobank Supporting Rare Disease Research In Dermatopathology. Our Experience In Establishing A Biobank.

Beleut M, Seclaman E, Baudis M, Nicula A, and Solovan C

RoJCED 2, 202-206 (2015)

arrayMap 2014: an updated cancer genome resource.

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

Genomic instability of osteosarcoma cell lines in culture: impact on the prediction of metastasis relevant genes.

Muff R, Rath P, Ram Kumar RM, Husmann K, Born W, Baudis M, Fuchs B.

Progenetix: 12 years of oncogenomic data curation.

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

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.

Biopsying parapsoriasis: quo vadis? Are morphological stains enough or are ancillary tests needed?

Baderca F, Chiticariu E, Baudis M, Solovan C.

SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome.

Krieger M, Roos A, Stendel C, Claeys KG, Sonmez FM, Baudis M, Bauer P, Bornemann A, de Goede C, Dufke A, Finkel RS, Goebel HH, Häussler M, Kingston H, Kirschner J, Medne L, Muschke P, Rivier F, Rudnik-Schöneborn S, Spengler S, Inzana F, Stanzial F, Benedicenti F, Synofzik M, Lia Taratuto A, Pirra L, Tay SK, Topaloglu H, Uyanik G, Wand D, Williams D, Zerres K, Weis J, Senderek J.

Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas.

Martin-Guerrero I, Salaverria I, Burkhardt B, Szczepanowski M, Baudis M, Bens S, de Leval L, Garcia-Orad A, Horn H, Lisfeld J, Pellissery S, Klapper W, Oschlies I, Siebert R.

High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas.

Salaverria I, Martin-Guerrero I, Burkhardt B, Kreuz M, Zenz T, Oschlies I, Arnold N, Baudis M, Bens S, García-Orad A, Lisfeld J, Schwaenen C, Szczepanowski M, Wessendorf S, Pfreundschuh M, Trümper L, Klapper W, Siebert R.

PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts.

Bluwstein A, Kumar N, Léger K, Traenkle J, Oostrum Jv, Rehrauer H, Baudis M, Hottiger MO.

Molecular karyotyping as a relevant diagnostic tool in children with growth retardation with Silver-Russell features.

Spengler S, Begemann M, Ortiz Brüchle N, Baudis M, Denecke B, Kroisel PM, Oehl-Jaschkowitz B, Schulze B, Raabe-Meyer G, Spaich C, Blümel P, Jauch A, Moog U, Zerres K, Eggermann T.

2p21 Deletions in hypotonia-cystinuria syndrome.

Eggermann T, Spengler S, Venghaus A, Denecke B, Zerres K, Baudis M, Ensenauer R.

Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL.

Wernstedt A, Valtorta E, Armelao F, Togni R, Girlando S, Baudis M, Heinimann K, Messiaen L, Staehli N, Zschocke J, Marra G, Wimmer K.

DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis.

von Bueren AO, Gerss J, Hagel C, Cai H, Remke M, Hasselblatt M, Feuerstein BG, Pernet S, Delattre O, Korshunov A, Rutkowski S, Pfister SM, Baudis M.

arrayMap: a reference resource for genomic copy number imbalances in human malignancies.

Cai H, Kumar N, Baudis M.

Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data.

Kumar N, Cai H, von Mering C, Baudis M.

Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma.

Luebke AM, Baudis M, Matthaei H, Vashist YK, Verde PE, Hosch SB, Erbersdobler A, Klein CA, Izbicki JR, Knoefel WT, Stoecklein NH.

Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome.

Beleut M, Zimmermann P, Baudis M, Bruni N, Bühlmann P, Laule O, Luu VD, Gruissem W, Schraml P, Moch H.

Silver-Russell patients showing a broad range of ICR1 and ICR2 hypomethylation in different tissues.

Begemann M, Spengler S, Kanber D, Haake A, Baudis M, Leisten I, Binder G, Markus S, Rupprecht T, Segerer H, Fricke-Otto S, Mühlenberg R, Siebert R, Buiting K, Eggermann T.

CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations.

Kumar N, Rehrauer H, Cai H, Baudis M.

MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells.

Lacunza E, Baudis M, Colussi AG, Segal-Eiras A, Croce MV, Abba MC.

Increased expression of cellular retinol-binding protein 1 in laryngeal squamous cell carcinoma.

Peralta R, Baudis M, Vazquez G, Juárez S, Ortiz R, Decanini H, Hernandez D, Gallegos F, Valdivia A, Piña P, Salcedo M.

Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15).

Eggermann T, Spengler S, Bachmann N, Baudis M, Mau-Holzmann UA, Singer S, Rossier E.

Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome.

Spengler S, Schönherr N, Binder G, Wollmann HA, Fricke-Otto S, Mühlenberg R, Denecke B, Baudis M, Eggermann T.

Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region.

Eggermann T, Schönherr N, Spengler S, Jäger S, Denecke B, Binder G, Baudis M.

Quantifying cancer progression with conjunctive Bayesian networks.

Gerstung M, Baudis M, Moch H, Beerenwinkel N.

Inferring progression models for CGH data.

Liu J, Bandyopadhyay N, Ranka S, Baudis M, Kahveci T.

Recurrent loss, but lack of mutations, of the SMARCB1 tumor suppressor gene in T-cell prolymphocytic leukemia with TCL1A-TCRAD juxtaposition.

Bug S, Dürig J, Oyen F, Klein-Hitpass L, Martin-Subero JI, Harder L, Baudis M, Arnold N, Kordes U, Dührsen U, Schneppenheim R, Siebert R.

Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge.

Boerma EG, Siebert R, Kluin PM, Baudis M.

Chromosomal changes characterize head and neck cancer with poor prognosis.

Bauer VL, Braselmann H, Henke M, Mattern D, Walch A, Unger K, Baudis M, Lassmann S, Huber R, Wienberg J, Werner M, Zitzelsberger HF.

A 10.7 Mb interstitial deletion of 13q21 without phenotypic effect defines a further non-pathogenic euchromatic variant.

Roos A, Elbracht M, Baudis M, Senderek J, Schönherr N, Eggermann T, Schüler HM.

Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH.

Hoischen A, Ehrler M, Fassunke J, Simon M, Baudis M, Landwehr C, Radlwimmer B, Lichter P, Schramm J, Becker AJ, Weber RG.

Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma.

Nieländer I, Martín-Subero JI, Wagner F, Baudis M, Gesk S, Harder L, Hasenclever D, Klapper W, Kreuz M, Pott C, Martinez-Climent JA, Dreyling M, Arnold N, Siebert R.

Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32).

Dürig J, Bug S, Klein-Hitpass L, Boes T, Jöns T, Martin-Subero JI, Harder L, Baudis M, Dührsen U, Siebert R.

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

Baudis M.

ABCB1 over-expression and drug-efflux in acute lymphoblastic leukemia cell lines with t(17;19) and E2A-HLF expression.

Baudis M, Prima V, Tung YH, Hunger SP.

Distance-based clustering of CGH data.

Liu J, Mohammed J, Carter J, Ranka S, Kahveci T, Baudis M.

Allele-specific loss of heterozygosity in multiple colorectal adenomas: toward an integrated molecular cytogenetic map II.

Mao X, Hamoudi RA, Talbot IC, Baudis M.

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

Baudis M.

Genetic losses in breast cancer: toward an integrated molecular cytogenetic map.

Mao X, Hamoudi RA, Zhao P, Baudis M.

Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma.

Vandesompele J, Baudis M, De Preter K, Van Roy N, Ambros P, Bown N, Brinkschmidt C, Christiansen H, Combaret V, Lastowska M, Nicholson J, O’Meara A, Plantaz D, Stallings R, Brichard B, Van den Broecke C, De Bie S, De Paepe A, Laureys G, Speleman F.

Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma.

Hidalgo A, Baudis M, Petersen I, Arreola H, Piña P, Vázquez-Ortiz G, Hernández D, González J, Lazos M, López R, Pérez C, García J, Vázquez K, Alatorre B, Salcedo M.

Randomized study to evaluate the use of high-dose therapy as part of primary treatment for “aggressive” lymphoma.

Kaiser U, Uebelacker I, Abel U, Birkmann J, Trümper L, Schmalenberg H, Karakas T, Metzner B, Hossfeld DK, Bischoff HG, Franke A, Reiser M, Müller P, Mantovani L, Grundeis M, Rothmann F, von Seydewitz CU, Mesters RM, Steinhauer EU, Krahl D, Schumacher K, Kneba M, Baudis M, Schmitz N, Pfab R, Köppler H, Parwaresch R, Pfreundschuh M, Havemann K.

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

Baudis M, Cleary ML.

Gain of chromosome arm 9p is characteristic of primary mediastinal B-cell lymphoma (MBL): comprehensive molecular cytogenetic analysis and presentation of a novel MBL cell line.

Bentz M, Barth TF, Brüderlein S, Bock D, Schwerer MJ, Baudis M, Joos S, Viardot A, Feller AC, Müller-Hermelink HK, Lichter P, Döhner H, Möller P.

Potential of chromosomal and matrix-based comparative genomic hybridization for molecular diagnostics in lymphomas.

Wessendorf S, Lichter P, Schwänen C, Fritz B, Baudis M, Walenta K, Kloess M, Döhner H, Bentz M.

Comparative genomic hybridization for the analysis of leukemias and lymphomas.

Baudis M, Bentz M.

t(11;14)-positive mantle cell lymphomas exhibit complex karyotypes and share similarities with B-cell chronic lymphocytic leukemia.

Bentz M, Plesch A, Bullinger L, Stilgenbauer S, Ott G, Müller-Hermelink HK, Baudis M, Barth TF, Möller P, Lichter P, Döhner H.

Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: toward a genetic model of meningioma progression.

Weber RG, Boström J, Wolter M, Baudis M, Collins VP, Reifenberger G, Lichter P.

High-level DNA amplifications are common genetic aberrations in B-cell neoplasms.

Werner CA, Döhner H, Joos S, Trümper LH, Baudis M, Barth TF, Ott G, Möller P, Lichter P, Bentz M.

Efficacy of current molecular cytogenetic protocols for the diagnosis of chromosome aberrations in tumor specimens.

Lichter P, Fischer K, Joos S, Fink T, Baudis M, Potkul RK, Ohl S, Solinas-Toldo S, Weber R, Stilgenbauer S, Bentz M, Döhner H.

Chromosome imbalances in papillary renal cell carcinoma and first cytogenetic data of familial cases analyzed by comparative genomic hybridization.

Bentz M, Bergerheim US, Li C, Joos S, Werner CA, Baudis M, Gnarra J, Merino MJ, Zbar B, Linehan WM, Lichter P.

Identification of genetic imbalances in malignant lymphoma using comparative genomic hybridization.

Bentz M, Döhner H, Werner CA, Huck K, Baudis M, Joos S, Schlegelberger B, Trümper LH, Feller AC, Pfreundschuh M.