The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

Kadir Caner Akdemir, Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G.W. Verhaak, Rameen Beroukhim, Peter J. Campbell, Lynda Chin, Jesse R. Dixon, P. Andrew Futreal, PCAWG Structural Variation Working Group, Kadir C. Akdemir, Eva G. Álvarez, Adrian Baez‐Ortega, Paul C. Boutros, , Ludmil B. Alexandrov

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Nature Genetics · Feb 5, 2020Peer-reviewedGenomics

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal S. Jain, Youngsook Lucy Jung, Lixing Yang, Dmitry A. Gordenin, Leszek J. Klimczak, Cheng‐Zhong Zhang, David S. Pellman, PCAWG Structural Variation Working Group, Kadir Caner Akdemir, Eva G. Álvarez, Adrian Baez‐Ortega, Rameen Beroukhim, , Kenneth Aldape

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Nature Genetics · Feb 5, 2020Peer-reviewedGenomics

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Yiqun Zhang, Fengju Chen, Nuno A. Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brāzma, PCAWG Transcriptome Working Group, Samirkumar B. Amin, Philip Awadalla, Peter J. Bailey, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, , Paul Alan Edwards

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

Bernardo Rodríguez–Martín, Eva G. Álvarez, Adrian Baez‐Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martín Santamarina, Young Seok Ju, Javier Temes, Daniel García Souto, Harald Detering, Yilong Li, Jorge Rodríguez‐Castro, Ana Dueso-Barroso, Alicia L. Bruzos, , the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

bioRxiv · Sep 7, 2018 · PreprintGenomics