ABSTRACT
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
Subject(s)
Mutation , Neoplasms/genetics , Telomere/genetics , Case-Control Studies , Co-Repressor Proteins/genetics , Genome, Human , Humans , Molecular Chaperones/genetics , RNA, Long Noncoding , Repetitive Sequences, Nucleic Acid , Telomerase/genetics , Whole Genome Sequencing , X-linked Nuclear Protein/geneticsABSTRACT
As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to â¼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
Subject(s)
High-Throughput Nucleotide Sequencing/methods , Leukemia, Lymphoid/genetics , Medulloblastoma/genetics , Mutation , Genome, Human , HumansABSTRACT
Early-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with "classical" (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age, and pursued comparative assessments with seven elderly-onset PCA genomes. Remarkable age-related differences in structural rearrangement (SR) formation became evident, suggesting distinct disease pathomechanisms. Whereas EO-PCAs harbored a prevalence of balanced SRs, with a specific abundance of androgen-regulated ETS gene fusions including TMPRSS2:ERG, elderly-onset PCAs displayed primarily non-androgen-associated SRs. Data from a validation cohort of > 10,000 patients showed age-dependent androgen receptor levels and a prevalence of SRs affecting androgen-regulated genes, further substantiating the activity of a characteristic "androgen-type" pathomechanism in EO-PCA.
Subject(s)
Gene Rearrangement , Genomics , Oncogene Proteins, Fusion/genetics , Prostatic Neoplasms/genetics , Receptors, Androgen/genetics , Serine Endopeptidases/genetics , Trans-Activators/genetics , Adult , Aged , Aged, 80 and over , Computational Biology , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Transcriptional Regulator ERGABSTRACT
Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.
Subject(s)
Cerebellar Neoplasms/genetics , Genome, Human/genetics , Medulloblastoma/genetics , Aging/genetics , Amino Acid Sequence , Cell Transformation, Neoplastic , Cerebellar Neoplasms/classification , Cerebellar Neoplasms/diagnosis , Cerebellar Neoplasms/pathology , Child , Chromatin/metabolism , Chromosomes, Human/genetics , DEAD-box RNA Helicases/genetics , DNA Helicases/genetics , DNA-Binding Proteins/genetics , Genomics , Hedgehog Proteins/metabolism , High-Throughput Nucleotide Sequencing , Histone Demethylases/genetics , Humans , Medulloblastoma/classification , Medulloblastoma/diagnosis , Medulloblastoma/pathology , Methylation , Mutation/genetics , Mutation Rate , Neoplasm Proteins/genetics , Nuclear Proteins/genetics , Oncogene Proteins, Fusion/genetics , Patched Receptors , Patched-1 Receptor , Phosphoprotein Phosphatases/genetics , Polyploidy , Receptors, Cell Surface/genetics , Sequence Analysis, RNA , Signal Transduction , T-Box Domain Proteins/genetics , Transcription Factors/genetics , Wnt Proteins/metabolism , beta Catenin/geneticsABSTRACT
Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the approximately 21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.
