Genetics and pharmacogenomics of diffuse gliomas

Thuijl, Hinke F. van; Ylstra, Bauke; Würdinger, Tom; Nieuwenhuizen, D. van; Heimans, Jan J.; Wesseling, Pieter; Reijneveld, Jaap C.

doi:10.1016/j.pharmthera.2012.09.002

Cited by 9 publications

(17 citation statements)

References 128 publications

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“…Projects investigating cancers with long survival, such as diffuse low-grade gliomas (LGGs) with a subset of patients surviving > 25 yr after diagnosis (van Thuijl et al 2012), require long-term clinical follow-up. Archival FFPE tissue is often the only source of material for study (Blow 2007).…”

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confidence: 99%

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

et al. 2014

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Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with~0.13 genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.

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confidence: 99%

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

et al. 2014

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“…Only after many years were mutations in CIC and FUBP1 associated with codeletion of chromosomal arms 1p and 19q [18,19]. In total 148 genes are located on 10q25.2-qter, including MGMT, DMBT1 and ERCC6 [16,20,21], while the usual suspect, PTEN, is located more proximal to the centromere [16] and is preferentially lost in higher grade gliomas [4].…”

Section: Discussionmentioning

confidence: 99%

“…The disease course of patients with LGGs is correlated with gene mutations, such as in p53 and IDH1, hypermethylation of MGMT as well as chromosomal copy number aberrations (CNAs). Regarding the latter, assessment of combined loss of 1p and 19q currently is implemented in routine clinical care in specific glioma subgroups given its favorable prognostic and predictive value [3,4]. Other CNAs, such as losses of chromosomes 10 and 11p, have been reported to be prognostically unfavorable, but have not been introduced into clinical practice yet, possibly due the limited number of samples included in the studies and/or lack of validation [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

et al. 2014

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Background: The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behavior and can thereby complement the prognostically favorable 1p/19q co-deletion.

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“…IDH1 mutations are heterozygous, and these are involving an amino acid substitution (glycine to arginine) in the active site of the enzyme in codon 132 (R132H). This mutation results in the abnormal production of 2-hydroxyglutarate, which causes histone and deoxyribonucleic acid (DNA) methylation, hence promoting tumorigenesis [27], while IDH2 variants are reported to influence angiogenesis, apoptosis, and glucose metabolism [28].…”

Section: Idh1 and Idh2mentioning

confidence: 99%

The Systemic Treatment of Glioma

Camargo¹

2019

Primary Intracranial Tumors

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Gliomas have been treated by a specialized team including neurosurgery, radiation therapy, and neuro-oncology, as well as depending on integrated sophisticated facilities and multi-professional team. Despite these huge efforts to glioma treatment, glioblastoma, one of the most frequent gliomas, has median life expectance for just 15 months, so these results are still an unmet need. Related to the systemic treatment, some cancer approaches have been revolutionized with new strategies, such as immunotherapy, although in neuro-oncology, this alternative still has challenges to overcome. Throughout this chapter, relevant information and key points will be discussed to the best way to manage systemic treatment and improve glioma overall survival.

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Genetics and pharmacogenomics of diffuse gliomas

Cited by 9 publications

References 128 publications

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

The Systemic Treatment of Glioma

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