Mar Mallo

IJC Josep Carreras Leukemia Research Institute | IJC · Microarrays Unit

RNA-Sequencing (RNA-Seq) can identify gene fusions in tumors, but not all these fusions have functional consequences. Using multiple data bases, we have performed an in silico analysis of fusions detected by RNA-Seq in tumor samples from 139 newly diagnosed glioblastoma patients to identify in-frame fusions with predictable oncogenic potential. Amo...

e14039 Background: Glioblastoma (GB) is the most prevalent primary brain tumor in adults. The first-line treatment is based on standard brain surgery and adjuvant radio-chemotherapy. Indoleamine 2,3-dioxygenase 1 (IDO1) is a catabolic enzyme that plays a role in the metabolism of tryptophan (Trp), thereby promoting a state of immunosuppression. New...

Purpose: Glioblastoma is the most aggressive brain tumor in adults and has few therapeutic options. The study of molecular subtype classifications may lead to improved prognostic classification and identification of new therapeutic targets. The TCGA subtype classification has mainly been applied in USA clinical trials, while the IGS has mainly bee...

Purpose: Molecular subtype classifications in glioblastoma may detect therapy sensitivities. Immunohistochemistry would potentially allow the identification of molecular subtypes in routine clinical practice. Experimental design: Paraffin-embedded tumor samples of 124 uniformly treated, newly diagnosed glioblastoma patients were submitted to RNA...

Background & Aims: Hepatoblastoma (HB) is a rare disease. Nevertheless, it is the predominant pediatric liver cancer, with limited therapeutic options for patients with aggressive tumors. Herein, we aimed to uncover the mechanisms of HB pathobiology and to identify new biomarkers and therapeutic targets in a move towards precision medicine for pati...

Absence of the second X chromosome in Turner syndrome is generally well tolerated, but in cases of small fragments or rings derived from the X chromosome, the incidence of mental retardation and other unusual congenital abnormalities can be significantly higher. This investigation focuses on a 9-year-old female who was referred for molecular analys...

Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem ce...

mpileup changes in GBM associated genes. Number of mpileup substitutions with respect to the reference genome. Gray shaded areas indicate C>T and G>A changes. (DOCX)

C>T and G>A FFPE artefacts in GBM-associated genes. Number of SNP artefacts originated by C>T and G>A changes. We counted cases that were CC (GG) homozygous in the FF sample and CT (GA) or TT (AA) in the paired FFPE sample. (DOCX)

Excel sheets. There are five tabs: (A) Results of the differential gene sampling analysis. Genes are sorted by significance. (B) List of differentially sampled genes with FDR <0.05. (C) List of over-sampled genes in FFPE samples sorted by gene name. The majority are non-coding RNA belonging to specific gene families and have no functional annotatio...

Best gene predictors of GBM molecular classification. Grey shaded areas indicate genes included in Verhaak’s gene signature. (DOCX)

Statistical results. Results of statistical analyses of quality metrics. A one-tailed Fisher’s exact test was applied to each FF and FFPE pair. (XLSX)

Overlapping and non-overlapping SNPs in FF-FFPE pairs. Number of overlapping SNPs (shaded) and non-overlapping SNPs (non-shaded) for each FF-FFPE pair and each gene. 0/1 indicates a heterozygous SNP. 1/1 indicates a homozygous alternative. NA indicates not assessed. (DOCX)

Unlabelled: Identification of new treatments for relapsing pediatric cancer is an unmet clinical need and a societal challenge. Liver cancer occurrence in infancy, 1.5 for million children per year, falls far below the threshold of interest for dedicated drug development programs, and this disease is so rare that it is very difficult to gather eno...

Nonsynonymous TP53 exon 4 single-nucleotide polymorphism (SNP), R72P, is linked to cancer and mutagen susceptibility. R72P associations with specific cancer risk, particularly hematological malignancies, have been conflicting. Myelodysplastic syndrome (MDS) with chromosome 5q deletion is characterized by erythroid hypoplasia arising from lineage-sp...

Monosomal karyotype (MK) is associated with an adverse prognosis in patients in acute myeloid leukemia (AML). The present study analyzes the prognostic impact of MK in a cohort of primary, untreated patients with myelodysplastic syndromes (MDS). 431 patients were extracted from an international database. To analyze whether MK is an independent prog...

This cooperative study assessed prognostic factors for overall survival (OS) and risk of transformation to acute myeloid leukemia (AML) in 541 patients with de novo myelodysplastic syndrome (MDS) and deletion 5q. Additional chromosomal abnormalities were strongly related to different patients' characteristics. In multivariate analysis, the most imp...

Deletion of the long arm of chromosome 5 is the most frequent chromosomal abnormality in MDS (10–15% of MDS cases). Patients with del(5q), particularly those with the ‘5q-syndrome’ have a much better prognosis than other MDS subtypes. Although the presence of additional chromosome abnormalities (ACA), apart from 5q-, has been suggested to negativel...

Introduction: Several recent publications have advanced our knowledge of the prognostic significance of clonal cytogenetic abnormalities in MDS, yet the genetic risk assessment of the rare karyotypic aberrations in MDS patients (pts) remains unknown. Using the German-Austrian (G-A) Cytogenetics Database, we previously defined 24 cytogenetic prognos...