Sergi Villatoro - Academia.edu (original) (raw)

Papers by Sergi Villatoro

Briefings in Functional Genomics, May 20, 2015

Polymorphic inversions are a type of structural variants that are difficult to analyze owing to t... more Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies.

Translational lung cancer research, Oct 1, 2016

Lung cancer is the most common cancer and the first cause of cancer deaths worldwide (1). NSCLC i... more Lung cancer is the most common cancer and the first cause of cancer deaths worldwide (1). NSCLC is the predominant subtype of lung cancer, being adenocarcinoma the most common histology. Unfortunately, almost half of NSCLC patients are diagnosed at advanced stage and have poor prognosis and limited options for treatment, traditionally restricted to chemotherapy (2). However, in recent years, the identification of prognostic and predictive biomarkers has led to improvements in outcome and has set allowed the application of personalized medicine approaches in NSCLC patients. More than 50% of advanced NSCLC patients harbor a driver genetic alteration that, if targetable, changes the therapeutic panorama (3). For this reason, implementing resources for quick, cost-effective, multiplex detection of alterations has recently gained importance for cancer diagnostics.

Medicina Clinica, Nov 1, 2009

BackgroundThe Prader-Willi syndrome (PWS) is a disease of genetic origin. It is characterized by ... more BackgroundThe Prader-Willi syndrome (PWS) is a disease of genetic origin. It is characterized by neonatal hypotonia, hypogonadism, hiperfagia leading to obesity, low stature, developmental delay, moderate mental retardation, abnormal behavior and characteristic facial appearance. It is caused by the loss or the inactivation of paternal genes of the imprinted region 15q11-13. There are different genetic causes: paternal 15q11-q13 deletion in

BMC Genomics, Nov 28, 2008

Background: The technological evolution of platforms for detecting genome-wide copy number imbala... more Background: The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susceptibility. Multiplex Ligation-dependent Probe Amplification (MLPA) is a targeted method to assess copy number differences for up to 40 genomic loci in one single experiment. Although specific MLPA assays can be ordered from MRC-Holland (the proprietary company of the MLPA technology), custom designs are also developed in many laboratories worldwide. After our own experience, an important drawback of custom MLPA assays is the time spent during the design of the specific oligonucleotides that are used as probes. Due to the large number of probes included in a single assay, a number of restrictions need to be met in order to maximize specificity and to increase success likelihood. Results: We have developed a web tool for facilitating and optimising custom probe design for MLPA experiments. The algorithm only requires the target sequence in FASTA format and a set of parameters, that are provided by the user according to each specific MLPA assay, to identify the best probes inside the given region. Conclusion: To our knowledge, this is the first available tool for optimizing custom probe design of MLPA assays. The ease-of-use and speed of the algorithm dramatically reduces the turn around time of probe design. ProSeeK will become a useful tool for all laboratories that are currently using MLPA in their research projects for CNV studies.

European Journal of Medical Genetics, 2007

PradereWilli syndrome (PWS) and Angelman syndrome (AS) are genetic disorders caused by a deficien... more PradereWilli syndrome (PWS) and Angelman syndrome (AS) are genetic disorders caused by a deficiency of imprinted gene expression from the paternal or maternal chromosome 15, respectively. This deficiency is due to the deletion of the 15q11-q13 region, parental uniparental disomy of the chromosome 15, or imprinting defect (ID). Mutation of the UBE3A gene causes approximately 10% of AS cases. In this present study, we describe the molecular analysis and phenotypes of two PWS patients and four AS patients with ID. One of the PWS patients has a non-familial imprinting center (IC) deletion and displayed a severe phenotype with an atypical PWS appearance, hyperactivity and psychiatric vulnerability. The other PWS and AS patients did not present genetic abnormalities in the IC, suggesting an epimutation as the genetic cause. The methylation pattern of two AS patients showed a faint maternal band

American Journal of Medical Genetics, 2005

We applied comparative genomic hybridization (CGH) in six patients with de novo prenatal or postn... more We applied comparative genomic hybridization (CGH) in six patients with de novo prenatal or postnatal extra marker chromosomes (MC). In four cases, MCs were mosaic and in one of them, the MC was detected in less than 50% of the cells. In three cases, CGH identified the origin of the extra MCs. In the other three, two prenatal cases and one child with an abnormal phenotype, CGH showed normal profiles. Among these cases, a normal profile and entirely C-band positive was identified suggesting that MC did not contain euchromatin. Genetic imbalances detected by CGH were as follow: a gain of 8p10-p12 in a boy with facial dysmorphism, hyperactivity and speech delay, a gain of 8q10-q12 in a healthy man with a history of spontaneous abortions, and a gain of 15q11-q13 in a girl with speech delay, and motor skill and object manipulation difficulties. Clinical data of these patients were compared with those reported in the literature. We conclude that CGH is a very useful and powerful tool for characterizing prenatal or postnatal MCs, even when the mosaicism is present and the MCs are present in less than 50% of the cells.

Annals of Oncology, 2017

In a significant percentage of advanced non-small-cell lung cancer (NSCLC) patients, tumor tissue... more In a significant percentage of advanced non-small-cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses. We prospectively analyzed if circulating-free DNA (cfDNA) purified from blood can be used as a surrogate in this setting to select patients for treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). Blood samples were collected in 119 hospitals from 1138 advanced NSCLC patients at presentation (n = 1033) or at progression to EGFR-TKIs (n = 105) with no biopsy or insufficient tumor tissue. Serum and plasma were sent to a central laboratory, cfDNA purified and EGFR mutations analyzed and quantified using a real-time PCR assay. Response data from a subset of patients (n = 18) were retrospectively collected. Of 1033 NSCLC patients at presentation, 1026 were assessable; with a prevalence of males and former or current smokers. Sensitizing mutations were found in the cfDNA of 113 patients (11%); with a majority of females, never smokers and exon 19 deletions. Thirty-one patients were positive only in plasma and 11 in serum alone and mutation load was higher in plasma and in cases with exon 19 deletions. More than 50% of samples had <10 pg mutated genomes/µl with allelic fractions below 0.25%. Patients treated first line with TKIs based exclusively on EGFR positivity in blood had an ORR of 72% and a median PFS of 11 months. Of 105 patients screened after progression to EGFR-TKIs, sensitizing mutations were found in 56.2% and the p.T790M resistance mutation in 35.2%. Large-scale EGFR testing in the blood of unselected advanced NSCLC patients is feasible and can be used to select patients for targeted therapy when testing cannot be done in tissue. The characteristics and clinical outcomes to TKI treatment of the EGFR-mutated patients identified are undistinguishable from those positive in tumor.

Background: Surgical resection remains the best treatment option for early-stage endometrial (CE)... more Background: Surgical resection remains the best treatment option for early-stage endometrial (CE), colorectal (CRC) and lung cancer (LC) patients. However, a proportion of patients (p) develop tumor recurrence, even after curative resection. Peritoneal or pleural lavages may be performed during surgery but little data is available about their potential as liquid biopsies with predictive value for recurrence. This proof-of concept study aimed to determine if somatic mutations can be detected in these lavages. Methods: We analyzed mutations in paired surgical biopsies, blood and peritoneal or pleural lavages supernatants in an early-stage cohort of 25 EC, 12 CRC and 19 LC p. Molecular characterization of surgical biopsies was performed using the GeneReader NGS platform (Qiagen) and the Actionable Insight Tumor Panel, which includes 12 genes (KRAS, NRAS, KIT, BRAF, PDGFRA, ALK, EGFR, ERBB2, PIK3CA, ERBB3, ESR1, and RAF1). cfDNA was purified from blood and lavages using an automatic extractor and the hotspot mutations identified in tumor tissue were tested using a sensitive Taqman assay for codons 12, 13, and 61 in KRAS, codons 542, 545 and 1047 in PIK3CA and codon 600 in BRAF. Results: NGS of tumor biopsies revealed hotspot KRAS, PIK3CA or BRAF mutations in a total of 11/25 (44%) early-stage EC p, 7/12 (58%) early-stage CRC p and 6/19 (32%) early-stage LC p. In peritoneal lavages, hotspot mutations were found in 6/11 (55%) EC p and 2/7 (29%) CRC p and, in pleural lavages, hotspot mutations appeared in 2/6 (33%) LC p. Furthermore, 2/11 (18%) blood samples from EC p, 1/7 (14%) blood samples from CRC p and 1/6 (17%) blood samples from LC p were positive. Conclusions: Our study reveals that mutational analysis in peritoneal or pleural lavages from early stage tumors is feasible and that mutations are more frequently detected in lavages than in blood. Further research will determine if positivity in blood or lavages is associated with early relapse. Citation Format: Núria Jordana Ariza, Mónica Garzón Ibañez, Alejandro Martinez-Bueno, Sonia Gatius Caldero, Clara Mayo de las casas, Ana Velasco, Maria Ruiz, Berta Roman Canal, Jordi Bertran Alamillo, Sonia Rodríguez Muñoz, Raquel Campos Fuentes, Beatriz García, Ariadna Balada Bel, Sergi Villatoro, Miguel Ángel Molina-Vila, Xavier Matias-Guiu. Utility of peritoneal and pleural lavages for detection of somatic alterations: A proof-of-concept study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3643.

Clinical Research (Excluding Clinical Trials), 2019

Neuro-Oncology, 2018

Local recurrence free survival (LRFS), distance progression-free survival (PFS) and overall survi... more Local recurrence free survival (LRFS), distance progression-free survival (PFS) and overall survival (OS) were calculated with IBM SPSS Statistics 21.0. Survival curves were generated using Kaplan-Meier method. Surgery resection, histopathological grade WHO classification and RT dose in local recurrence were analyzed. The impact of clinical and therapeutic variables on survival was evaluated by log-rank test. RESULTS: With a median age at diagnosis 44 (23-78) years old. Pts were 2 females and 10 males. Anatomical sites were 1 pt supratentorial; 6 pts infratentorial and 4 pts spinal cord. Staging included in 75% pts lumbar puncture and cranial/neuroaxis MRI. GTR was achieved in 77% of pts. WHO grade was III in 3 pts; grade II in 7 pts and 2 pts grade I. Median RT dose was 54Gy (50.4-59.4) with 2 pts with boost to posterior fossa and one pt 36 Gy for neuroaxis. The 5 and 10-year OS were 78% and 23% respectively, calculated from the surgery data to the last follow-up/death. 5-years free-local recurrence survival (FLRS) 73% calculated from the surgery date to the local recurrence date; with a 5-years distant progression-free survival (PFS) 100%. In this analysis 5-year LRFS was 67% for STR and 80% for GTR (p=0.715); 5-year LRFS was 100% pts WHO I; 0% pts WHO II; 75% pts WHO III (p=0.712) and 5-year LRFS RT doses were 100% > 54 Gy and 75% ≤54Gy (p=0.035). CONCLUSION: Current analysis includes only 12 pts with different anatomical sites ET, with heterogeneous behaviors, has no power to reveal optimum RT dose nor identify pts WHO grade that deferral post-operatory RT. Our 5 year OS likewise publications for adult. Genetic classification can accrue ET, resulting in more precise diagnostics, sharpen prognostic and improved therapy, beeing now surgery and RT therapeutic mainstays.

Cancer Research, 2018

Translational Cancer Research, 2018

Background: In a significant percentage of advanced non-small cell lung cancer (NSCLC) patients, ... more Background: In a significant percentage of advanced non-small cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses at time to progression. We prospectively analyzed the appearance of genetic alterations associated with resistance in liquid biopsies of advanced NSCLC patients progressing to targeted therapies using the NGS platform. Methods: A total of 24 NSCLC patients were included in the study, 22 progressing to tyrosine kinase inhibitors and two to other treatments. Liquid biopsies samples were obtained and analyzed using the GeneRead TM QIAact Lung DNA UMI Panel, designed to enrich specific target regions and containing 550 variant positions in 19 selected genes frequently altered in lung cancer tumors. Previously, a retrospective validation of the panel was performed in clinical samples. Results: Of the 21 patients progressing to tyrosine kinase inhibitors with valid results in liquid biopsy, NGS analysis identified a potential mechanism of resistance in 12 (57%). The most common were acquired mutations in ALK and EGFR, which appeared in 8/21 patients (38%), followed by amplifications in 5/21 patients (24%), and KRAS mutations in one patient (5%). Loss of the p.T790M was also identified in two patients progressing to osimertinib. Three of the 21 (14%) patients presented two or more concomitant alterations associated with resistance. Finally, an EGFR amplification was found in the only patient progressing to immunotherapy included in the study. Conclusions: NGS analysis in liquid biopsies of patients progressing to targeted therapies using the GeneReader platform is feasible and can help the oncologist to make treatment decisions. S4 Mayo de las Casas et al. NGS analysis of liquid biopsies after progression to targeted therapy

Expert Review of Molecular Diagnostics, 2017

ABSTRACT Introduction: Collection of tumor samples is not always feasible in non-small cell lung ... more ABSTRACT Introduction: Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients. Expert commentary: Detection of somatic alterations in cfDNA is already in use in clinical practice and provides valuable information for patient management. Monitoring baseline alterations and emergence of resistance mutations is one of the most important clinical applications and can be used to non-invasively track disease evolution. Today, different technologies are available for cfDNA analysis, including whole-genome or exome sequencing and targeted methods that focus on a selection of genes of interest in a specific disease. In the case of Next Generation Sequencing (NGS) approaches, in depth coverage of candidate mutation loci can be achieved by selecting a limited number of targeted genes.

Cancer Research, 2017

Background: Mutations in the KRAS proto-oncogene, GTPase (KRAS) are driver alterations in several... more Background: Mutations in the KRAS proto-oncogene, GTPase (KRAS) are driver alterations in several tumors, such as non-small-cell lung (NSCLC) and colorectal cancer (CRC). However, their role as a prognostic marker in liquid biopsies is unclear. We studied the status of KRAS mutations in the peripheral blood of advanced NSCLC and colorectal cancer patients visited in our hospital and evaluated its potential value as a monitoring marker in the clinical practice. Methods: We developed a sensitive TaqMan assay, in the presence of a PNA clamp, for the determination of KRAS mutations (codons 12, 13 and 61) in circulating-free DNA (cfDNA). The assay detected 2.5 pg mutated DNA/µL and a ratio of KRAS mutated versus wild type allele of 1:20000 and was validated in 80 cancer patients previously genotyped in tumor tissue showing a clinical sensitivity of 72.5% and specificity of 100%. cfDNA was isolated from serum and plasma specimens, using an automatic extractor and mutational analyses were ...

Translational Lung Cancer Research, 2016

PLoS ONE, 2009

Background: Understanding the genetic contribution to phenotype variation of human groups is nece... more Background: Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. Methodology/Principal Findings: We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH) in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space) within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs) translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. Conclusions: Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.

BMC Genomics, 2008

Background The technological evolution of platforms for detecting genome-wide copy number imbalan... more Background The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susceptibility. Multiplex Ligation-dependent Probe Amplification (MLPA) is a targeted method to assess copy number differences for up to 40 genomic loci in one single experiment. Although specific MLPA assays can be ordered from MRC-Holland (the proprietary company of the MLPA technology), custom designs are also developed in many laboratories worldwide. After our own experience, an important drawback of custom MLPA assays is the time spent during the design of the specific oligonucleotides that are used as probes. Due to the large number of probes included in a single assay, a number of restrictions need to be met in order to maximize specificity and to increase success li...