Silvia Tore

@article{nokey,

title = {Comparison between Three Different Techniques for the Detection of EGFR Mutations in Liquid Biopsies of Patients with Advanced Stage Lung Adenocarcinoma},

author = {Casula Milena and Pisano Marina and Paliogiannis Panagiotis and Colombino Maria and Sini Maria Cristina and Zinellu Angelo},

year  = {2023},

date = {2023-03-29},

urldate = {2023-03-29},

journal = {International Journal of Molecular Sciences},

volume = {24},

number = {6410},

abstract = {Oncogenic mutations in the EGFR gene are targets of tyrosine kinase inhibitors (TKIs) in lung adenocarcinoma (LC) patients and their search is mandatory to make decisions on treatment strategies. Liquid biopsy of circulating tumour DNA (ctDNA) is increasingly used to detect EGFR mutations including main activating alterations (exon 19 deletions and exon 21 L858R mutation) and T790M mutation which is the most common mechanism of acquired resistance to first- and second-generation TKIs. In this study we prospectively compared three different techniques for EGFR mutation detection in liquid biopsies of such patients. Fifty-four ctDNA samples from 48 consecutive advanced LC patients treated with TKIs were tested for relevant EGFR mutations with Therascreen® EGFR Plasma RGQ-PCR Kit (Qiagen). Samples were subsequently tested with two different technologies with the aim to compare the EGFR detection rates: real-time PCR based Idylla™ ctEGFR mutation assay (Biocartis) and next-generation sequencing (NGS) system with Ion AmpliSeq Cancer Hotspot panel (ThermoFisher). A high concordance rate for main druggable EGFR alterations was observed with the two real-time PCR-based assays ranging from 100% for T790M mutation to 94% for L858R variant and 85% for exon 19 deletions. Conversely lower concordance rates were found between real-time PCR approaches and the NGS method (L858R: 88%; exon19-dels: 74%; T790M: 37.5%). Our results evidenced an equivalent detection ability between PCR-based techniques for circulating EGFR mutations. The NGS assay allowed detection of a wider range of EGFR mutations but showed a poor ability to detect T790M.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kottgen_genome-wide_2013,

title = {Genome-wide association analyses identify 18 new loci associated with serum urate concentrations},

author = {K{ö}ttgen, Anna and Albrecht, Eva and Teumer, Alexander and Vitart, Veronique and Krumsiek, Jan and Hundertmark, Claudia and Pistis, Giorgio and Ruggiero, Daniela and ... and Tore, Silvia and ... and Ripatti, Samuli and Soranzo, Nicole and Toniolo, Daniela and Chasman, Daniel I and Raitakari, Olli and Kao, W H Linda and Ciullo, Marina and Fox, Caroline S and Caulfield, Mark and Bochud, Murielle and Gieger, Christian},

doi = {10.1038/ng.2500},

issn = {1546-1718},

year  = {2013},

date = {2013-02-01},

urldate = {2013-02-01},

journal = {Nature Genetics},

volume = {45},

number = {2},

pages = {145--154},

abstract = {Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SFMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional excretion of urate. Network analyses implicate the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. New candidate genes for serum urate concentration highlight the importance of metabolic control of urate production and excretion, which may have implications for the treatment and prevention of gout.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21283782,

title = {Application of a new method for GWAS in a related case/control sample with known pedigree structure: identification of new loci for nephrolithiasis},

author = {Tore, S. and Casula, S. and Casu, G. and Concas, M. P. and Pistidda, P. and Persico, I. and Sassu, A. and Maestrale, G. B. and Mele, C. and Caruso, M. R. and Bonerba, B. and Usai, P. and Deiana, I. and Thornton, T. and Pirastu, M. and Forabosco, P.},

year  = {2011},

date = {2011-01-01},

journal = {PLoS Genet},

volume = {7},

number = {1},

pages = {e1001281},

abstract = {In contrast to large GWA studies based on thousands of individuals and large meta-analyses combining GWAS results, we analyzed a small case/control sample for uric acid nephrolithiasis. Our cohort of closely related individuals is derived from a small, genetically isolated village in Sardinia, with well-characterized genealogical data linking the extant population up to the 16(th) century. It is expected that the number of risk alleles involved in complex disorders is smaller in isolated founder populations than in more diverse populations, and the power to detect association with complex traits may be increased when related, homogeneous affected individuals are selected, as they are more likely to be enriched with and share specific risk variants than are unrelated, affected individuals from the general population. When related individuals are included in an association study, correlations among relatives must be accurately taken into account to ensure validity of the results. A recently proposed association method uses an empirical genotypic covariance matrix estimated from genome-screen data to allow for additional population structure and cryptic relatedness that may not be captured by the genealogical data. We apply the method to our data, and we also investigate the properties of the method, as well as other association methods, in our highly inbred population, as previous applications were to outbred samples. The more promising regions identified in our initial study in the genetic isolate were then further investigated in an independent sample collected from the Italian population. Among the loci that showed association in this study, we observed evidence of a possible involvement of the region encompassing the gene LRRC16A, already associated to serum uric acid levels in a large meta-analysis of 14 GWAS, suggesting that this locus might lead a pathway for uric acid metabolism that may be involved in gout as well as in nephrolithiasis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}