Andrea Angius

@article{Atzeni2024-tj,

title = {A novel affordable and reliable framework for accurate detection  and comprehensive analysis of somatic mutations in cancer},

author = {Rossano Atzeni and Matteo Massidda and Enrico Pieroni and Vincenzo Rallo and Massimo Pisu and Andrea Angius},

year  = {2024},

date = {2024-07-01},

urldate = {2024-07-01},

journal = {Int. J. Mol. Sci.},

volume = {25},

number = {15},

pages = {8044},

publisher = {MDPI AG},

abstract = {Äccurate detection and analysis of somatic variants in cancer 

 involve multiple third-party tools with complex dependencies and 

 configurations, leading to laborious, error-prone, and 

 time-consuming data conversions. This approach lacks accuracy, 

 reproducibility, and portability, limiting clinical application. 

 Musta was developed to address these issues as an end-to-end 

 pipeline for detecting, classifying, and interpreting cancer 

 mutations. Musta is based on a Python command-line tool designed 

 to manage tumor-normal samples for precise somatic mutation 

 analysis. The core is a Snakemake-based workflow that covers all 

 key cancer genomics steps, including variant calling, mutational 

 signature deconvolution, variant annotation, driver gene 

 detection, pathway analysis, and tumor heterogeneity estimation. 

 Musta is easy to install on any system via Docker, with a 

 Makefile handling installation, configuration, and execution, 

 allowing for full or partial pipeline runs. Musta has been 

 validated at the CRS4-NGS Core facility and tested on large 

 datasets from The Cancer Genome Atlas and the Beijing Institute 

 of Genomics. Musta has proven robust and flexible for somatic 

 variant analysis in cancer. It is user-friendly, requiring no 

 specialized programming skills, and enables data processing with 

 a single command line. Its reproducibility ensures consistent 

 results across users following the same protocol."},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pala_population-_2017,

title = {Population- and individual-specific regulatory variation in Sardinia},

author = {Mauro Pala and Zachary Zappala and Mara Marongiu and Xin Li and Joe R Davis and Roberto Cusano and Francesca Crobu and Kimberly R Kukurba and Michael J Gloudemans and Frederic Reinier and Riccardo Berutti and Maria G Piras and Antonella Mulas and Magdalena Zoledziewska and Michele Marongiu and Elena P Sorokin and Gaelen T Hess and Kevin S Smith and Fabio Busonero and Andrea Maschio and Maristella Steri and Carlo Sidore and Serena Sanna and Edoardo Fiorillo and Michael C Bassik and Stephen J Sawcer and Alexis Battle and John Novembre and Chris Jones and Andrea Angius and Gon{ç}alo R Abecasis and David Schlessinger and Francesco Cucca and Stephen B Montgomery},

doi = {10.1038/ng.3840},

issn = {1546-1718},

year  = {2017},

date = {2017-05-01},

journal = {Nature Genetics},

volume = {49},

number = {5},

pages = {700--707},

abstract = {Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia. Using family relationships, we identified 809 segregating expression outliers (median z score of 2.97), averaging 13.3 genes per individual. Outlier genes were enriched for proximal rare variants, providing a new approach to study large-effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{angius_bi-allelic_2016,

title = {Bi-allelic Mutations in KLHL7 Cause a Crisponi/CISS1-like Phenotype Associated with Early-Onset Retinitis Pigmentosa},

author = {Andrea Angius and Paolo Uva and Insa Buers and Manuela Oppo and Alessandro Puddu and Stefano Onano and Ivana Persico and Angela Loi and Loredana Marcia and Wolfgang H{ö}hne and Gianmauro Cuccuru and Giorgio Fotia and Manila Deiana and Mara Marongiu and Hatice Tuba Atalay and Sibel Inan and Osama {El Assy} and Leo M E Smit and Ilyas Okur and Koray Boduroglu and G{ü}len Eda Utine and Esra Kılı{ç} and Giuseppe Zampino and Giangiorgio Crisponi and Laura Crisponi and Frank Rutsch},

doi = {10.1016/j.ajhg.2016.05.026},

issn = {1537-6605},

year  = {2016},

date = {2016-07-01},

journal = {American Journal of Human Genetics},

volume = {99},

number = {1},

pages = {236--245},

abstract = {Crisponi syndrome (CS)/cold-induced sweating syndrome type 1 (CISS1) is a very rare autosomal-recessive disorder characterized by a complex phenotype with high neonatal lethality, associated with the following main clinical features: hyperthermia and feeding difficulties in the neonatal period, scoliosis, and paradoxical sweating induced by cold since early childhood. CS/CISS1 can be caused by mutations in cytokine receptor-like factor 1 (CRLF1). However, the physiopathological role of CRLF1 is still poorly understood. A subset of CS/CISS1 cases remain yet genetically unexplained after CRLF1 sequencing. In five of them, exome sequencing and targeted Sanger sequencing identified four homozygous disease-causing mutations in kelch-like family member 7 (KLHL7), affecting the Kelch domains of the protein. KLHL7 encodes a BTB-Kelch-related protein involved in the ubiquitination of target proteins for proteasome-mediated degradation. Mono-allelic substitutions in other domains of KLHL7 have been reported in three families affected by a late-onset form of autosomal-dominant retinitis pigmentosa. Retinitis pigmentosa was also present in two surviving children reported here carrying bi-allelic KLHL7 mutations. KLHL7 mutations are thus associated with a more severe phenotype in recessive than in dominant cases. Although these data further support the pathogenic role of KLHL7 mutations in a CS/CISS1-like phenotype, they do not explain all their clinical manifestations and highlight the high phenotypic heterogeneity associated with mutations in KLHL7.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sidore_genome_2015,

title = {Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers},

author = {Carlo Sidore and Fabio Busonero and Andrea Maschio and Eleonora Porcu and Silvia Naitza and Magdalena Zoledziewska and Antonella Mulas and Giorgio Pistis and Maristella Steri and Fabrice Danjou and Alan Kwong and Vicente Diego {Ortega Del Vecchyo} and Charleston W K Chiang and Jennifer Bragg-Gresham and Maristella Pitzalis and Ramaiah Nagaraja and Brendan Tarrier and Christine Brennan and Sergio Uzzau and Christian Fuchsberger and Rossano Atzeni and Frederic Reinier and Riccardo Berutti and Jie Huang and Nicholas J Timpson and Daniela Toniolo and Paolo Gasparini and Giovanni Malerba and George Dedoussis and Eleftheria Zeggini and Nicole Soranzo and Chris Jones and Robert Lyons and Andrea Angius and Hyun M Kang and John Novembre and Serena Sanna and David Schlessinger and Francesco Cucca and Gon{ç}alo R Abecasis},

doi = {10.1038/ng.3368},

issn = {1546-1718},

year  = {2015},

date = {2015-11-01},

journal = {Nature Genetics},

volume = {47},

number = {11},

pages = {1272--1281},

abstract = {We report ∼17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from previous sequencing-based compilations and are enriched for predicted functional consequences. Furthermore, ∼76,000 variants common in our sample (frequency >5%) are rare elsewhere (<0.5% in the 1000 Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. We observe 14 signals, including 2 major new loci, for lipid levels and 19 signals, including 2 new loci, for inflammatory markers. The new associations would have been missed in analyses based on 1000 Genomes Project data, underlining the advantages of large-scale sequencing in this founder population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{francalacci_low-pass_2013,

title = {Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny},

author = {Paolo Francalacci and Laura Morelli and Andrea Angius and Riccardo Berutti and Frederic Reinier and Rossano Atzeni and Rosella Pilu and Fabio Busonero and Andrea Maschio and Ilenia Zara and Daria Sanna and Antonella Useli and Maria Francesca Urru and Marco Marcelli and Roberto Cusano and Manuela Oppo and Magdalena Zoledziewska and Maristella Pitzalis and Francesca Deidda and Eleonora Porcu and Fausto Poddie and Hyun Min Kang and Robert Lyons and Brendan Tarrier and Jennifer Bragg Gresham and Bingshan Li and Sergio Tofanelli and Santos Alonso and Mariano Dei and Sandra Lai and Antonella Mulas and Michael B Whalen and Sergio Uzzau and Chris Jones and David Schlessinger and Gon{ç}alo R Abecasis and Serena Sanna and Carlo Sidore and Francesco Cucca},

doi = {10.1126/science.1237947},

issn = {1095-9203},

year  = {2013},

date = {2013-08-01},

journal = {Science (New York, N.Y.)},

volume = {341},

number = {6145},

pages = {565--569},

abstract = {Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population textasciitilde7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of textasciitilde180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA-based estimates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}