Silvia Buonaiuto
A5069262323- Genomic variations and chromosomal abnormalities
- Prenatal Screening and Diagnostics
- Pancreatic and Hepatic Oncology Research
- Chromosomal and Genetic Variations
- Reproductive Biology and Fertility
- Cancer Cells and Metastasis
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Genetic Syndromes and Imprinting
- Genomics and Chromatin Dynamics
- Liver Disease Diagnosis and Treatment
- Assisted Reproductive Technology and Twin Pregnancy
- Evolution and Genetic Dynamics
- Genetics and Neurodevelopmental Disorders
- Genetic factors in colorectal cancer
- Pancreatic function and diabetes
- Renal and related cancers
- Cancer Genomics and Diagnostics
- Genetic Mapping and Diversity in Plants and Animals
- BRCA gene mutations in cancer
- Liver physiology and pathology
- Cancer, Lipids, and Metabolism
- Congenital heart defects research
- Genetic Associations and Epidemiology
- CRISPR and Genetic Engineering
University of Tennessee Health Science Center
2024
Institute of Genetics and Biophysics
2020-2024
National Research Council
2020-2024
University of Campania "Luigi Vanvitelli"
2021-2022
University of Naples Federico II
2019
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. contains 47 phased, diploid assemblies from cohort of genetically diverse individuals. These cover more than 99% the expected sequence and are accurate at structural base-pair levels. Based on alignments assemblies, we generated that captures known variants haplotypes, reveals novel alleles structurally complex loci, adds 119 million base pairs euchromatic polymorphic 1,529 gene...
Abstract Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared pattern SNVs between unique duplicated regions 3,4 We find that are elevated 60% to estimate at least 23% this increase is due interlocus gene conversion (IGC) with up 4.3 megabase pairs SD sequence...
Tumor-initiating cells (TIC), also known as cancer stem cells, are considered a specific subpopulation of necessary for initiation and metastasis; however, the mechanisms by which they acquire metastatic traits not well understood.LAMC2 transcriptional levels were evaluated using publicly available transcriptome data sets, LAMC2 immunohistochemistry was performed tissue microarray composed PDAC normal pancreas tissues. Silencing tracing lentiviral shRNA constructs CRISPR/Cas9-mediated...
Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer with an aggressive metastatic phenotype and very poor clinical prognosis. Interestingly, a lower occurrence of PDAC has been described in individuals severe long-standing asthma. Here we explored potential link between glucocorticoid (GC) budesonide, first-line therapy to treat Methods We tested effect budesonide classical GCs on morphology, proliferation, migration invasiveness patient-derived cells...
Abstract The Biorepository and Integrative Genomics (BIG) Initiative in Tennessee has developed a pioneering resource to address gaps genomic research by linking genomic, phenotypic, environmental data from diverse Mid-South population, including underrepresented groups. We analyzed 13,152 genomes BIG found significant genetic diversity, with 50% of participants inferred have non-European or several types admixed ancestry. Ancestry within the cohort is stratified, distinct geographic...
The apple does not fall far from the tree is an old idiom that encapsulates a key concept: being related extends beyond merely sharing genetic material. It often implies common environment, including culture, language, dietary habits, and geographical location. In this study, we show analysis of relatedness can serve as indicator health conditions by capturing combined influences inheritance shared environmental factors. We mapped genomic data electronic records 13k individuals in...
Abstract The Biorepository and Integrative Genomics (BIG) Initiative in Tennessee has developed a pioneering resource to address gaps genomic research by linking genomic, phenotypic, environmental data from diverse Mid-South population, including underrepresented groups. We analyzed 13,152 exomes BIG found significant genetic diversity, with 50% of participants inferred have non-European or several types admixed ancestry. Ancestry within the cohort is stratified, distinct geographic...
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed k-mer indexing strategy for comparative analysis across multiple assemblies, including pangenome reference, GRCh38, and CHM13, telomere-to-telomere assembly. Our approach enabled us to identify valuable collection universally conserved sequences all referred as...
Endoderm-derived organs as liver and pancreas are potential targets for regenerative therapies, thus, there is great interest in understanding the pathways that regulate induction specification of this germ layer. Currently, knowledge molecular mechanisms guide vivo endoderm restricted by lack early specific markers. Nephrocan (Nepn) a gene whose expression characterizes stages murine (E7.5–11.5) encodes secreted N-glycosylated protein. In present study, we report identification new...
Abstract Miscarriage is the spontaneous termination of a pregnancy before 24 weeks gestation. We studied genome euploid miscarried embryos from mothers in range healthy adult individuals to understand genetic susceptibility miscarriage not caused by chromosomal aneuploidies. developed gp , pipeline that we used prioritize 439 unique variants 399 genes, including genes known be associated with miscarriages. Among prioritized found STAG2 coding for cohesin complex subunit, which inactivation...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21, and 22 share large homologous regions, including ribosomal DNA repeats extended segmental duplications (Floutsakou et al. 2013; van Sluis 2019). While complete assembly these regions in Telomere-to-Telomere consortium’s CHM13 provided a model their homology (Nurk 2022), it remained unclear if patterns were ancestral or maintained by ongoing recombination exchange. Here, we show that contain pseudo-homologous (PHRs)...
ABSTRACT Miscarriage is the spontaneous termination of a pregnancy before 24 weeks gestation. We studied genome euploid miscarried embryos from mothers in range healthy adult individuals to understand genetic susceptibility miscarriage not caused by chromosomal aneuploidies. developed GP, pipeline that we used prioritize 439 unique variants 399 genes, including genes known be associated with miscarriages. Among prioritized found STAG2 coding for cohesin complex subunit, which inactivation...
ABSTRACT Tumor-initiating cells (TIC), also known as cancer stem cells, are considered a specific subpopulation of necessary for initiation and metastasis. Here, we report LAMC2-positive cell population, which is endowed with enhanced self-renewal capacity, sufficient tumor initiation, differentiation, driving Mechanistically, mRNA profiling these indicate prominent squamous signature, differentially activated pathways critical growth metastasis, including deregulation the TGF-β signaling...
ABSTRACT OBJECTIVE To develop a methodology for case selection and whole-exome sequencing (WES) analysis in infertile women due to recurrent oocyte maturation defects(OOMD) and/or preimplantation embryo lethality (PREMBL). DESIGN Retrospective cohort study. SETTING IVF patients attending the Istanbul Memorial Hospital (2015-2021). WES bioinformatics were performed at Igenomix National Research Council, Italy. PATIENTS A statistical identification of endophenotypes (recurrent low rate, LMR,...
Abstract Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with 5-year survival rate of <8%, characterized by extensive fibrosis, which causes chemotherapy failure and tumor progression. stellate cells (PSCs) are the major cellular stromal component in PDAC, contributes to extracellular matrix (ECM) deposition development. L1 cell adhesion molecule (L1CAM) expression generally associated metastases poor prognosis different human tumors, while its role PDAC remains...
Abstract Study question Do whole-exome sequencing (WES) data from infertile women provide valuable information for the discovery of genes/pathways involved in extreme IVF phenotypes, i.e. oocyte/embryo developmental arrest? Summary answer The development a specific bioinformatic WES pipeline revealed known and new candidate isolated failure,providing foundation to scale up research. What is already use has made it possible identify infertility phenotypes such as recurrent low oocytes...