Publications by authors named "Pilar Alvarino"
Human virome studies are gaining attention as viruses are increasingly acknowledged as key modulators of microbial communities and human health. However, viral metagenomics presents distinct challenges, including the low abundance and diversity of viruses in biological samples, the lack of universal marker genes, and protocol-induced biases. Although various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these often fail to replicate the complexity and heterogeneity of natural viromes.
View Article and Find Full Text PDFDifferential performance of strategies for single-cell whole-genome amplification.
Cell Rep Methods
April 2025
Single-cell genomics enables studying tissues and organisms at the highest resolution. However, since a cell contains a small amount of DNA, single-cell DNA sequencing (scDNA-seq) typically requires single-cell whole-genome amplification (scWGA). Unfortunately, scWGA methods introduce technical biases that complicate the interpretation of scDNA-seq data.
View Article and Find Full Text PDFArticle Synopsis
- The study examines how social restrictions and different variants, specifically Alpha, Delta, and Omicron-BA.1, affected the spread of SARS-CoV-2 in Galicia, Spain.
- Using genomic data and mobility statistics, the research found that initial variant introductions mostly came from other Spanish regions and France, later shifting to include imports from Portugal and the U.S.
- Despite the number of introductions, most did not contribute significantly to the pandemic's evolution in Galicia, but major coastal cities were identified as key areas for viral transmission.
Article Synopsis
- The study investigates how social restrictions and different variants, specifically Alpha, Delta, and Omicron, affected SARS-CoV-2 transmission in Galicia, Spain.
- Using genomic data and mobility information, the research shows that the Alpha variant initially spread from other Spanish regions and France, while later variants saw increased influences from Portugal and the USA.
- Key coastal cities in Galicia were identified as significant hubs for the virus's dissemination, underscoring the importance of regional connectivity for public health strategies.
Article Synopsis
- - Transmissible cancers like bivalve transmissible neoplasia (BTN) can spread between marine organisms, particularly affecting species like the common cockle (Cerastoderma edule) along the Atlantic coasts of Europe and Africa.
- - Researchers examined over 6,800 cockles, diagnosed 390 cases of BTN tumors, and analyzed genomic variation in 61 tumors, confirming the presence of two BTN lineages with links to blood cell origins.
- - The study found significant genomic instability in the BTN tumors, including whole-genome duplications and mutations, and suggested a long history of clonal evolution in these transmissible cancers.
Article Synopsis
- The study investigates how analyzing circulating tumor cells (CTCs) from blood can provide valuable insights into cancer treatment effectiveness and survival predictions for metastatic colorectal cancer (mCRC) patients.
- Researchers compared different methods for collecting CTCs—CellSearch, Parsortix, and FACS—and found that the genomic mutations varied based on the method used.
- Results showed that CTCs from Parsortix and CellSearch methods presented genomic features similar to those of the primary tumors, while FACS enrichment resulted in misleading diversity estimates due to sequencing errors; this underscores the potential of CTC analysis in personalizing cancer treatment.
Article Synopsis
- - The recurrence of tumor cells in metastatic colorectal cancer (mCRC) poses a major challenge even after surgical removal of metastases, highlighting the need to study the evolution of these recurrent tumors.
- - A unique dataset from single-cell whole-genome sequencing of recurrent liver lesions in an mCRC patient revealed that a certain tumor lineage survived surgery and continued to evolve, despite undergoing chemotherapy for two years.
- - The study found that chemotherapy significantly contributed to mutations in tumor cells, suggesting that some mCRC subclones can migrate and adapt after treatment, leading to rapid regrowth of tumors.
Article Synopsis
- Human mitochondria can be genetically different within the same person, a situation called heteroplasmy, particularly prevalent in cancer.
- In a study of colorectal cancer patients, researchers sequenced individual mitochondrial genomes from normal and tumor cells and found that both types of cells carry diverse mitochondrial genetic variations.
- The study indicates that this variation can exist before cancer starts and persist in certain tumor cell groups, but the somatic mutations observed in these cells don't seem to significantly contribute to cancer development.