Browsing Other ICR Research by author "Zapata Ortiz, Luis"
Now showing items 1-10 of 10
-
Allele balance bias identifies systematic genotyping errors and false disease associations.
Muyas, F; Bosio, M; Puig, A; Susak, H; Domènech, L; et al. (WILEY, 2019-01-01)In recent years, next-generation sequencing (NGS) has become a cornerstone of clinical genetics and diagnostics. Many clinical applications require high precision, especially if rare events such as somatic mutations in ... -
Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms.
Zapata, L; Ding, J; Willing, E-M; Hartwig, B; Bezdan, D; et al. (NATL ACAD SCIENCES, 2016-07-12)Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually ... -
Evolutionary dynamics of neoantigens in growing tumors.
Lakatos, E; Williams, MJ; Schenck, RO; Cross, WCH; Househam, J; et al. (NATURE PORTFOLIO, 2020-10-01)Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of ... -
Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios.
Williams, MJ; Zapata, L; Werner, B; Barnes, CP; Sottoriva, A; et al. (ELIFE SCIENCES PUBLICATIONS LTD, 2020-03-30)The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in ... -
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.
Zapata, L; Pich, O; Serrano, L; Kondrashov, FA; Ossowski, S; et al. (BMC, 2018-05-31)BACKGROUND: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic ... -
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.
Tarbier, M; Mackowiak, SD; Frade, J; Catuara-Solarz, S; Biryukova, I; et al. (NATURE RESEARCH, 2020-10-28)Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply ... -
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues.
Muyas, F; Zapata, L; Guigó, R; Ossowski, S (BMC, 2020-05-27)BACKGROUND: Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of ... -
Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes.
Zapata, L; Susak, H; Drechsel, O; Friedländer, MR; Estivill, X; et al. (NATURE PORTFOLIO, 2017-10-13)Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell ... -
Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence.
Fiedler, D; Heselmeyer-Haddad, K; Hirsch, D; Hernandez, LS; Torres, I; et al. (WILEY, 2019-04-01)Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence ... -
Very large hidden genetic diversity in one single tumor: evidence for tumors-in-tumor.
Chen, B; Wu, X; Ruan, Y; Zhang, Y; Cai, Q; et al. (OXFORD UNIV PRESS, 2022-12-12)Despite the concern of within-tumor genetic diversity, this diversity is in fact limited by the kinship among cells in the tumor. Indeed, genomic studies have amply supported the 'Nowell dogma' whereby cells of the same ...