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2.
Mol Cell Proteomics ; 22(4): 100506, 2023 04.
Article in English | MEDLINE | ID: mdl-36796642

ABSTRACT

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past 2 decades. However, improvement in the accuracy of prediction algorithms is needed for clinical applications like the development of personalized cancer vaccines, the discovery of biomarkers for response to immunotherapies, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic Human Leukocyte Antigen (HLA) Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA allele to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC diversity in the training data and extend allelic coverage in underprofiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.17-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.


Subject(s)
Neoplasms , Peptides , Humans , Peptides/metabolism , Histocompatibility Antigens Class I/metabolism , Histocompatibility Antigens Class II , Major Histocompatibility Complex , HLA Antigens/genetics , HLA Antigens/metabolism
3.
Nat Commun ; 13(1): 1925, 2022 04 12.
Article in English | MEDLINE | ID: mdl-35414054

ABSTRACT

Human leukocyte antigen loss of heterozygosity (HLA LOH) allows cancer cells to escape immune recognition by deleting HLA alleles, causing the suppressed presentation of tumor neoantigens. Despite its importance in immunotherapy response, few methods exist to detect HLA LOH, and their accuracy is not well understood. Here, we develop DASH (Deletion of Allele-Specific HLAs), a machine learning-based algorithm to detect HLA LOH from paired tumor-normal sequencing data. With cell line mixtures, we demonstrate increased sensitivity compared to previously published tools. Moreover, our patient-specific digital PCR validation approach provides a sensitive, robust orthogonal approach that could be used for clinical validation. Using DASH on 610 patients across 15 tumor types, we find that 18% of patients have HLA LOH. Moreover, we show inflated HLA LOH rates compared to genome-wide LOH and correlations between CD274 (encodes PD-L1) expression and microsatellite instability status, suggesting the HLA LOH is a key immune resistance strategy.


Subject(s)
Loss of Heterozygosity , Neoplasms , Algorithms , HLA Antigens/genetics , Histocompatibility Antigens Class I/genetics , Histocompatibility Antigens Class II , Humans , Loss of Heterozygosity/genetics , Machine Learning , Microsatellite Repeats/genetics , Neoplasms/genetics
4.
Hipertens. riesgo vasc ; 39(2): 95-97, abr.-jun. 2022. ilus
Article in Spanish | IBECS | ID: ibc-203959

ABSTRACT

El síndrome de encefalopatía posterior reversible (PRES) constituye una entidad clínico-radiológica relacionada con múltiples etiologías con hallazgos similares en neuroimagen. Su incidencia es desconocida y su patogenia es multifactorial, englobando fenómenos de disfunción endotelial y autorregulación del flujo cerebral, entre otros. Existe una gran variedad de condiciones asociadas, siendo las más frecuentes la hipertensión, eclampsia y la terapia inmunosupresora, junto con otros fármacos, drogas, enfermedades autoinmunes e incluso la uremia. Presentamos el caso de un síndrome de encefalopatía posterior reversible secundario a afectación renal como forma de debut de una amiloidosis AL.(AU)


Posterior reversible encephalopathy syndrome (PRES) is a clinical and radiological entity linked to multiple aetiologies with similar neuroimaging findings. Its incidence is unknown, and its pathogenesis is multifactorial, encompassing phenomena of endothelial dysfunction and cerebral flow autoregulation, inter alia. There is a wide variety of associated conditions, the most frequent being hypertension, eclampsia, and immunosuppressive therapy, along with other drugs, autoimmune diseases, and even uraemia. We present the case of a reversible posterior encephalopathy syndrome secondary to renal involvement as a debut form of AL amyloidosis.(AU)


Subject(s)
Humans , Female , Aged , Hypertension/complications , Immunoglobulin Light-chain Amyloidosis/complications , Neuroimaging/adverse effects , Posterior Leukoencephalopathy Syndrome/diagnostic imaging , Posterior Leukoencephalopathy Syndrome/etiology , Posterior Leukoencephalopathy Syndrome/pathology , Women , Humans , Pregnancy
5.
Hipertens Riesgo Vasc ; 39(2): 95-97, 2022.
Article in Spanish | MEDLINE | ID: mdl-34973898

ABSTRACT

Posterior reversible encephalopathy syndrome (PRES) is a clinical and radiological entity linked to multiple aetiologies with similar neuroimaging findings. Its incidence is unknown, and its pathogenesis is multifactorial, encompassing phenomena of endothelial dysfunction and cerebral flow autoregulation, inter alia. There is a wide variety of associated conditions, the most frequent being hypertension, eclampsia, and immunosuppressive therapy, along with other drugs, autoimmune diseases, and even uraemia. We present the case of a reversible posterior encephalopathy syndrome secondary to renal involvement as a debut form of AL amyloidosis.


Subject(s)
Hypertension , Immunoglobulin Light-chain Amyloidosis , Posterior Leukoencephalopathy Syndrome , Female , Humans , Hypertension/complications , Immunoglobulin Light-chain Amyloidosis/complications , Neuroimaging/adverse effects , Posterior Leukoencephalopathy Syndrome/diagnostic imaging , Posterior Leukoencephalopathy Syndrome/etiology , Posterior Leukoencephalopathy Syndrome/pathology , Pregnancy
6.
Clin Cancer Res ; 27(15): 4265-4276, 2021 08 01.
Article in English | MEDLINE | ID: mdl-34341053

ABSTRACT

PURPOSE: While immune checkpoint blockade (ICB) has become a pillar of cancer treatment, biomarkers that consistently predict patient response remain elusive due to the complex mechanisms driving immune response to tumors. We hypothesized that a multi-dimensional approach modeling both tumor and immune-related molecular mechanisms would better predict ICB response than simpler mutation-focused biomarkers, such as tumor mutational burden (TMB). EXPERIMENTAL DESIGN: Tumors from a cohort of patients with late-stage melanoma (n = 51) were profiled using an immune-enhanced exome and transcriptome platform. We demonstrate increasing predictive power with deeper modeling of neoantigens and immune-related resistance mechanisms to ICB. RESULTS: Our neoantigen burden score, which integrates both exome and transcriptome features, more significantly stratified responders and nonresponders (P = 0.016) than TMB alone (P = 0.049). Extension of this model to include immune-related resistance mechanisms affecting the antigen presentation machinery, such as HLA allele-specific LOH, resulted in a composite neoantigen presentation score (NEOPS) that demonstrated further increased association with therapy response (P = 0.002). CONCLUSIONS: NEOPS proved the statistically strongest biomarker compared with all single-gene biomarkers, expression signatures, and TMB biomarkers evaluated in this cohort. Subsequent confirmation of these findings in an independent cohort of patients (n = 110) suggests that NEOPS is a robust, novel biomarker of ICB response in melanoma.


Subject(s)
Drug Resistance, Neoplasm/immunology , Melanoma/drug therapy , Melanoma/immunology , Models, Immunological , Forecasting , Humans , Treatment Outcome
7.
Mol Cell Proteomics ; 20: 100111, 2021.
Article in English | MEDLINE | ID: mdl-34126241

ABSTRACT

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass-spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past two decades. However, improvement in the sensitivity and specificity of prediction algorithms is needed for clinical applications such as the development of personalized cancer vaccines, the discovery of biomarkers for response to checkpoint blockade, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic HLA Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA alleles to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC-binding pocket diversity in the training data and extend allelic coverage in under profiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.15-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.


Subject(s)
Antigens, Neoplasm , Major Histocompatibility Complex , Models, Theoretical , Peptides , Algorithms , Antigen Presentation , Cell Line , Humans , Proteome , Transcriptome
8.
Tech Coloproctol ; 24(10): 1001-1015, 2020 10.
Article in English | MEDLINE | ID: mdl-32666362

ABSTRACT

BACKGROUND: Preoperative or neoadjuvant chemotherapy (NAC) has emerged as a novel alternative to treat locally advanced colon cancer (LACC), as in other gastrointestinal malignancies. However, evidence of its efficacy and safety has not yet been gathered in the literature. The aim of the present study was to perform an extensive review of the scientific evidence for NAC in patients with LACC. METHODS: PubMed, EMBASE, MEDLINE and Cochrane Library were searched for a systematic review of the literature from 2010 to 2019. Six eligible studies were included, with a total of 27,937 patients, 1232 of them (4.4%) treated with NAC. There were only one randomized controlled trial, three phase II non-randomized single arm studies and two retrospective studies. RESULTS: The baseline computed tomography scan showed that most of patients had a T3 tumor. The completion rate of the planned neoadjuvant treatment ranged from 52.5 to 93.8%. Between 97.2 and 100% of patients had the scheduled surgery. The median tumor volume reduction after NAC ranged from 62.5 to 63.7%. The anastomotic leak rate in the NAC group ranged from 0 to 7%, with no cases of postoperative mortality. There was major pathological tumor regression in 4-34.7% of cases. Between 84 and 100% of NAC patients had R0-surgery. Survival after NAC seems to be encouraging although significant improvement has only been proven in T4b tumours. CONCLUSIONS: According to our systematic review, the NAC may be a safe and effective emerging therapeutic alternative for treating LACC. This approach, which is still being tested, increases the reliance on accurate radiological staging.


Subject(s)
Colonic Neoplasms , Neoadjuvant Therapy , Antineoplastic Combined Chemotherapy Protocols , Chemotherapy, Adjuvant , Colonic Neoplasms/drug therapy , Colonic Neoplasms/pathology , Humans , Neoplasm Staging , Retrospective Studies
9.
J Hered ; 111(2): 216-226, 2020 04 02.
Article in English | MEDLINE | ID: mdl-32072169

ABSTRACT

A goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated with this variation in UI, but the mechanistic connection between these intra- and inter-specific pollen rejection behaviors is poorly understood in most instances. We generated an F2 population between SI and SC genotypes of a single species, Solanum pennellii, to examine the genetic basis of intraspecific variation in UI against other species, and to determine whether loci underlying SI are genetically associated with this variation. We found that F2 individuals vary in the rate at which UI rejection occurs. One large effect QTL detected for this trait co-localized with the SI-determining S-locus. Moreover, individuals that expressed S-RNase-the S-locus protein involved in SI pollen rejection-in their styles had much more rapid UI responses compared with those without S-RNase protein. Our analysis shows that intraspecific variation at mate choice loci-in this case at loci that prevent self-fertilization-can contribute to variation in the expression of interspecific isolation, including postmating prezygotic barriers. Understanding the nature of such intraspecific variation can provide insight into the accumulation of these barriers between diverging lineages.


Subject(s)
Genetic Variation , Pollen/genetics , Self-Incompatibility in Flowering Plants , Solanum/genetics , Genes, Plant , Genetics, Population , Genotype , Solanum lycopersicum/genetics , Quantitative Trait Loci , Reproduction
10.
BMC Biol ; 18(1): 1, 2020 01 02.
Article in English | MEDLINE | ID: mdl-31898513

ABSTRACT

BACKGROUND: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. RESULTS: We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. CONCLUSIONS: Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.


Subject(s)
Anopheles/genetics , Biological Evolution , Chromosomes , Genetic Techniques/instrumentation , Genomics/methods , Synteny , Animals , Chromosome Mapping
11.
PLoS One ; 13(12): e0208901, 2018.
Article in English | MEDLINE | ID: mdl-30566479

ABSTRACT

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.


Subject(s)
Ethnicity/genetics , Genetic Predisposition to Disease , Genetic Variation , Genome, Human , Animals , Female , Genome-Wide Association Study , Humans , Male , Neanderthals/genetics , Serbia/ethnology
13.
Angiología ; 68(6): 478-483, nov.-dic. 2016. graf, tab
Article in Spanish | IBECS | ID: ibc-157711

ABSTRACT

OBJETIVOS: Valorar la utilidad clínica de la introducción rutinaria del mapeo ecográfico de extremidades superiores en el estudio preoperatorio de los pacientes candidatos a un acceso vascular (AV) para hemodiálisis. MATERIAL Y MÉTODOS: Estudio unicéntrico retrospectivo de 4 años de duración. Incluimos pacientes con enfermedad renal crónica terminal (ERCT) candidatos a un AV para hemodiálisis, excluyendo a aquellos con fístulas arteriovenosas (FAV) previas en la misma extremidad superior. Dos grupos de estudio: exploración física (EF: junio de 2011-febrero de 2014) y mapeo ecográfico (ECO: marzo de 2014-junio de 2015). Analizamos: variables demográficas, comorbilidad y tipo de AV. En el subgrupo FAV radiocefálicas, analizamos la tasa de permeabilidad inmediata (48 h), precoz (4 semanas), tardía (6 meses) y los procedimientos realizados. RESULTADOS: Estudiamos a 81 pacientes (EF: 42; ECO: 39), de los que el 63% eran hombres, con una edad media de 66,5±13,1 años. El 81% fueron izquierdos. No se evidenciaron diferencias significativas entre los grupos respecto a demografía, comorbilidad ni etiología de la ERCT. Tipo de AV (EF vs. ECO): FAVRC* (47,6 vs. 69,2%; *p < 0,05); húmero-cefálicas* (38,1 vs. 10,3%); húmero-basílicas (11,9 vs. 17.9%) y prótesis húmero-axilares (2,4 vs. 2,6%). Tasa de permeabilidad FAV radiocefálicas: inmediata (90 vs. 85,2%); precoz (75 vs. 100%*) y tardía (55 vs. 88,9%*), respectivamente. Solo observamos un mayor número de AV realizados en otros territorios (25 vs. 3,7%*) en el grupo EF de las FAV radiocefálicas. CONCLUSIONES: En nuestro centro, la introducción rutinaria del mapeo ecográfico de las extremidades superiores en el estudio preoperatorio de los pacientes candidatos a un AV permitió optimizar el territorio vascular distal y mejorar la permeabilidad precoz y tardía de las fístulas radiocefálica


OBJECTIVES: To assess the clinical usefulness of routine doppler ultrasound vascular mapping of upper extremities before creating a vascular access (VA) for haemodialysis. MATERIAL AND METHODS: A retrospective single-centre study conducted over a four-year period including end-stage renal disease (ESRD) patients referred to for VA creation for haemodialysis. Patients with previous VA in the same upper extremities were excluded. Two study groups were formed: Physical examination (PE: June 2011-February 2014) and ultrasound mapping (US: March 2014-June 2015). An analysis was performed on the demographic variables, comorbidities and AV location. The results of the patency rates of the radio-cephalic fistulae (RCF) subgroup were recorded, immediately (48 h), early (4 weeks), and late (6 months). RESULTS: The study included a total 81 patients (42 PE, 39 US), with 63% males. The mean age was 66.5±13.1 years, and 81% were affected on the left side. There were no significant differences between the groups as regards, demographics, comorbidities, or ESRD aetiology. The VA type (PE vs. US): 47.6 vs. 69.2% radio-cephalic fistula* (*P<.05), 38.1 vs. 10.3% brachial-cephalic fistula*, 11.9 vs. 17.9% brachiobasilic fistula, and 2.4 vs. 2.6% humeral-axillary grafts. RCF patency rates: Immediate 90 vs. 85.2%, early 75 vs. 100%*, and late 88.9 vs. 55%*; respectively. However, an increase in AV performed in other territories was observed in PE group (25 vs. 3.7%*) in RCF. CONCLUSIONS: Routine doppler ultrasound mapping of upper extremities before VA creation in our centre allowed the distal vascular territory to be optimised, and improved the primary patency rates of both early and late radio-cephalic fistulas


Subject(s)
Humans , Male , Female , Ultrasonography/methods , Preoperative Care/methods , Renal Dialysis/methods , Renal Dialysis/standards , Arteriovenous Fistula/complications , Arteriovenous Fistula/pathology , Permeability , Renal Insufficiency, Chronic/pathology , Ultrasonography/instrumentation , Preoperative Care/standards , Renal Dialysis/classification , Renal Dialysis , Arteriovenous Fistula/classification , Arteriovenous Fistula/metabolism , Renal Insufficiency, Chronic/metabolism , Retrospective Studies
14.
Gigascience ; 5(1): 31, 2016 07 19.
Article in English | MEDLINE | ID: mdl-27435057

ABSTRACT

BACKGROUND: Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species. RESULTS: We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on both simulated and real datasets, we show that it is highly accurate and that it achieves greater accuracy and contiguity when compared with other existing methods. CONCLUSION: AGOUTI is a powerful and effective scaffolder and, unlike most scaffolders, is expected to be more effective in larger genomes because of the commensurate increase in intron length. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the number of gene models by hundreds or thousands. The software is available free of charge under the MIT license.


Subject(s)
Computational Biology/methods , Gene Expression Profiling/methods , Molecular Sequence Annotation/methods , Algorithms , Genome , High-Throughput Nucleotide Sequencing/methods , Sequence Analysis, RNA/methods , Software
16.
G3 (Bethesda) ; 4(4): 669-79, 2014 Apr 16.
Article in English | MEDLINE | ID: mdl-24531727

ABSTRACT

Current de novo whole-genome sequencing approaches often are inadequate for organisms lacking substantial preexisting genetic data. Problems with these methods are manifest as: large numbers of scaffolds that are not ordered within chromosomes or assigned to individual chromosomes, misassembly of allelic sequences as separate loci when the individual(s) being sequenced are heterozygous, and the collapse of recently duplicated sequences into a single locus, regardless of levels of heterozygosity. Here we propose a new approach for producing de novo whole-genome sequences-which we call recombinant population genome construction-that solves many of the problems encountered in standard genome assembly and that can be applied in model and nonmodel organisms. Our approach takes advantage of next-generation sequencing technologies to simultaneously barcode and sequence a large number of individuals from a recombinant population. The sequences of all recombinants can be combined to create an initial de novo assembly, followed by the use of individual recombinant genotypes to correct assembly splitting/collapsing and to order and orient scaffolds within linkage groups. Recombinant population genome construction can rapidly accelerate the transformation of nonmodel species into genome-enabled systems by simultaneously producing a high-quality genome assembly and providing genomic tools (e.g., high-confidence single-nucleotide polymorphisms) for immediate applications. In populations segregating for important functional traits, this approach also enables simultaneous mapping of quantitative trait loci. We demonstrate our method using simulated Illumina data from a recombinant population of Caenorhabditis elegans and show that the method can produce a high-fidelity, high-quality genome assembly for both parents of the cross.


Subject(s)
Genome , Recombination, Genetic , Alleles , Animals , Caenorhabditis elegans , Genetic Linkage , Genotype , High-Throughput Nucleotide Sequencing , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Sequence Analysis, DNA
17.
Rev. esp. investig. quir ; 14(4): 203-207, oct.-dic. 2011. tab
Article in Spanish | IBECS | ID: ibc-99574

ABSTRACT

INTRODUCCIÓN. El cáncer gástrico sigue siendo hoy en día uno de los cánceres más frecuentes con aproximadamente 870.000 nuevos casos y 650.000 muertes cada año. OBJETIVO. El objetivo del trabajo es analizar la mortalidad en el postoperatorio inmediato y las variables asociadas. MATERIAL Y MÉTODOS. Estudio retrospectivo, con fases de prospectivo sobre 454 pacientes sometidos a cirugía por adenocarcinoma gástrico. RESULTADOS. Se incluyeron un total de 454 pacientes, 264 varones y 190 mujeres. Pico de mayor incidencia en la séptima década de la vida, con una media de 70 años y una desviación típica de 10 y rango de 30 a 92 años. En ella se expone que un 76% de los tumores presentaron localización baja (cuerpo-antro), frente a un 22% localización alta (cardias-fundus). Se realizaron 45,2% de gastrectomías subtotales. 35,3% de gastrectomías totales y un 19,6% (laparotomía y gastroyeyunostomía). Se encontró afectación ganglionar en 249 pacientes (54,8%), metástasis hepáticas en 8,1% y en un 15,4% metástasis peritoneales. En este estudio el porcentaje de exitus en el postoperatorio fue de 10,1% del total de pacientes frente a un 8,7% en el de cirugía curativa. La edad, la esplenectomía y el estadio IV obtuvieron resultados significativos en el análisis multivariante. CONCLUSIONES. El estadio IV, la realización de esplenectomía y la edad se asocian de forma independiente con mayor mortalidad en el postoperatorio inmediato. Estas tres variables son predictivas, de forma independiente, de la mortalidad en el postoperatorio (AU)


INTRODUCCIÓN. Gastric cancer remains today one of the most common cancers with approximately 870,000 new cases and 650,000 deaths each year. OBJECTIVE. The study aims to analyze mortality in the immediate postoperative period and associated variables. METHODS. Retrospective study with prospective phases of 454 patients undergoing surgery for gastric adenocarcinoma. RESULTS. A total of 454 patients, 264 men and 190 women. There is a higher incidence peak in the seventh decade of life, with an average of 70 years and a standard deviation of 10 and range 30 to 92 years. It shows that 76% of tumors had low location (body-antrum), compared with 22% upper localization (cardia-fundus). 45.2% were performed subtotal gastrectomy, total gastrectomy 35.3% and 19.6% (laparotomy and gastrojejunostomy). Lymph node was found in 249 patients (54.8%), liver metastases in 8.1% and peritoneal metastases in 15.4%. In this study, the percentage of exitus in the postoperative period was 10.1% of patients compared to 8.7% for curative surgery. Age, splenectomy and stage IV results were significant in the multivariate analysis. CONCLUSIONS. Stage IV, the performance of splenectomy and age were independently associated with increased mortality in the immediate postoperative period. These three variables are predictive, independently of mortality in postoperatory (AU)


Subject(s)
Humans , Postoperative Complications/mortality , Stomach Neoplasms/surgery , Gastrectomy , Retrospective Studies , Splenectomy
20.
Rev. esp. investig. quir ; 11(3): 117-118, jul.-sept. 2008. ilus
Article in Spanish | IBECS | ID: ibc-87311

ABSTRACT

La invaginación intestinal es una patología frecuente en el niño pero muy infrecuente en el adulto. El mecanismo exacto que precipita la invaginación es todavía desconocido, aunque la mayoría de los casos en los adultos se deben a una tumoración que ejerce como cabeza de la misma. El tratamiento en éstos es siempre quirúrgico y la controversia radica en si se puede desinvaginar antes de la resección. Presentamos el caso de una invaginación ileocólica cuya causa desencadenante fue un tumor miofibroblástico inflamatorio (AU)


Intestinal intussusception is a frequent pathology in children but very rare in adults. The exact mechanism that precipitates this pathology is yet unknown althought in most cases in adults it is due to a neoplasm that acts as the lead point of the intussusception. Treatment in these cases is always surgical and controversy lies in the possibility of initial reduction followed by a more limited resection. We present the case of an ileocolic intussusception that was caused by a inflammatory myofibroblastic tumor (AU)


Subject(s)
Humans , Female , Adult , Intussusception/surgery , Neoplasms, Muscle Tissue/surgery , Risk Factors
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