Search results for "SNP"
showing 10 items of 366 documents
SNPs detection by eBWT positional clustering
2019
Sequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, there is a growing interest in alignment-free and reference-free variants calling methods that only make use of (suitably indexed) raw reads data. We develop the positional clustering theory that (i) describes how the extended Burrows–Wheeler Transform (eBWT) of a collection of reads tends to cluster together bases that cover the same genome position (ii) predicts the size of such clusters, and (iii) exhibits an elegant and precise LCP array based procedure to locate such clusters in the e…
Influencia de los polimorfismos genéticos en la Leucemia Mieloide Crónica
2016
La leucemia mieloide crónica (LMC) es una neoplasia mieloproliferativa crónica de carácter clonal con origen en una célula madre pluripotencial común a las tres series hematopoyéticas. La historia natural de la LMC progresa desde una fase crónica relativamente benigna a la aparición de una fase terminal o de crisis blástica caracterizada por un cuadro de insuficiencia medular, similar al de las leucemias agudas y generalmente refractario al tratamiento. La enfermedad se caracteriza por la presencia de una alteración citogenética, el cromosoma Filadelfia (Ph), producto de una translocación recíproca entre los cromosomas 9 y 22 en las células hematopoyéticas, que genera el oncogén BCR/ABL, da…
Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chicke…
2023
Abstract Background Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homoz…
Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
2017
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the more than 100,000 years old trans-Atlantic separation of Atlantic co…
Association of a single nucleotide polymorphism of RANK gene with blood pressure in Spanish women
2020
Abstract In addition to governing key functions in bone metabolism and the immune system, the RANK/RANKL/OPG system plays a role in the vascular system, particularly in vascular calcification and atherosclerosis. Given that these 2 phenotypes are considered a major cause of high blood pressure (BP), in this study we analyzed the association of SNPs in RANK and OPG genes with blood pressure. An observational study was conducted of 2 SNPs in the RANK gene (rs884205 and rs78326403) and 1 in the OPG gene (rs4876869) with systolic (SBP) and diastolic blood pressure (DBP) in a cohort of 695 women. Data analysis revealed a statistically significant association between the SNP rs884205 and BP press…
Variants translating reduced expression of the beta estrogen receptor gene were associated with increased carotid intima media thickness : a cross-se…
2021
Abstract Background There is debate on the role of estrogens in modulating the risk for atherosclerosis in women. Our purpose was to investigate whether the size of the estrogenic impact was independently associated with variation of carotid intima-media thickness (IMT) in healthy late postmenopausal women. The levels of circulating estrogens have been used in previous studies but the influence of SNPs of the estrogen receptors (ER) α and β has not been investigated.Methods We performed a crossed-sectional study of 91 women in a university hospital. We used a double approach in which, in addition to the measurement of estradiol levels by ultrasensitive methods, genetic variants (SNPs) assoc…
New loci associated with kidney function and chronic kidney disease
2010
Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea 60 ml/min/1.73 m 2; n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide-significant loci (P 5 × 10 8) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or…
Association between CCK-AR gene and schizophrenia with auditory hallucinations
2007
[Objective]: Previous studies on a possible association between CCK-AR polymorphisms and schizophrenia have been controversial. The aim of the present study was to assess a potential association between schizophrenic patients with auditory hallucinations and polymorphisms of the CCK-AR gene.
Association analysis between gene variants of the tyrosine hydroxylase and the serotonin transporter in borderline personality disorder.
2010
For patients with borderline personality disorder (BPD), we previously reported an independent effect of the catechol-o-methyl-transferase (COMT) low-activity (Met(158)) allele and an interaction with the low-expression allele of the deletion/insertion (short/long or S/L, resp.) polymorphism in the serotonin transporter-linked promoter region (5-HTTLPR). The purpose of the present study was to extend these findings to the tyrosine hydroxylase (TH) Val(81)Met single nucleotide polymorphism (SNP), the 5-HTTLPR S/L polymorphism incorporating the recently described functional A/G SNP within the long allele of the 5-HTTLPR (rs25531) as well as the variable number of tandem repeat (VNTR) polymorp…