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Search Results: 1 - 10 of 689 matches for " Francesc Calafell "
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Genetic studies of the Roma (Gypsies): a review
Luba Kalaydjieva, David Gresham, Francesc Calafell
BMC Medical Genetics , 2001, DOI: 10.1186/1471-2350-2-5
Abstract: Recent medical genetic research has identified a number of novel, or previously known but rare conditions, caused by private founder mutations. A summary of the findings, provided in this review, should assist diagnosis and counselling in affected families, and promote future collaborative research. The available incomplete epidemiological data suggest a non-random distribution of disease-causing mutations among Romani groups.Although far from systematic, the published information indicates that medical genetics has an important role to play in improving the health of this underprivileged and forgotten people of Europe. Reported carrier rates for some Mendelian disorders are in the range of 5 -15%, sufficient to justify newborn screening and early treatment, or community-based education and carrier testing programs for disorders where no therapy is currently available. To be most productive, future studies of the epidemiology of single gene disorders should take social organisation and cultural anthropology into consideration, thus allowing the targeting of public health programs and contributing to the understanding of population structure and demographic history of the Roma.The Roma (Gypsies) became one of the peoples of Europe around one thousand years ago, when they first arrived in the Balkans [1,2]. The current size of the European Romani population, around 8 million [2], is equivalent to that of an average European country (Figure 1). While human rights and socio-economic issues related to the Roma are increasingly becoming the focus of political debate and media coverage throughout Europe, their poor health status [[3-6]] is rarely discussed and still awaits the attention of the medical profession.This review of genetic studies of the Roma was prompted by two recent developments: (i) Studies conducted over the last decade have resulted in the identification of a number of novel single gene disorders and disease-causing mutations. The accumulating data are al
Factores genéticos en casos graves de gripe (H1N1) 2009
Calafell i Majó,Francesc; González Candelas,Fernando;
Revista Espa?ola de Salud Pública , 2011, DOI: 10.1590/S1135-57272011000100004
Abstract: the pandemic influenza (h1n1) 2009 raised a number of issues, of which we address the following: why did between 25 and 30% of severe influenza cases show no obvious risk factor? we hypothesize that an element that can contribute to the answer are host genetic risk factors involved in poor disease progression. several indications led us to this hypothesis: i) studies of familial aggregation in iceland and utah mormons show some heritability of influenza mortality; ii) nearly 300 known human genes are necessary for the replication of the influenza virus, and iii) the most severe cases of influenza a (h1n1) 2009 showed a deregulation of the adaptive immune system. we are addressing this problem through a case-control design (hospitalized cases of influenza (h1n1) 2009 confirmed against outpatient cases, also confirmed for (h1n1) 2009), which will be genotyped for more than a million single nucleotide polymorphisms (snps) and copy number variations (cnvs).
A New Method to Reconstruct Recombination Events at a Genomic Scale
Marta Melé,Asif Javed,Marc Pybus,Francesc Calafell,Laxmi Parida ,Jaume Bertranpetit ,The Genographic Consortium
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1001010
Abstract: Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.
Nicaraguan population data on LDLR, GYPA, D7S8, HBGG, GC and HLA-DQA1 loci
Bernal Morera,Gerardo Sánchez-Rivera,Gerardo Jiménez-Arce,Francesc Calafell
Revista de Biología Tropical , 2001,
Abstract: Nicaraguans have become the most numerous and fastest increasing minority in Costa Rica: at present they represent around 6 % of the total population of the country. We have analyzed the allele and genotype frequencies of six PCR-based genetic markers (LDLR, GYPA, HBGG, D7S8, GC, and HLA-DQA1) in 100 unrelated Nicaraguans living in Costa Rica. All loci studied were in Hardy-Weinberg equilibrium. Some statistical parameters of forensic interest were also calculated (h, PD and CE). Allele frequencies of the markers HLA-DQA1 and GYPAwere found to be significantly different between the populations of Nicaragua and Costa Rica. Nevertheless, genetic distances showed that Nicaragua is close to other Hispanic-admixed populations like those from Argentina, Chile, Colombia, Costa Rica, and USA Hispanics. The loci set was assessed to be useful for paternity testing and individual identification in the Nicaraguan population residing in Costa Rica Los nicaragüenses se han convertido en el grupo minoritario más numeroso y creciente en Costa Rica y en la actualidad representan alrededor del 6 % de la población total del país. Analizamos las frecuencias alélicas y genotípicas de seis marcadores genéticos (LDLR, GYPA, HBGG, D7S8, GC y HLA-DQA1) basados en la PCR en 100 nicaragüenses no emparentados, residentes en Costa Rica. Todos los loci estudiados cumplieron con el equilibrio de Hardy-Weinberg. También se calcularon algunos parámetros estadísticos de interés forense (h, PD y EC). Se encontró que las frecuencias alélicas de los marcadores HLA-DQA1 y GYPA presentan diferencias significativas entre las poblaciones de Nicaragua y Costa Rica. Sin embargo, el análisis de distancias genéticas mostró que la población de Nicaragua es cercana a otras de origen hispano mestizo como las poblaciones de Argentina, Chile, Colombia, Costa Rica y los hispanos de Estados Unidos. Este conjunto de loci fue validado como útil para la realización de pruebas de paternidad y para la identificación de individuos en la población nicaragüense residente en Costa Rica
A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin
Marc Garcia-Garcerà, Koldo Garcia-Etxebarria, Mireia Coscollà, Amparo Latorre, Francesc Calafell
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0074914
Abstract: In the last decade, an extensive effort has been made to characterize the human microbiota, due to its clinical and economic interests. However, a metagenomic approach to the skin microbiota is hampered by the high proportion of host DNA that is recovered. In contrast with the burgeoning field of gut metagenomics, skin metagenomics has been hindered by the absence of an efficient method to avoid sequencing the host DNA. We present here a method for recovering microbial DNA from skin samples, based on a combination of molecular techniques. We have applied this method to mouse skin, and have validated it by standard, quantitative PCR and amplicon sequencing of 16S rRNA. The taxonomic diversity recovered was not altered by this new method, as proved by comparing the phylogenetic structure revealed by 16S rRNA sequencing in untreated vs. treated samples. As proof of concept, we also present the first two mouse skin metagenomes, which allowed discovering new taxa (not only prokaryotes but also viruses and eukaryots) not reachable by 16S rRNA sequencing, as well as to characterize the skin microbiome functional landscape. Our method paves the way for the development of skin metagenomics, which will allow a much deeper knowledge of the skin microbiome and its relationship with the host, both in a healthy state and in relation to disease.
Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba
Isabel Mendizabal, Karla Sandoval, Gemma Berniell-Lee, Francesc Calafell, Antonio Salas, Antonio Martínez-Fuentes, David Comas
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-213
Abstract: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively.While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.At the time of the arrival of Columbus to Cuba in 1492, two different Native American groups inhabited the island: the Ciboneys, spread across the whole island, and the Tainos, mainly occupying the Central and Eastern regions of Cuba [1]. Although not much is known of Ciboney culture including their language, it is known that their economy was based on hunter-gathering (mainly fishing and hunting) and lacked pottery, unlike the Tainos, who were sedentary people living in large settlements and whose culture was supported by technically advanced agriculture. The social organization of the Tainos was based on chiefdoms, in which the caciques were the social authority. The Tainos spoke Arawakan, a language belonging to both the Equatorial sub-family and the Equatorial-Tucanoan family [1].Who first colonized the Caribbean islands is still a matter of debate. Geographical, archaeological and linguistic evidence [2-4], as well as ancient DNA data [5,6] suggest that the Caribbean was most likely populated by successive waves of migration originating in the Lower Orinoco Valley in South America, taking advantage of the close geographical proximity of the islands in the Caribbean. Therefo
Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22
Anna González-Neira, Francesc Calafell, Arcadi Navarro, Oscar Lao, Howard Cann, David Comas, Jaume Bertranpetit
Human Genomics , 2004, DOI: 10.1186/1479-7364-1-6-399
Abstract:
Nicaraguan population data on LDLR, GYPA, D7S8, HBGG, GC and HLA-DQA1 loci
Morera,Bernal; Sánchez-Rivera,Gerardo; Jiménez-Arce,Gerardo; Calafell,Francesc; Morales-Cordero,Ana Isabel;
Revista de Biología Tropical , 2001,
Abstract: nicaraguans have become the most numerous and fastest increasing minority in costa rica: at present they represent around 6 % of the total population of the country. we have analyzed the allele and genotype frequencies of six pcr-based genetic markers (ldlr, gypa, hbgg, d7s8, gc, and hla-dqa1) in 100 unrelated nicaraguans living in costa rica. all loci studied were in hardy-weinberg equilibrium. some statistical parameters of forensic interest were also calculated (h, pd and ce). allele frequencies of the markers hla-dqa1 and gypawere found to be significantly different between the populations of nicaragua and costa rica. nevertheless, genetic distances showed that nicaragua is close to other hispanic-admixed populations like those from argentina, chile, colombia, costa rica, and usa hispanics. the loci set was assessed to be useful for paternity testing and individual identification in the nicaraguan population residing in costa rica
Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics
Marc García-Garcerà, Elena Gigli, Federico Sanchez-Quinto, Oscar Ramirez, Francesc Calafell, Sergi Civit, Carles Lalueza-Fox
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024161
Abstract: Background Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. Methodology/Principals Findings To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. Conclusions We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5′ and 3′ ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
Allelic and genotypic associations of DRD2 TaqI A polymorphism with heroin dependence in Spanish subjects: a case control study
Jose Perez de los Cobos, Montserrat Baiget, Joan Trujols, Nuria Sinol, Victor Volpini, Enrique Banuls, Francesc Calafell, Elena Luquero, Elisabeth del Rio, Enric Alvarez
Behavioral and Brain Functions , 2007, DOI: 10.1186/1744-9081-3-25
Abstract: We compared two samples of unrelated Spanish individuals, all of European origin: 281 methadone-maintained heroin-dependent patients (207 males and 74 females) who frequently used non-opioid substances, and 145 control subjects (98 males and 47 females).The A1-A1 genotype was detected in 7.1% of patients and 1.4% of controls (P = 0.011, odds ratio = 5.48, 95% CI 1.26–23.78). Although the A1 allele was not associated with heroin dependence in the entire sample, the frequency of A1 allele was higher in male patients than in male controls (24.4% vs. 16.3%, P = 0.024, odds ratio = 1.65, 95% CI 1.07–2.57). A logistic regression analysis showed an interaction between DRD2 alleles and gender (odds ratio = 1.77, 95% CI 1.15–2.70).Our results indicate that, in Spanish individuals, genotypes of the DRD2 TaqI A polymorphism contribute to variations in the risk of heroin dependence, while single alleles contribute only in males.A better understanding of the etiology of heroin dependence is crucial for improving the prevention and treatment of this severe mental disorder. Genes that could be risk factors for heroin dependence have not been consistently identified; however, genetic epidemiology studies have shown that they do have an impact. These studies, with one exception [1], also suggest that such genetic factors are mainly nonspecific, because they also confer vulnerability to other substance use disorders (SUD) [2-4].The gene coding for the dopamine receptor D2 (DRD2) could be involved in heroin dependence and other SUD as a nonspecific genetic factor, because opioids and other substances of abuse induce some of their rewarding effects through the mesolimbic dopamine system [5,6]. Preclinical research supports this hypothesis. An absence of opioid-rewarding effects has been reported in mice lacking DRD2 [7].The DRD2 TaqI A is a SNP with two variants: A1, the less frequent allele, and A2. The A1 allele is associated with a reduction in the density of D2 receptors at the str
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