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308 results on '"Labuda, D."'

3. Fraction of informative recombinations: a heuristic approach to analyze recombination rates

Author

Lefebvre, J.-F. and Labuda, D.

Subjects
Genetic recombination -- Research, Heuristic -- Genetic aspects, Nucleotide sequence -- Evaluation, Biological sciences
Abstract

In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 AfricanAmericans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates ([[rho].sub.obs]) of 0.85 and 0.37 [kb.sup.1] in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of [[rho].sub.obs] varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed ~80% of recombinations in one-third and ~50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.

Published
2008

6. Age and origin of major Smith-Lemli-Opitz syndrome (SLOS) mutations in European populations

Author

Witsch-Baumgartner, M, Schwentner, I, Gruber, M, Benlian, P, Bertranpetit, J, Bieth, E, Chevy, F, Clusellas, N, Estivill, X, Gasparini, G, Giros, M, Kelley, R I, Krajewska-Walasek, M, Menzel, J, Miettinen, T, Ogorelkova, M, Rossi, M, Scala, I, Schinzel, A, Schmidt, K, Schönitzer, D, Seemanova, E, Sperling, K, Syrrou, M, Talmud, P J, Wollnik, B, Krawczak, M, Labuda, D, and Utermann, G

Published
2008
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9. Lipid processing and lipoprotein synthesis by the developing human fetal colon

Author

Levy, E., Loirdighi, N., Thibault, L., Nguyen, T.D., Labuda, D., Delvin, E., and Menard, D.

Subjects
Colon (Anatomy) -- Physiological aspects, Gastrointestinal mucosa -- Physiological aspects, Lipids in nutrition -- Physiological aspects, Biological sciences
Abstract

The role of the colon in nutrition was determined by investigating its contribution to lipid processing and lipoprotein synthesis in the developing human fetal colon. The results showed that the colon is involved in the synthesis of lipids, lipoproteins and major apoproteins. It was also suggested that the colon is involved in the transport of lipids and lipoproteins in the gastrointestinal mucosa.

Published
1996

11. The genomic history of Southeastern Europe

Author

Mathieson, I., Roodenberg, S., Posth, C., Szécsényi-Nagy, A., Rohland, N., Mallick, S., Olalde, I., Broomandkhoshbacht, N., Cheronet, O., Fernandes, D., Ferry, M., Gamarra, B., Fortes, G., Haak, W., Harney, E., Krause-Kyora, B., Kucukkalipci, I., Michel, M., Mittnik, A., Nägele, K., Novak, M., Oppenheimer, J., Patterson, N., Pfrengle, S., Sirak, K., Stewardson, K., Vai, S., Alexandrov, S., Alt, K., Andreescu, R., Antonović, D., Ash, A., Atanassova, N., Bacvarov, K., Gusztáv, M., Bocherens, H., Bolus, M., Boroneanţ, A., Boyadzhiev, Y., Budnik, A., Burmaz, J., Chohadzhiev, S., Conard, N., Cottiaux, R., Čuka, M., Cupillard, C., Drucker, D., Elenski, N., Francken, M., Galabova, B., Ganetovski, G., Gely, B., Hajdu, T., Handzhyiska, V., Harvati, K., Higham, T., Iliev, S., Janković, I., Karavanić, I., Kennett, D., Komšo, D., Kozak, A., Labuda, D., Lari, M., Lazar, C., Leppek, M., Leshtakov, K., Vetro, D., Los, D., Lozanov, I., Malina, M., Martini, F., McSweeney, K., Meller, H., Menđušić, M., Mirea, P., Moiseyev, V., Petrova, V., Price, T., Simalcsik, A., Sineo, L., Šlaus, M., Slavchev, V., Stanev, P., Starović, A., Szeniczey, T., Talamo, S., Teschler-Nicola, M., Thevenet, C., Valchev, I., Valentin, F., Vasilyev, S., Veljanovska, F., Venelinova, S., Veselovskaya, E., Viola, B., Virag, C., Zaninović, J., Zäuner, S., Stockhammer, P., Catalano, G., Krauß, R., Caramelli, D., Zariņa, G., Gaydarska, B., Lillie, M., Nikitin, A., Potekhina, I., Papathanasiou, A., Borić, D., Bonsall, C., Krause, J., Pinhasi, R., and Reich, D.

Published
2017

12. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, S, Li, H, Lipson, M, Mathieson, I, Gymrek, M, Racimo, F, Zhao, M, Chennagiri, N, Nordenfelt, S, Tandon, A, Skoglund, P, Lazaridis, I, Sankararaman, S, Fu, Q, Rohland, N, Renaud, G, Erlich, Y, Willems, T, Gallo, C, Spence, JP, Song, YS, Poletti, G, Balloux, F, van Driem, G, de Knijff, P, Romero, IG, Jha, AR, Behar, DM, Bravi, CM, Capelli, C, Hervig, T, Moreno-Estrada, A, Posukh, OL, Balanovska, E, Balanovsky, O, Karachanak-Yankova, S, Sahakyan, H, Toncheva, D, Yepiskoposyan, L, Tyler-Smith, C, Xue, Y, Abdullah, MS, Ruiz-Linares, A, Beall, CM, Di Rienzo, A, Jeong, C, Starikovskaya, EB, Metspalu, E, Parik, J, Villems, R, Henn, BM, Hodoglugil, U, Mahley, R, Sajantila, A, Stamatoyannopoulos, G, Wee, JTS, Khusainova, R, Khusnutdinova, E, Litvinov, S, Ayodo, G, Comas, D, Hammer, MF, Kivisild, T, Klitz, W, Winkler, CA, Labuda, D, Bamshad, M, Jorde, LB, Tishkoff, SA, Watkins, WS, Metspalu, M, Dryomov, S, Sukernik, R, Singh, L, Thangaraj, K, Paeaebo, S, Kelso, J, Patterson, N, Reich, D, Mallick, S, Li, H, Lipson, M, Mathieson, I, Gymrek, M, Racimo, F, Zhao, M, Chennagiri, N, Nordenfelt, S, Tandon, A, Skoglund, P, Lazaridis, I, Sankararaman, S, Fu, Q, Rohland, N, Renaud, G, Erlich, Y, Willems, T, Gallo, C, Spence, JP, Song, YS, Poletti, G, Balloux, F, van Driem, G, de Knijff, P, Romero, IG, Jha, AR, Behar, DM, Bravi, CM, Capelli, C, Hervig, T, Moreno-Estrada, A, Posukh, OL, Balanovska, E, Balanovsky, O, Karachanak-Yankova, S, Sahakyan, H, Toncheva, D, Yepiskoposyan, L, Tyler-Smith, C, Xue, Y, Abdullah, MS, Ruiz-Linares, A, Beall, CM, Di Rienzo, A, Jeong, C, Starikovskaya, EB, Metspalu, E, Parik, J, Villems, R, Henn, BM, Hodoglugil, U, Mahley, R, Sajantila, A, Stamatoyannopoulos, G, Wee, JTS, Khusainova, R, Khusnutdinova, E, Litvinov, S, Ayodo, G, Comas, D, Hammer, MF, Kivisild, T, Klitz, W, Winkler, CA, Labuda, D, Bamshad, M, Jorde, LB, Tishkoff, SA, Watkins, WS, Metspalu, M, Dryomov, S, Sukernik, R, Singh, L, Thangaraj, K, Paeaebo, S, Kelso, J, Patterson, N, and Reich, D

Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

13. Founder effect in North-Eastern Quebec and the extent of the genetic signature associated with the myotonic dystrophy mutation

Author

Yotova, V., Zietkiewicz, E., Lemieux-Blanchard, E., Labuda, M., Bourgeois, S., Labuda, D., Fortin, J., Lepage, P., Hudson, T.J., Lescault, A., and Laberge, C.

Subjects
Human genetics -- Research, Myotonic dystrophy -- Genetic aspects, French-Canadians -- Diseases, Genetic disorders -- Demographic aspects, Human population genetics -- Research, Biological sciences
Published
2001

14. A nuclear marker for the southern route out of Africa

Author

Lovell, A.D., Zietkiewicz, E., Yotova, V., Batzer, M., and Labuda, D.

Subjects
Middle East -- Emigration and immigration, Africa -- Emigration and immigration, Human genetics -- Usage, Emigration and immigration -- Research, Prehistoric peoples -- Emigration and immigration, Genetic markers -- Usage, Anthropological research -- Genetic aspects, Genetic research -- Usage, Biogeography -- Research, Gene frequency -- Research, Cladistic analysis -- Usage, Ethnohistory -- Research, Biological sciences
Published
2001

16. Founder effects and the peopling of the New World

Author

Bourgeois, S., Zietkiewicz, E., Yotova, V., Michalski, R., Ruiz-Linares, A., and Labuda, D.

Subjects
Human genetics -- Research, Biological diversity -- Research, Native Americans -- Physiological aspects, Biological sciences
Published
2001

19. Reconstructing Native American population history

Author

Reich, D., Patterson, N., Campbell, D., Tandon, A., Mazieres, S., Ray, N., Parra, M.V., Rojas, W., Duque, C., Mesa, N., García, L.F., Triana, O., Blair, S., Maestre, A., Dib, J.C., Bravi, C.M., Bailliet, G., Corach, D., Hünemeier, T., Bortolini, M.C., Salzano, F.M., Petzl-Erler, M.L., Acuña-Alonzo, V., Aguilar-Salinas, C., Canizales-Quinteros, S., Tusié-Luna, T., Riba, L., Rodríguez-Cruz, M., Lopez-Alarcón, M., Coral-Vazquez, R., Canto-Cetina, T., Silva-Zolezzi, I., Fernandez-Lopez, J.C., Contreras, A.V., Jimenez-Sanchez, G., Gómez-Vázquez, M.J., Molina, J., Carracedo, A., Salas, A., Gallo López-Aliaga, Carla Maria, Poletti, G., Witonsky, D.B., Alkorta-Aranburu, G., Sukernik, R.I., Osipova, L., Fedorova, S.A., Vasquez, R., Villena, M., Moreau, C., Barrantes, R., Pauls, D., Excoffier, L., Bedoya, G., Rothhammer, F., Dugoujon, J.-M., Larrouy, G., Klitz, W., Labuda, D., Kidd, J., Kidd, K., Di Rienzo, A., Freimer, N.B., Price, A.L., and Ruiz-Linares, A.

Subjects
Gene Flow, Canada, Genotype, Life History, Population Dynamics, Review, Eskimo, Divergence, Arctic, Progeny, Isthmus Of Panama, Polymorphism, Migration, Language, Ancestry, Inheritance, Asian, Data Set, Population Dispersion, Dispersal, South America, Siberia, Panama [Central America], Genetic Variability, Archaeology, American Indian, Single Nucleotide Polymorphism, purl.org/pe-repo/ocde/ford#3.01.00 [https], Demographic History, Reconstruction, Indigenous Population
Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call First American. However, speakers of Eskimog-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Published
2012

20. Contraste de diversité génétique chez les populations amérindiennes

Author

Yang, NN, Mazières, S, Bravi, CM, Ray, N, Wang, S, Burley, MW, Bedoya, G, Rojas, W, Parra, MV, Molina, JA, Gallo, C, Poletti, G, Hill, K, Hurtado, AM, Petzl-Erler, ML, Tsuneto, LT, Klitz, W, Barrantes, R, Llop, E, Rothhammer, F, Labuda, D, Salzano, FM, Bortolini, MC, Excoffier, L, Dugoujon JM and Ruiz-Linares, A, Mazières, Stéphane, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, ComputingMilieux_MISCELLANEOUS, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology
Abstract

International audience

Published
2011

22. Mutability of Y-chromosomal microsatellites: Rates, characteristics, molecular bases, and rorensic implications

Author

Ballantyne, K. (Kaye), Goedbloed, M.A. (Miriam), Fang, R.N. (Rixun), Schaap, O. (Onno), Lao Grueso, O. (Oscar), Wollstein, A. (Andreas), Choi, Y. (Ying), Duijn, K. (Kate) van, Vermeulen, M. (Mark), Brauer, S. (Silke), Decorte, R. (Ronny), Poetsch, M. (Micaela), Wurmb-Schwark, N. (Nicole) von, Knijff, P. (Peter) de, Labuda, D. (Damian), Vézina, H. (Hélne), Knoblauch, H. (Hans), Lessig, R. (Rüdiger), Roewer, L. (Lutz), Ploski, R. (Rafal), Dobosz, T. (Tadeusz), Henke, J. (Jürgen), Furtado, M.R. (Manohar), Kayser, M.H. (Manfred), Ballantyne, K. (Kaye), Goedbloed, M.A. (Miriam), Fang, R.N. (Rixun), Schaap, O. (Onno), Lao Grueso, O. (Oscar), Wollstein, A. (Andreas), Choi, Y. (Ying), Duijn, K. (Kate) van, Vermeulen, M. (Mark), Brauer, S. (Silke), Decorte, R. (Ronny), Poetsch, M. (Micaela), Wurmb-Schwark, N. (Nicole) von, Knijff, P. (Peter) de, Labuda, D. (Damian), Vézina, H. (Hélne), Knoblauch, H. (Hans), Lessig, R. (Rüdiger), Roewer, L. (Lutz), Ploski, R. (Rafal), Dobosz, T. (Tadeusz), Henke, J. (Jürgen), Furtado, M.R. (Manohar), and Kayser, M.H. (Manfred)

Abstract

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10-4(95% credible interval [CI], 1.38 × 10-5- 2.02 × 10-3) to 7.44 × 10-2(95% CI, 6.51 × 10-2- 9.09 × 10-2) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Published
2010
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26. Diversity in the human genome

Author

Yotova, V, Zietkiewicz, E, Batzer, M, Kidd, Kk, Tishkoff, S, Modiano, David, Scozzari, Rosaria, Moisan, J. P., Jaruzelska, J, Labuda, M, Roman, Ma, and Labuda, D.

Published
1996

27. An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations

Author

Yotova, V., primary, Lefebvre, J.-F., additional, Moreau, C., additional, Gbeha, E., additional, Hovhannesyan, K., additional, Bourgeois, S., additional, Bedarida, S., additional, Azevedo, L., additional, Amorim, A., additional, Sarkisian, T., additional, Avogbe, P. H., additional, Chabi, N., additional, Dicko, M. H., additional, Kou' Santa Amouzou, E. S., additional, Sanni, A., additional, Roberts-Thomson, J., additional, Boettcher, B., additional, Scott, R. J., additional, and Labuda, D., additional

Published
2011
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28. Age and origin of major Smith-Lemli-Opitz syndrome (SLOS) mutations in European populations

Author

Witsch-Baumgartner, M, primary, Schwentner, I, additional, Gruber, M, additional, Benlian, P, additional, Bertranpetit, J, additional, Bieth, E, additional, Chevy, F, additional, Clusellas, N, additional, Estivill, X, additional, Gasparini, G, additional, Giros, M, additional, Kelley, R I, additional, Krajewska-Walasek, M, additional, Menzel, J, additional, Miettinen, T, additional, Ogorelkova, M, additional, Rossi, M, additional, Scala, I, additional, Schinzel, A, additional, Schmidt, K, additional, Schonitzer, D, additional, Seemanova, E, additional, Sperling, K, additional, Syrrou, M, additional, Talmud, P J, additional, Wollnik, B, additional, Krawczak, M, additional, Labuda, D, additional, and Utermann, G, additional

Published
2007
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31. Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity

Author

Fuselli, S, primary, Gilman, R H, additional, Chanock, S J, additional, Bonatto, S L, additional, De Stefano, G, additional, Evans, C A, additional, Labuda, D, additional, Luiselli, D, additional, Salzano, F M, additional, Soto, G, additional, Vallejo, G, additional, Sajantila, A, additional, Pettener, D, additional, and Tarazona-Santos, E, additional

Published
2006
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46. Parental smoking, CYP1A1 genetic polymorphisms and childhood leukemia (Québec, Canada).

Author

Infante-Rivard, Claire, Krajinovic, Maja, Labuda, Damian, Sinnett, Daniel, Infante-Rivard, C, Krajinovic, M, Labuda, D, and Sinnett, D

Subjects
ALLELES, COMPARATIVE studies, DISEASE susceptibility, FATHERS, GENETIC polymorphisms, LYMPHOBLASTIC leukemia, RESEARCH methodology, MEDICAL cooperation, OXIDOREDUCTASES, PASSIVE smoking, RESEARCH, SMOKING, LOGISTIC regression analysis, EVALUATION research, CASE-control method, PRENATAL exposure delayed effects, ODDS ratio
Abstract

Objective: To evaluate the effect of parental smoking on childhood acute lymphoblastic leukemia and to determine if it is modified by child genetic polymorphisms.Methods: We carried out a case-control study in Quebec, Canada, including 491 incident cases aged 0-9 years and as many healthy controls matched on age and sex. Each parent was interviewed separately with respect to smoking habits during and after pregnancy. In addition, we carried out a case-only substudy with 158 cases classified according to presence or absence of the alleles *2A, *2B, and *4 in the CYP1A1 gene.Results: There were small risk increases with maternal smoking during the later trimesters. Interaction odds ratios were increased (although often not significantly) for the CYP1A1*4 allele at high levels of maternal smoking in the last trimesters and at low level of paternal postnatal smoking, and decreased for the CYP1A1*2B allele. The latter appeared to confer a protective advantage at low levels for maternal prenatal smoking and at high levels for paternal postnatal smoking.Conclusions: Reported smoking habits showed no association with leukemia; risks for genetic polymorphisms lacked precision but indicated that the effect of parental smoking could be modified by variant alleles in the CYP1A1 gene. [ABSTRACT FROM AUTHOR]

Published
2000
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50. Allelic losses and DNA methylation at DNA mismatch repair loci in sporadic colorectal cancer.

Author

Benachenhou, N, Guiral, S, Gorska-Flipot, I, Michalski, R, Labuda, D, and Sinnett, D

Abstract

Normal and tumor DNA samples of 35 patients with sporadic colorectal carcinoma were analyzed for microsatellite alterations at 12 markers linked to mismatch repair loci: hMLH1, hMSH2, hMSH3, hMSH6, hPMS1 and hPMS2. Remarkably, no correlation was observed between the replication error phenotype (RER+) and allelic losses at these loci. Hemizygous deletions, seen in 6/35 (17%) informative cases at hMLH1, 4/27 (15%) at hMSH2/hMSH6 and 6/34 (18%) at hMSH3, were rarely found in RER+ tumors. Since mismatch repair protein components act in molecular complexes of defined stoichiometry we propose that hemizygous deletion of the corresponding loci may be involved in colorectal tumorigenesis through defects in cellular functions other than replication error correction. The analysis of the methylation status of the promoter region of hMLH1 revealed that methylation might be an important mechanism of this locus inactivation in RER+ sporadic colorectal cancer. [ABSTRACT FROM PUBLISHER]

Published
1998
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