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Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C, Wang J, Wang W, Xun X. The sheep genome reference sequence: a work in progress. Anim Genet 2010; 41:449-53. [DOI: 10.1111/j.1365-2052.2010.02100.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Faraut T, de Givry S, Hitte C, Lahbib-Mansais Y, Morisson M, Milan D, Schiex T, Servin B, Vignal A, Galibert F, Yerle M. Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals. Cytogenet Genome Res 2009; 126:21-33. [DOI: 10.1159/000245904] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2009] [Indexed: 11/19/2022] Open
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Abstract
MOTIVATION Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering. RESULTS In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model. AVAILABILITY The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.
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Affiliation(s)
- T Faraut
- Laboratoire de génétique cellulaire BP 52627, 31326 Castanet Tolosan, France.
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Bosak N, Yamomoto R, Fujisaki S, Faraut T, Kiuchi S, Hiraiwa H, Hayashi T, Yasue H. A dense comparative gene map between human chromosome 19q13.3-->q13.4 and a homologous segment of swine chromosome 6. Cytogenet Genome Res 2005; 108:317-21. [PMID: 15627751 DOI: 10.1159/000081525] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Accepted: 06/30/2004] [Indexed: 11/19/2022] Open
Abstract
The human chromosome (HSA)19q region has been shown to correspond to swine chromosome (SSC) 6q11-->q21 by bi-directional chromosomal painting and gene mapping. However, since the precise correspondence has not been determined, 26 genes localized in HSA19q13.3-->q13.4 were assigned to the SSC6 region mainly by radiation hybrid (RH) mapping, and additionally, by somatic cell hybrid panel (SCHP) mapping, and fluorescent in situ hybridization (FISH). Out of the 26 genes, 24 were assigned to a swine RH map with LOD scores greater than 6 (threshold of significance). The most likely order of the 24 genes along SSC6 was calculated by CarthaGene, revealing that the order is essentially the same as that in HSA19q13.3-->q13.4. For AURKC and RPS5 giving LOD scores not greater than 6, SCHP mapping and FISH were additionally performed; SCHP mapping assigned AURKC and RPS5 to SSC6q22-->q23 and SSC6q21, respectively, which is consistent with the observation of FISH. Consequently, all the genes (26 genes) examined in the present study were shown to localize in SSC6q12-->q23, and the order of the genes along the chromosomes was shown to be essentially the same in swine and human, though several intrachromosomal rearrangements were observed between the species.
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Affiliation(s)
- N Bosak
- Genome Research Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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Pinton A, Faraut T, Yerle M, Gruand J, Pellestor F, Ducos A. Comparison of male and female meiotic segregation patterns in translocation heterozygotes: a case study in an animal model (Sus scrofa domestica L.). Hum Reprod 2005; 20:2476-82. [PMID: 15878917 DOI: 10.1093/humrep/dei067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The comparison of male and female meiotic segregation patterns for individuals carrying identical reciprocal translocations has been rarely reported in mammalian species. The main comparative study involving males and females with comparable genetic background has been performed in the mouse. Swine is another relevant animal model species for meiotic studies. Here we present the segregation patterns determined for sows carrying one of the two following reciprocal translocations: 38, XX, rcp(3;15)(q27;q13), and 38, XX, rcp(12;14)(q13;q21). These segregation data were compared to those previously obtained for closely related boars carrying the same balanced chromosomal rearrangements. METHODS Dual colour in situ hybridization of whole chromosome painting probes was carried out on metaphases of in vitro-matured oocytes II. Segregation results were obtained for 118 and 206 metaphases II respectively for the two translocations. RESULTS Significant differences between sexes were demonstrated for both rearrangements. For instance, for the 3/15 translocation, the chromosomally unbalanced gametes were of different origin: preponderance of the adjacent-I segregation in the male (31.4%), and of the adjacent-II (14.3%) and 3:1 (14.3%) segregations in females. For the 12/14 translocation, the proportion of balanced gametes was greater in males than in females (75.9 and 59.4% respectively). CONCLUSION This study is a new scientific contribution to compare the segregation patterns of male and female carriers of identical chromosomal rearrangements. The results obtained are consistent with those previously reported in mice. Hypotheses to interpret the observed differences between the two translocations, as well as between the male and female segregation patterns, are formulated and discussed.
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Affiliation(s)
- A Pinton
- UMR INRA-ENVT Cytogénétique des Populations Animales, Toulouse, France.
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Pinton A, Ducos A, Yerle M, Faraut T, Pellestor F. Male and female segregation profiles in two reciprocal translocations t(12;14)(q13;q21) t(3;15)(q27;q13) in the pig species. Fertil Steril 2004. [DOI: 10.1016/j.fertnstert.2004.07.729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bosak N, Faraut T, Mikawa S, Uenishi H, Kiuchi S, Hiraiwa H, Hayashi T, Yasue H. Construction of a high-resolution comparative gene map between swine chromosome region 6q11-->q21 and human chromosome 19 q-arm by RH mapping of 51 genes. Cytogenet Genome Res 2004; 102:109-15. [PMID: 14970688 DOI: 10.1159/000075734] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2003] [Accepted: 07/28/2003] [Indexed: 11/19/2022] Open
Abstract
A comprehensive and comparative map was constructed for the porcine chromosome (SSC) 6q11-->q21 region, where the gene(s) responsible for the maldevelopment of embryos are localized using swine populations of the National Institute of Animal Industry, Japan (NIAI). Since the chromosomal region corresponds to a region of human chromosome (HSA) 19q13.1-->q13.3 based on bi-directional chromosome painting, primer pairs were designed from porcine cDNA sequences identified, on a sequence comparison basis, as being transcripts from genes orthologous to those in the HSA region. Fifty-one genes were successfully assigned to a swine radiation hybrid (RH) map with LOD scores greater than 6. ERF and PSMD8 genes were assigned to SSC4 and SSC1, respectively. The remaining 49 genes were assigned to SSC6, demonstrating that the synteny between the SSC6 and HSA19 chromosomal regions is essentially conserved, therefore confirming, the results of bi-directional chromosome painting. However, when examined precisely, rearrangements have apparently occurred within the region of conserved synteny. For the ERF and PSMD8 genes assigned to SSCs other than SSC6, additional mapping using somatic cell hybrid (SCH) panels was performed to confirm the results of RH-mapping.
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Affiliation(s)
- N Bosak
- Genome Research Department, National Institute of Agrobiological Sciences, Ikenodai, Tsukuba, Ibaraki, Japan
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Morisson M, Jiguet-Jiglaire C, Lemiere A, Leroux S, Faraut T, Yerle M, Vignal A. A radiation hybrid panel and its use in developing a gene map of the chicken. Br Poult Sci 2004; 44:797-8. [PMID: 14965119 DOI: 10.1080/00071660410001666853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M Morisson
- I.N.R.A.-Laboratoire de Génétique Cellulaire, 31326 Castanet-Tolosan
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Robic A, Faraut T, Iannuccelli N, Lahbib-Mansais Y, Cantegrel V, Alexander L, Milan D. A new contribution to the integration of human and porcine genome maps: 623 new points of homology. Cytogenet Genome Res 2004; 102:100-8. [PMID: 14970687 DOI: 10.1159/000075733] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Accepted: 07/28/2003] [Indexed: 11/19/2022] Open
Abstract
In this study we examined homologies between 1,735 porcine microsatellites and human sequence. For 1,710 microsatellites we directly used the sequence flanking the repeat available in GenBank. For a set of 305 microsatellites, a BAC library was screened and end-sequencing provided 461 additional sequences. Altogether 2,171 porcine sequences were tentatively aligned with the sequence of the human genome using the fasta program. Human homologies were observed for 652 microsatellite loci and porcine chromosome assignments available for 623 microsatellites provide useful links in the human and pig comparative map. Moreover for 92 STS, a significant sequence similarity was detected using at least two sequences and in all cases corresponding human locations were consistent. The present study allowed the integration of anonymous markers and the porcine linkage map into the framework of the comparative data between human and porcine genomes (http://w3.toulouse.inra.fr/lgc/pig/msat/). Moreover all conserved syntenic segments were defined on human chromosomes.
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Affiliation(s)
- A Robic
- Institut National de la Recherche Agronomique, Laboratoire de Génétique Cellulaire, BP27, Castanet Tolosan, France.
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Faraut T, Mermet MA, Demongeot J, Cohen O. Cooperation of selection and meiotic mechanisms in the production of imbalances in reciprocal translocations. Cytogenet Cell Genet 2000; 88:15-21. [PMID: 10773657 DOI: 10.1159/000015476] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have used data from chromosomally unbalanced offspring observed at birth, as well as data from sperm chromosome analysis, to study the meiotic segregation of reciprocal translocations. Using data from a total of 1,597 unbalanced children, we have observed an excess in maternal origin for all modes of imbalance. This excess is particularly marked for the 3:1 unbalanced mode, for which we have also observed a maternal age effect, indicating a close relationship with autosomal trisomies. In addition, a statistical analysis of data from 34 different published studies using sperm chromosome analysis has demonstrated that factors which, for reasons of viability, produce a predisposition for a particular mode of imbalance at birth also appear to favor meiotic production of this type of imbalance. Thus the production of unbalanced gametes of a particular type is influenced by the size of the imbalance.
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Affiliation(s)
- T Faraut
- TIMC-IMAG CNRS UMR 5525, Université Joseph Fourier, Faculté de Médecine de Grenoble, La Tronche, France.
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Faraut T, Cans C, Althuser M, Jouk PS. [Combined use of nuchal translucency, gestational age and maternal age for evaluation of the risk of trisomy 21]. J Gynecol Obstet Biol Reprod (Paris) 1999; 28:439-45. [PMID: 10566163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
PURPOSE Despite the definition of new screening policies for fetal trisomies, based on nuchal translucency thickness (NT) or maternal serum, the prevalence of trisomy 21 remains high. We propose a strategy based on a combination of maternal age, gestational age and NT, measured at the first trimester ultrasound examination, for the assessment of risk. METHODS We present, in this paper, a characterisation of the physiological increase of fetal NT between the 10th and the 14th week of gestation, in a preliminary study of 266 echographic examinations. Next we propose a calculation of the simultaneous risk of trisomy 21 based on marginal risks for maternal age and increased NT values available in the literature. RESULTS AND CONCLUSION We propose to define a high-risk group associated to the NT marker by using a cut-off risk of 1/250 for the simultaneous risk. This criteria may, as well, be expressed by a pathological threshold of NT varying with maternal age and gestational age. Without questioning that women aged of 38 years or older are a high-risk group, this approach should allow an improvement of the prenatal screening for trisomy 21.
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Affiliation(s)
- T Faraut
- Techniques de l'Imagerie de la Modélisation et de la Cognition (TIMC), Faculté de Médecine, La Tronche
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