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157 results on '"Nijman, Isaäc J."'

2. Multiplex spatial omics reveals changes in immune-epithelial crosstalk during inflammation and dysplasia development in chronic IBD patients

Author

CMM, CMM Groep Vercoulen, Cancer, MS MDL 1, Infection & Immunity, CMM USEQ Facility, Unit Opleiding MDL, CTI, CTI Computational Immunology Core, Pathologie Pathologen staf, Baars, Matthijs J.D., Floor, Evelien, Sinha, Neeraj, ter Linde, José J.M., van Dam, Stephanie, Amini, Mojtaba, Nijman, Isaäc J., ten Hove, Joren R., Drylewicz, Julia, Offerhaus, G. Johan A., Laclé, Miangela M., Oldenburg, Bas, Vercoulen, Yvonne, CMM, CMM Groep Vercoulen, Cancer, MS MDL 1, Infection & Immunity, CMM USEQ Facility, Unit Opleiding MDL, CTI, CTI Computational Immunology Core, Pathologie Pathologen staf, Baars, Matthijs J.D., Floor, Evelien, Sinha, Neeraj, ter Linde, José J.M., van Dam, Stephanie, Amini, Mojtaba, Nijman, Isaäc J., ten Hove, Joren R., Drylewicz, Julia, Offerhaus, G. Johan A., Laclé, Miangela M., Oldenburg, Bas, and Vercoulen, Yvonne

Published
2024

3. Pseudobudding: ruptured glands do not represent true tumor buds

Author

Haddad, Tariq Sami, primary, van den Dobbelsteen, Luuk, additional, Öztürk, Sonay K, additional, Geene, Robin, additional, Nijman, Isaäc J, additional, Verrijp, Kiek, additional, Jamieson, Nigel B, additional, Wood, Colin, additional, van Vliet, Shannon, additional, Reuvers, Luuk, additional, Achouiti, Soumia, additional, Rutgers, Natasja, additional, Brouwer, Nelleke, additional, Simmer, Femke, additional, Zlobec, Inti, additional, Lugli, Alessandro, additional, and Nagtegaal, Iris D, additional

Published
2023
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4. Pseudobudding: ruptured glands do not represent true tumor buds

Author

Haddad, Tariq Sami, van den Dobbelsteen, Luuk, Öztürk, Sonay K, Geene, Robin, Nijman, Isaäc J, Verrijp, Kiek, Jamieson, Nigel B, Wood, Colin, van Vliet, Shannon, Reuvers, Luuk, Achouiti, Soumia, Rutgers, Natasja, Brouwer, Nelleke, Simmer, Femke, Zlobec, Inti, Lugli, Alessandro, and Nagtegaal, Iris D

Subjects
570 Life sciences, biology, 610 Medicine & health
Abstract

Tumor budding (TB) is a strong biomarker of poor prognosis in colorectal cancer and other solid cancers. TB is defined as isolated single cancer cells or clusters of up to four cancer cells at the invasive tumor front. In areas with a large inflammatory response at the invasive front, single cells and cell clusters surrounding fragmented glands are observed appearing like TB. Occurrence of these small groups is referred to as pseudobudding (PsB), which arises due to external influences such as inflammation and glandular disruption. Using a combination of orthogonal approaches, we show that there are clear biological differences between TB and PsB. TB is representative of active invasion by presenting features of epithelial-mesenchymal transition and exhibiting increased deposition of extracellular matrix within the surrounding tumor microenvironment (TME), whereas PsB represents a reactive response to heavy inflammation where increased levels of granulocytes within the surrounding TME are observed. Our study provides evidence that areas with a strong inflammatory reaction should be avoided in the routine diagnostic assessment of TB. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Published
2023
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5. Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability

Author

Monroe, Glen R., Frederix, Gerardus W., Savelberg, Sanne M.C., de Vries, Tamar I., Duran, Karen J., van der Smagt, Jasper J., Terhal, Paulien A., van Hasselt, Peter M., Kroes, Hester Y., Verhoeven-Duif, Nanda M., Nijman, Isaäc J., Carbo, Ellen C., van Gassen, Koen L., Knoers, Nine V., Hövels, Anke M., van Haelst, Mieke M., Visser, Gepke, and van Haaften, Gijs

Published
2016
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7. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

Author

Lenstra, J.A., Tigchelaar, J., Biebach, I., Hallsson, J.H., Kantanen, J., Nielsen, V.H., Pompanon, F., Naderi, S., Rezaei, H.R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., VosLoohuis, M., van Straten, M., de Poel, E.A., Windig, J., Oldenbroek, K., AboShehada, Mahamoud, Marsan, Paolo Ajmone, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, BejaPereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régis, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, DʼUrso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, MarieLouise, IbeaghaAwemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andreas, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stéphane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgios, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesus, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, ObexerRuff, Gabriela, Papachristoforou, Christos, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, MariaEva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, and Zundel, Stéphanie

Published
2017
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9. Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.

Author

Nijman, Isaäc J., Rosen, Benjamin D., Bardou, Philippe, Faraut, Thomas, Cumer, Tristan, Daly, Kevin G., Zheng, Zhuqing, Cai, Yudong, Asadollahpour, Hojjat, Kul, Bengi Çınar, Zhang, Wei‐Yi, E., Guangxin, Ayin, A., Baird, Hayley, Bakhtin, Meirat, Bâlteanu, Valentin A., Barfield, Diana, Berger, Beate, Blichfeldt, Thor, and Boink, Geert

Subjects
*GOATS, *HAPLOGROUPS, *HAPLOTYPES, *GENE flow, *FOSSIL DNA, *CROSSBREEDING
Abstract

By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y‐chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y‐chromosomal variants from whole‐genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present‐day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male‐mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo‐Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y‐chromosomal variants for reconstructing the history of domestic species with a wide geographical range. [ABSTRACT FROM AUTHOR]

Published
2022
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10. Investigation of Genetic Modifiers of Copper Toxicosis in Labrador Retrievers

Author

Wu, Xiaoyan, den Boer, Elise R, Vos-Loohuis, Manon, Monroe, Glen R, Nijman, Isaäc J, van Steenbeek, F.G., Leegwater, Peter A J, Fieten, Hille, Interne geneeskunde GD, dCSCA AVR, dCSCA RMSC-1, CS_Genetics, Interne geneeskunde GD, dCSCA AVR, dCSCA RMSC-1, and CS_Genetics

Subjects
0301 basic medicine, medicine.medical_specialty, Cirrhosis, 040301 veterinary sciences, ATP7A, Biology, Article, General Biochemistry, Genetics and Molecular Biology, RETN, 0403 veterinary science, Labrador retriever, 03 medical and health sciences, Internal medicine, ATP7B, medicine, Allele, lcsh:Science, Ecology, Evolution, Behavior and Systematics, Wilson disease, Fatty liver, Genetic disorder, Paleontology, 04 agricultural and veterinary sciences, Menkes disease, medicine.disease, 030104 developmental biology, Endocrinology, Space and Planetary Science, copper, dog, Labrador Retriever, lcsh:Q, Resistin, copper toxicosis
Abstract

Copper toxicosis is a complex genetic disorder in Labrador retrievers characterized by hepatic copper accumulation eventually leading to liver cirrhosis. The variation of hepatic copper levels in Labrador retrievers has been partly explained by mutations in ATP7A c.980C&gt, T and ATP7B c.4358G&gt, A. To further elucidate the genetic background of this disease, we used targeted Next Generation Sequencing (NGS) in a cohort of 95 Labrador retrievers to analyze 72 potential modifier genes for variations associated with hepatic copper levels. Variants associated with copper levels were subsequently evaluated in a replication cohort of 144 Labrador retrievers. A total of 44 variants in 25 different genes were identified, of which four showed significant association with copper levels. Of the four variants found associated with hepatic copper levels in the NGS cohort, one was validated in the replication cohort. The non-reference allele of the variant NC_006602.3.g.52434480C&gt, T in RETN resulting in amino-acid change p.Leu7Phe was associated with decreased hepatic copper levels. In humans, resistin is associated with severity of non-alcoholic fatty liver disease, fibrosis, cirrhosis and mitochondrial dysfunction in hepatocytes. Further studies are needed to investigate the biological function of RETN p.Leu7Phe in the development of copper toxicosis in Labrador retrievers.

Published
2020

11. Investigation of Genetic Modifiers of Copper Toxicosis in Labrador Retrievers

Author

Interne geneeskunde GD, dCSCA AVR, dCSCA RMSC-1, CS_Genetics, Wu, Xiaoyan, den Boer, Elise R, Vos-Loohuis, Manon, Monroe, Glen R, Nijman, Isaäc J, van Steenbeek, F.G., Leegwater, Peter A J, Fieten, Hille, Interne geneeskunde GD, dCSCA AVR, dCSCA RMSC-1, CS_Genetics, Wu, Xiaoyan, den Boer, Elise R, Vos-Loohuis, Manon, Monroe, Glen R, Nijman, Isaäc J, van Steenbeek, F.G., Leegwater, Peter A J, and Fieten, Hille

Published
2020

16. Characterization of 37 Breed-Specific Single-Nucleotide Polymorphisms in Sheep

Author

Pariset, Lorraine, Cappuccio, Irene, Ajmone-Marsan, Paolo, Bruford, Michael, Dunner, Susana, Cortes, Oscar, Erhardt, Georg, Prinzenberg, Eva-Maria, Gutscher, Katja, Joost, Stephane, Pinto-Juma, Gabriela, Nijman, Isaäc J., Lenstra, Johannes A., Perez, Trinidad, Valentini, Alessio, and Consortium, Econogene

Published
2006

17. Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data

Author

Fokkema, Ivo F.A.C., van der Velde, Kasper J., Slofstra, Mariska K., Ruivenkamp, Claudia A.L., Vogel, Maartje J., Pfundt, Rolph, Blok, Marinus J., Lekanne Deprez, Ronald H., Waisfisz, Quinten, Abbott, Kristin M., Sinke, Richard J., Rahman, Rubayte, Nijman, Isaäc J., de Koning, Bart, Thijs, Gert, Wieskamp, Nienke, Moritz, Ruben J.G., Charbon, Bart, Saris, Jasper J., den Dunnen, Johan T., Laros, Jeroen F.J., Swertz, Morris A., van Gijn, Marielle E., Fokkema, Ivo F.A.C., van der Velde, Kasper J., Slofstra, Mariska K., Ruivenkamp, Claudia A.L., Vogel, Maartje J., Pfundt, Rolph, Blok, Marinus J., Lekanne Deprez, Ronald H., Waisfisz, Quinten, Abbott, Kristin M., Sinke, Richard J., Rahman, Rubayte, Nijman, Isaäc J., de Koning, Bart, Thijs, Gert, Wieskamp, Nienke, Moritz, Ruben J.G., Charbon, Bart, Saris, Jasper J., den Dunnen, Johan T., Laros, Jeroen F.J., Swertz, Morris A., and van Gijn, Marielle E.

Published
2019

18. Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data

Author

CMM USEQ Facility, Cancer, Genetica, Infection & Immunity, Fokkema, Ivo F.A.C., van der Velde, Kasper J., Slofstra, Mariska K., Ruivenkamp, Claudia A.L., Vogel, Maartje J., Pfundt, Rolph, Blok, Marinus J., Lekanne Deprez, Ronald H., Waisfisz, Quinten, Abbott, Kristin M., Sinke, Richard J., Rahman, Rubayte, Nijman, Isaäc J., de Koning, Bart, Thijs, Gert, Wieskamp, Nienke, Moritz, Ruben J.G., Charbon, Bart, Saris, Jasper J., den Dunnen, Johan T., Laros, Jeroen F.J., Swertz, Morris A., van Gijn, Marielle E., CMM USEQ Facility, Cancer, Genetica, Infection & Immunity, Fokkema, Ivo F.A.C., van der Velde, Kasper J., Slofstra, Mariska K., Ruivenkamp, Claudia A.L., Vogel, Maartje J., Pfundt, Rolph, Blok, Marinus J., Lekanne Deprez, Ronald H., Waisfisz, Quinten, Abbott, Kristin M., Sinke, Richard J., Rahman, Rubayte, Nijman, Isaäc J., de Koning, Bart, Thijs, Gert, Wieskamp, Nienke, Moritz, Ruben J.G., Charbon, Bart, Saris, Jasper J., den Dunnen, Johan T., Laros, Jeroen F.J., Swertz, Morris A., and van Gijn, Marielle E.

Published
2019

20. Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data

Author

Fokkema, Ivo F. A. C., primary, Velde, Kasper J., additional, Slofstra, Mariska K., additional, Ruivenkamp, Claudia A. L., additional, Vogel, Maartje J., additional, Pfundt, Rolph, additional, Blok, Marinus J., additional, Lekanne Deprez, Ronald H., additional, Waisfisz, Quinten, additional, Abbott, Kristin M., additional, Sinke, Richard J., additional, Rahman, Rubayte, additional, Nijman, Isaäc J., additional, Koning, Bart, additional, Thijs, Gert, additional, Wieskamp, Nienke, additional, Moritz, Ruben J. G., additional, Charbon, Bart, additional, Saris, Jasper J., additional, den Dunnen, Johan T., additional, Laros, Jeroen F. J., additional, Swertz, Morris A., additional, and Gijn, Marielle E., additional

Published
2019
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21. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

Author

Scheres Ben, Heidstra Renze, Benjamins Rene, van Dijken Anja, Nijman Isaäc J, Mokry Michal, and Cuppen Edwin

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Phenotype-driven forward genetic experiments are powerful approaches for linking phenotypes to genomic elements but they still involve a laborious positional cloning process. Although sequencing of complete genomes now becomes available, discriminating causal mutations from the enormous amounts of background variation remains a major challenge. Method To improve this, we developed a universal two-step approach, named 'fast forward genetics', which combines traditional bulk segregant techniques with targeted genomic enrichment and next-generation sequencing technology Results As a proof of principle we successfully applied this approach to two Arabidopsis mutants and identified a novel factor required for stem cell activity. Conclusion We demonstrated that the 'fast forward genetics' procedure efficiently identifies a small number of testable candidate mutations. As the approach is independent of genome size, it can be applied to any model system of interest. Furthermore, we show that experiments can be multiplexed and easily scaled for the identification of multiple individual mutants in a single sequencing run.

Published
2011
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22. Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats

Author

Nijman Isaäc J, Homberg Judith, Kuijpers Sylvia, and Cuppen Edwin

Subjects
Genetics, QH426-470
Abstract

Abstract Background Genetic variation in the regulatory region of the human serotonin transporter gene (SLC6A4) has been shown to affect brain functionality and personality. However, large heterogeneity in its biological effects is observed, which is at least partially due to genetic modifiers. To gain insight into serotonin transporter (SERT)-specific genetic modifiers, we studied an intercross between the Wistar SERT-/- rat and the behaviorally and genetically divergent Brown Norway rat, and performed a QTL analysis. Results In a cohort of >150 intercross SERT-/- and control (SERT+/+) rats we characterized 12 traits that were previously associated with SERT deficiency, including activity, exploratory pattern, cocaine-induced locomotor activity, and abdominal and subcutaneous fat. Using 325 genetic markers, 10 SERT-/--specific quantitative trait loci (QTLs) for parameters related to activity and exploratory pattern (Chr.1,9,11,14), and cocaine-induced anxiety and locomotor activity (Chr.5,8) were identified. No significant QTLs were found for fat parameters. Using in silico approaches we explored potential causal genes within modifier QTL regions and found interesting candidates, amongst others, the 5-HT1D receptor (Chr. 5), dopamine D2 receptor (Chr. 8), cannabinoid receptor 2 (Chr. 5), and genes involved in fetal development and plasticity (across chromosomes). Conclusions We anticipate that the SERT-/--specific QTLs may lead to the identification of new modulators of serotonergic signaling, which may be targets for pharmacogenetic and therapeutic approaches.

Published
2010
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23. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island

Author

Bonten Marc JM, Nijman Isaäc J, Hendrickx Antoni PA, Schapendonk Claudia ME, Vrijenhoek Joyce EP, Boekhorst Jos, Riley David R, Top Janetta, van Schaik Willem, Tettelin Hervé, and Willems Rob JL

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.

Published
2010
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24. A genome-wide SNP panel for mapping and association studies in the rat

Author

Guryev Victor, Verheul Mark, Kuipers Sylvia, Nijman Isaäc J, and Cuppen Edwin

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The laboratory rat (Rattus norvegicus) is an important model for human disease, and is extensively used for studying complex traits for example in the physiological and pharmacological fields. To facilitate genetic studies like QTL mapping, genetic makers that can be easily typed, like SNPs, are essential. Results A genome-wide set of 820 SNP assays was designed for the KASPar genotyping platform, which uses a technique based on allele specific oligo extension and energy transfer-based detection. SNPs were chosen to be equally spread along all chromosomes except Y and to be polymorphic between Brown Norway and SS or Wistar rat strains based on data from the rat HapMap EU project. This panel was tested on 38 rats of 34 different strains and 3 wild rats to determine the level of polymorphism and to generate a phylogenetic network to show their genetic relationships. As a proof of principle we used this panel to map an obesity trait in Zucker rats and confirmed significant linkage (LOD 122) to chromosome 5: 119–129 Mb, where the leptin receptor gene (Lepr) is located (chr5: 122 Mb). Conclusion We provide a fast and cost-effective platform for genome-wide SNP typing, which can be used for first-pass genetic mapping and association studies in a wide variety of rat strains.

Published
2008
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27. Characterization of 37 Breed-Specific Single-Nucleotide Polymorphisms in Sheep

Author

Pariset, Lorraine, Cappuccio, Irene, Ajmone-Marsan, Paolo, Bruford, Michael, Dunner, Susana, Cortes, Oscar, Erhardt, Georg, Prinzenberg, Eva-Maria, Gutscher, Katja, Joost, Stephane, Pinto-Juma, Gabriela, Nijman, Isaäc J., Lenstra, Johannes A., Perez, Trinidad, Valentini, Alessio, Consortium, Econogene, Pariset, Lorraine, Cappuccio, Irene, Ajmone-Marsan, Paolo, Bruford, Michael, Dunner, Susana, Cortes, Oscar, Erhardt, Georg, Prinzenberg, Eva-Maria, Gutscher, Katja, Joost, Stephane, Pinto-Juma, Gabriela, Nijman, Isaäc J., Lenstra, Johannes A., Perez, Trinidad, Valentini, Alessio, and Consortium, Econogene

Abstract

We identified 37 single-nucleotide polymorphisms (SNPs) in sheep and screened 16 individuals from 8 different sheep breeds selected throughout Europe. Population genetic measures based on the genotyping of about 30 sheep from the same 8 breeds are reported. To date, there are no sheep SNPs documented in the National Center for Biotechnology Information dbSNP database. Therefore, the markers presented here contribute significantly to those currently available

Published
2017

28. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

Author

Lenstra, J. A, Tigchelaar, J., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., Abo Shehada, Mahamoud, Ajmone Marsan, Paolo, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, Beja Pereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régi, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, D'Urso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, Marie Louise, Ibeagha Awemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andrea, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stephane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgio, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesu, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, Obexer Ruff, Gabriela, Papachristoforou, Christo, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Null, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, Maria Eva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, Zundel, Stéphanie, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Canali, Gabriele (ORCID:0000-0001-9244-8184), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Lenstra, J. A, Tigchelaar, J., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., Abo Shehada, Mahamoud, Ajmone Marsan, Paolo, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, Beja Pereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régi, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, D'Urso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, Marie Louise, Ibeagha Awemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andrea, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stephane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgio, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesu, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, Obexer Ruff, Gabriela, Papachristoforou, Christo, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Null, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, Maria Eva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, Zundel, Stéphanie, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Canali, Gabriele (ORCID:0000-0001-9244-8184), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)

Abstract

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.

Published
2017

29. Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity

Author

Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M, DDD Study, Sub Cell Biology, and Celbiologie

Subjects
Journal Article
Abstract

We identified de novo nonsense variants in KIDINS220/ARMS in three unrelated patients with spastic paraplegia, intellectual disability, nystagmus, and obesity (SINO). KIDINS220 is an essential scaffold protein coordinating neurotrophin signal pathways in neurites and is spatially and temporally regulated in the brain. Molecular analysis of patients' variants confirmed expression and translation of truncated transcripts similar to recently characterized alternative terminal exon splice isoforms of KIDINS220 KIDINS220 undergoes extensive alternative splicing in specific neuronal populations and developmental time points, reflecting its complex role in neuronal maturation. In mice and humans, KIDINS220 is alternative spliced in the middle region as well as in the last exon. These full-length and KIDINS220 splice variants occur at precise moments in cortical, hippocampal, and motor neuron development, with splice variants similar to the variants seen in our patients and lacking the last exon of KIDINS220 occurring in adult rather than in embryonic brain. We conducted tissue-specific expression studies in zebrafish that resulted in spasms, confirming a functional link with disruption of the KIDINS220 levels in developing neurites. This work reveals a crucial physiological role of KIDINS220 in development and provides insight into how perturbation of the complex interplay of KIDINS220 isoforms and their relative expression can affect neuron control and human metabolism. Altogether, we here show that de novo protein-truncating KIDINS220 variants cause a new syndrome, SINO. This is the first report of KIDINS220 variants causing a human disease.

Published
2016

31. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease

Author

van der Crabben, Saskia N, Hennus, Marije P, McGregor, Grant A, Ritter, Deborah I, Nagamani, Sandesh C S, Wells, Owen S, Harakalova, Magdalena, Chinn, Ivan K, Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M, Terheggen-Lagro, Suzanne W, van Lieshout, Stef, van Roosmalen, Markus J, Renkens, Ivo, Duran, Karen, Nijman, Isaäc J., Kloosterman, Wigard P, Hennekam, Eric, Orange, Jordan S, van Hasselt, Peter M, Wheeler, David A, Palecek, Jan J, Lehmann, Alan R, Oliver, Antony W, Pearl, Laurence H, Plon, Sharon E, Murray, Johanne M, van Haaften, Gijs, van der Crabben, Saskia N, Hennus, Marije P, McGregor, Grant A, Ritter, Deborah I, Nagamani, Sandesh C S, Wells, Owen S, Harakalova, Magdalena, Chinn, Ivan K, Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M, Terheggen-Lagro, Suzanne W, van Lieshout, Stef, van Roosmalen, Markus J, Renkens, Ivo, Duran, Karen, Nijman, Isaäc J., Kloosterman, Wigard P, Hennekam, Eric, Orange, Jordan S, van Hasselt, Peter M, Wheeler, David A, Palecek, Jan J, Lehmann, Alan R, Oliver, Antony W, Pearl, Laurence H, Plon, Sharon E, Murray, Johanne M, and van Haaften, Gijs

Published
2016

32. Targeted sequencing of 351 candidate genes for epileptic encephalopathy in a large cohort of patients

Author

de Kovel, Carolien G F, Brilstra, Eva H, van Kempen, Marjan J A, Van't Slot, Ruben, Nijman, Isaäc J., Afawi, Zaid, De Jonghe, Peter, Djémié, Tania, Guerrini, Renzo, Hardies, Katia, Helbig, Ingo, Hendrickx, Rik, Kanaan, Moine, Kramer, Uri, Lehesjoki, Anna-Elina E, Lemke, Johannes R, Marini, Carla, Mei, Davide, Møller, Rikke S, Pendziwiat, Manuela, Stamberger, Hannah, Suls, Arvid, Weckhuysen, Sarah, Koeleman, Bobby P C, EuroEPINOMICS RES Consortium, de Kovel, Carolien G F, Brilstra, Eva H, van Kempen, Marjan J A, Van't Slot, Ruben, Nijman, Isaäc J., Afawi, Zaid, De Jonghe, Peter, Djémié, Tania, Guerrini, Renzo, Hardies, Katia, Helbig, Ingo, Hendrickx, Rik, Kanaan, Moine, Kramer, Uri, Lehesjoki, Anna-Elina E, Lemke, Johannes R, Marini, Carla, Mei, Davide, Møller, Rikke S, Pendziwiat, Manuela, Stamberger, Hannah, Suls, Arvid, Weckhuysen, Sarah, Koeleman, Bobby P C, and EuroEPINOMICS RES Consortium

Published
2016

33. Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity

Author

Sub Cell Biology, Celbiologie, Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M, DDD Study, Sub Cell Biology, Celbiologie, Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M, and DDD Study

Published
2016

34. Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity

Author

Genetica Groep Van Haaften, Circulatory Health, Genetica Sectie Genoomdiagnostiek, Child Health, Cardiologie Arts-onderzoekers, CMM Groep Cuppen, Cancer, TN groep Joëls, Medische Fysiologie, Genetica, CMM Sectie Genomics and Bioinformatics, Genetica Klinische Genetica, Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M, DDD Study, Genetica Groep Van Haaften, Circulatory Health, Genetica Sectie Genoomdiagnostiek, Child Health, Cardiologie Arts-onderzoekers, CMM Groep Cuppen, Cancer, TN groep Joëls, Medische Fysiologie, Genetica, CMM Sectie Genomics and Bioinformatics, Genetica Klinische Genetica, Josifova, Dragana J, Monroe, Glen R, Tessadori, Federico, de Graaff, Esther, van der Zwaag, Bert, Mehta, Sarju G, Harakalova, Magdalena, Duran, Karen J, Savelberg, Sanne M C, Nijman, Isaäc J, Jungbluth, Heinz, Hoogenraad, Casper C, Bakkers, Jeroen, Knoers, Nine V, Firth, Helen V, Beales, Philip L, van Haaften, Gijs, van Haelst, Mieke M, and DDD Study

Published
2016

35. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease

Author

Metabole ziekten patientenzorg, Intensive care patientenzorg, Other research (not in main researchprogram), Infection & Immunity, Cardiologie Arts-onderzoekers, Genetica Sectie Genoomdiagnostiek, Brain, Immuno/reuma patientenzorg, Child Health, Genetica, CMM Groep Kloosterman, Genetica Groep Van Haaften, CMM Groep Cuppen, Cancer, Genetica Medische Informatica, Genetica Klinische Genetica, CMM Sectie Genomics and Bioinformatics, van der Crabben, Saskia N, Hennus, Marije P, McGregor, Grant A, Ritter, Deborah I, Nagamani, Sandesh C S, Wells, Owen S, Harakalova, Magdalena, Chinn, Ivan K, Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M, Terheggen-Lagro, Suzanne W, van Lieshout, Stef, van Roosmalen, Markus J, Renkens, Ivo, Duran, Karen, Nijman, Isaäc J., Kloosterman, Wigard P, Hennekam, Eric, Orange, Jordan S, van Hasselt, Peter M, Wheeler, David A, Palecek, Jan J, Lehmann, Alan R, Oliver, Antony W, Pearl, Laurence H, Plon, Sharon E, Murray, Johanne M, van Haaften, Gijs, Metabole ziekten patientenzorg, Intensive care patientenzorg, Other research (not in main researchprogram), Infection & Immunity, Cardiologie Arts-onderzoekers, Genetica Sectie Genoomdiagnostiek, Brain, Immuno/reuma patientenzorg, Child Health, Genetica, CMM Groep Kloosterman, Genetica Groep Van Haaften, CMM Groep Cuppen, Cancer, Genetica Medische Informatica, Genetica Klinische Genetica, CMM Sectie Genomics and Bioinformatics, van der Crabben, Saskia N, Hennus, Marije P, McGregor, Grant A, Ritter, Deborah I, Nagamani, Sandesh C S, Wells, Owen S, Harakalova, Magdalena, Chinn, Ivan K, Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M, Terheggen-Lagro, Suzanne W, van Lieshout, Stef, van Roosmalen, Markus J, Renkens, Ivo, Duran, Karen, Nijman, Isaäc J., Kloosterman, Wigard P, Hennekam, Eric, Orange, Jordan S, van Hasselt, Peter M, Wheeler, David A, Palecek, Jan J, Lehmann, Alan R, Oliver, Antony W, Pearl, Laurence H, Plon, Sharon E, Murray, Johanne M, and van Haaften, Gijs

Published
2016

36. Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability

Author

Genetica, CMM, Genetica Groep Van Haaften, Circulatory Health, Interne Geneeskunde Vasculaire, Child Health, Genetica Klinische Genetica, Metabole ziekten patientenzorg, Genetica Sectie Metabole Diagnostiek, Other research (not in main researchprogram), CMM Groep Cuppen, Cancer, Genetica Sectie Genoomdiagnostiek, CMM Sectie Genomics and Bioinformatics, Monroe, Glen R., Frederix, Gerardus W., Savelberg, Sanne M C, De Vries, Tamar I., Duran, Karen J., Van Der Smagt, Jasper J., Terhal, Paulien A., Van Hasselt, Peter M., Kroes, Hester Y., Verhoeven-Duif, Nanda M., Nijman, Isaäc J., Carbo, Ellen C., Van Gassen, Koen L., Knoers, Nine V., Hövels, Anke M., Van Haelst, Mieke M., Visser, Gepke, Van Haaften, Gijs, Genetica, CMM, Genetica Groep Van Haaften, Circulatory Health, Interne Geneeskunde Vasculaire, Child Health, Genetica Klinische Genetica, Metabole ziekten patientenzorg, Genetica Sectie Metabole Diagnostiek, Other research (not in main researchprogram), CMM Groep Cuppen, Cancer, Genetica Sectie Genoomdiagnostiek, CMM Sectie Genomics and Bioinformatics, Monroe, Glen R., Frederix, Gerardus W., Savelberg, Sanne M C, De Vries, Tamar I., Duran, Karen J., Van Der Smagt, Jasper J., Terhal, Paulien A., Van Hasselt, Peter M., Kroes, Hester Y., Verhoeven-Duif, Nanda M., Nijman, Isaäc J., Carbo, Ellen C., Van Gassen, Koen L., Knoers, Nine V., Hövels, Anke M., Van Haelst, Mieke M., Visser, Gepke, and Van Haaften, Gijs

Published
2016

37. Targeted sequencing of 351 candidate genes for epileptic encephalopathy in a large cohort of patients

Author

Genetica Klinische Genetica, Brain, Genetica Sectie Genoomdiagnostiek, Child Health, CMM Groep Cuppen, Cancer, Genetica Medische Informatica, Circulatory Health, de Kovel, Carolien G F, Brilstra, Eva H, van Kempen, Marjan J A, Van't Slot, Ruben, Nijman, Isaäc J., Afawi, Zaid, De Jonghe, Peter, Djémié, Tania, Guerrini, Renzo, Hardies, Katia, Helbig, Ingo, Hendrickx, Rik, Kanaan, Moine, Kramer, Uri, Lehesjoki, Anna-Elina E, Lemke, Johannes R, Marini, Carla, Mei, Davide, Møller, Rikke S, Pendziwiat, Manuela, Stamberger, Hannah, Suls, Arvid, Weckhuysen, Sarah, Koeleman, Bobby P C, EuroEPINOMICS RES Consortium, Genetica Klinische Genetica, Brain, Genetica Sectie Genoomdiagnostiek, Child Health, CMM Groep Cuppen, Cancer, Genetica Medische Informatica, Circulatory Health, de Kovel, Carolien G F, Brilstra, Eva H, van Kempen, Marjan J A, Van't Slot, Ruben, Nijman, Isaäc J., Afawi, Zaid, De Jonghe, Peter, Djémié, Tania, Guerrini, Renzo, Hardies, Katia, Helbig, Ingo, Hendrickx, Rik, Kanaan, Moine, Kramer, Uri, Lehesjoki, Anna-Elina E, Lemke, Johannes R, Marini, Carla, Mei, Davide, Møller, Rikke S, Pendziwiat, Manuela, Stamberger, Hannah, Suls, Arvid, Weckhuysen, Sarah, Koeleman, Bobby P C, and EuroEPINOMICS RES Consortium

Published
2016

38. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Author

Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, and Bovenberg, Jasper A.

Abstract

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value -4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C =0.135, βTC =0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR.

Published
2015

40. Loss-of-Function Mutations in the WNT Co-receptor LRP6 Cause Autosomal-Dominant Oligodontia

Author

Massink, Maarten P G, Creton, Marijn A., Spanevello, Francesca, Fennis, Willem M M, Cune, Marco S., Savelberg, Sanne M C, Nijman, Isaäc J., Maurice, Madelon M., vandenBoogaard, Marie José H, van Haaften, Gijs, Massink, Maarten P G, Creton, Marijn A., Spanevello, Francesca, Fennis, Willem M M, Cune, Marco S., Savelberg, Sanne M C, Nijman, Isaäc J., Maurice, Madelon M., vandenBoogaard, Marie José H, and van Haaften, Gijs

Published
2015

41. Mice lacking functional CD95-ligand display reduced proliferation of the intestinal epithelium without gross homeostatic alterations

Author

MS CGO, Cancer, Heelkunde Opleiding, Pathologie Laboratorium diagnostiek, CMM Groep Cuppen, Pathologie, Regenerative Medicine and Stem Cells, Divisie Beeld & Oncologie, MS HOD, Heelkunde Onderzoek, Trumpi, Kari, Steller, Ernst J A, de Leng, Wendy W, Raats, Daniëlle A, Nijman, Isaäc J, Morsink, Folkert H M, Borel Rinkes, Inne H M, Kranenburg, Onno, MS CGO, Cancer, Heelkunde Opleiding, Pathologie Laboratorium diagnostiek, CMM Groep Cuppen, Pathologie, Regenerative Medicine and Stem Cells, Divisie Beeld & Oncologie, MS HOD, Heelkunde Onderzoek, Trumpi, Kari, Steller, Ernst J A, de Leng, Wendy W, Raats, Daniëlle A, Nijman, Isaäc J, Morsink, Folkert H M, Borel Rinkes, Inne H M, and Kranenburg, Onno

Published
2015

42. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Author

CMM Groep Kaaij, CMM Groep Kloosterman, Child Health, Cancer, ZL Neuromusculaire Ziekten Medisch, Experimentele Afd. Cardiologie 1, CMM Groep Cuppen, JC onderzoeksprogramma Methodologie, Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., de Bakker, Paul I W, CMM Groep Kaaij, CMM Groep Kloosterman, Child Health, Cancer, ZL Neuromusculaire Ziekten Medisch, Experimentele Afd. Cardiologie 1, CMM Groep Cuppen, JC onderzoeksprogramma Methodologie, Van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, Van Enckevort, David J., Huffman, Jennifer E., White, Charles C., Feitosa, Mary F., Bartz, Traci M., Manichaikul, Ani, Joshi, Peter K., Peloso, Gina M., Deelen, Patrick, Van Dijk, Freerk, Willemsen, Gonneke, De Geus, Eco J., Milaneschi, Yuri, Penninx, Brenda W J H, Francioli, Laurent C., Menelaou, Androniki, Pulit, Sara L., Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A., Franco, Oscar H., Leach, Irene Mateo, Beekman, Marian, De Craen, Anton J M, Uh, Hae Won, Trochet, Holly, Hocking, Lynne J., Porteous, David J., Sattar, Naveed, Packard, Chris J., Buckley, Brendan M., Brody, Jennifer A., Bis, Joshua C., Rotter, Jerome I., Mychaleckyj, Josyf C., Campbell, Harry, Duan, Qing, Lange, Leslie A., Wilson, James F., Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F., Rich, Stephen S., Psaty, Bruce M., Borecki, Ingrid B., Kearney, Patricia M., Stott, David J., Cupples, L. Adrienne, Jukema, J. Wouter, Van Der Harst, Pim, Sijbrands, Eric J., Hottenga, Jouke Jan, Uitterlinden, Andre G., Swertz, Morris A., Van Ommen, Gert Jan B, De Bakker, Paul I W, Eline Slagboom, P., Boomsma, Dorret I., Wijmenga, Cisca, Van Duijn, Cornelia M., Neerincx, Pieter B T, Elbers, Clara C., Palamara, Pier Francesco, Peer, Itsik, Abdellaoui, Abdel, Kloosterman, Wigard P., Van Oven, Mannis, Vermaat, Martijn, Li, Mingkun, Laros, Jeroen F J, Stoneking, Mark, De Knijff, Peter, Kayser, Manfred, Veldink, Jan H., Van Den Berg, Leonard H., Byelas, Heorhiy, Den Dunnen, Johan T., Dijkstra, Martijn, Amin, Najaf, Van Der Velde, K. Joeri, Van Setten, Jessica, Kattenberg, Mathijs, Van Schaik, Barbera D C, Bot, Jan, Nijman, Isaäc J., Mei, Hailiang, Koval, Vyacheslav, Ye, Kai, Lameijer, Eric Wubbo, Moed, Matthijs H., Hehir-Kwa, Jayne Y., Handsaker, Robert E., Sunyaev, Shamil R., Sohail, Mashaal, Hormozdiari, Fereydoun, Marschall, Tobias, Schönhuth, Alexander, Guryev, Victor, Suchiman, H. Eka D, Wolffenbuttel, Bruce H., Platteel, Mathieu, Pitts, Steven J., Potluri, Shobha, Cox, David R., Li, Qibin, Li, Yingrui, Du, Yuanping, Chen, Ruoyan, Cao, Hongzhi, Li, Ning, Cao, Sujie, Wang, Jun, Bovenberg, Jasper A., and de Bakker, Paul I W

Published
2015

43. Loss-of-Function Mutations in the WNT Co-receptor LRP6 Cause Autosomal-Dominant Oligodontia

Author

Genetica Groep Van Haaften, Poli BT 9A-MFP, CMM Groep Maurice, MKA/BT Onderzoek, Other research (not in main researchprogram), CMM Groep Cuppen, Cancer, Regenerative Medicine and Stem Cells, Genetica Klinische Genetica, Child Health, Massink, Maarten P G, Creton, Marijn A., Spanevello, Francesca, Fennis, Willem M M, Cune, Marco S., Savelberg, Sanne M C, Nijman, Isaäc J., Maurice, Madelon M., vandenBoogaard, Marie José H, van Haaften, Gijs, Genetica Groep Van Haaften, Poli BT 9A-MFP, CMM Groep Maurice, MKA/BT Onderzoek, Other research (not in main researchprogram), CMM Groep Cuppen, Cancer, Regenerative Medicine and Stem Cells, Genetica Klinische Genetica, Child Health, Massink, Maarten P G, Creton, Marijn A., Spanevello, Francesca, Fennis, Willem M M, Cune, Marco S., Savelberg, Sanne M C, Nijman, Isaäc J., Maurice, Madelon M., vandenBoogaard, Marie José H, and van Haaften, Gijs

Published
2015

44. Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing

Author

STASSEN, JOOST H. M., SEIDL, MICHAEL F., VERGEER, PIM W. J., NIJMAN, ISAÄC J., SNEL, BEREND, CUPPEN, EDWIN, and VAN DEN ACKERVEKEN, GUIDO

Subjects
Peronospora, DNA, Complementary, Genome, Amino Acid Motifs, Molecular Sequence Data, High-Throughput Nucleotide Sequencing, Proteins, Original Articles, DNA, Lettuce, Markov Chains, Protein Structure, Tertiary, Plant Leaves, Consensus Sequence, Amino Acid Sequence, Transcriptome, Sequence Alignment, Phylogeny, Plant Diseases
Abstract

Lettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore‐derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene‐inducing peptide 1‐like proteins, glucanase inhibitors and lectins, and was enriched in cysteine‐rich proteins. Candidate host‐translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler‐like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.

Published
2012

45. Differentiation of European cattle by AFLP fingerprinting

Author

Negrini, Riccardo, Nijman, Isaäc J., Milanesi, Elisabetta, Moazami-Goudarzi, Katayoun, Williams, J. L., Erhardt, Georg, Dunner, Susana, Rodellar, Clementina, Valentini, Alessio, Bradley, Dan G., Olsaker, Ingrid, Kantanen, Juha, Ajmone-Marsan, Paolo, and Lenstra, Johannes A.

Subjects
Bovino, AFLP, Introgression, Introgressione, Cattle, Diversità genetica, Zebu, Amplified fragment length polymorphism, Genetic diversity
Abstract

The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19–22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.

Published
2011

46. Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity

Author

Naderi, Saeid, Rezaei, Hamid-Reza, Taberlet, Pierre, Zundel, Stéphanie, Rafat, Seyed-Abbas, Naghash, Hamid-Reza, El- Barody, Mohamed A. A., Ertugrul, Okan, Pompanon, François, Abo-Shehada, Mahamoud, Ajmone-Marsan, Paolo, Al Tarrayrah, Jamil, Baret, Philippe, Baumung, Roswitha, Beja-Pereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Bruford, Mike, Caloz, Régis, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Cortes, Oscar, Crepaldi, Paola, Dalamitra, Stella, Daniela, Krugmann, Dobi, Petrit, Dominik, Popielarczyk, Dunner, Susana, D'Urso, Giuseppe, England, Phillip, Erhardt, Georg, Prinzenberg, Eva-Maria, Ibeagha-Awemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andreas, Lühken, Gesine, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Brandt, Horst, Istvan, Anton, Juma, Gabriela, Joost, Stéphane, Jones, Sam, Karetsou, Katerina, Kliambas, Georgios, Koban, Evren, Kutita, Olga, Fesus, Lazlo, Lenstra, Johannes A., Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Glowatzki, Marie-Louise, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Obexer-Ruff, Gabriela, Papachristoforou, Christos, Pariset, Lorraine, Pellecchia, Marco, Peter, Christina, Perez, Trinidad, Pilla, Fabio, D'Andrea, Mariasilvia, Niznikowski, Roman, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, and Wiskin, Louise

Subjects
Domestic Goat, DNA mitocondriale, Mitochondrial DNA, Capra domestica
Abstract

From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings. The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HV segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals Conclusions/Significance. We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Published
2011

47. Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation

Author

Edwards, Ceiridwen J., Ginja, Catarina, Kantanen, Juha, Pérez-Pardal, Lucia, Tresset, Anne, Stock, Frauke, European Cattle Genetic Diversity Consortium, Gama, Luis T., Penedo, M. Cecilia T., Bradley, Daniel G., Lenstra, Johannes A., Nijman, Isaäc J., Moazami Goudarzi, Katayoun, Gautier 1, Mathieu, Laloë, Denis, Oulmouden, Ahmad, Levéziel, Hubert, Kivisild, Toomas, Smurfit Institute of Genetics, Trinity College Dublin, University of Oxford [Oxford], Veterinary Genetics Laboratory, University of California, Instituto Nacional dos Recursos Biológicos (INRB), Biotechnology and Food Research, Agrifood Research Finland, Servicio Regional de Investigacion y Desarollo Agroalimentario (SERIDA), Centre National de la Recherche Scientifique (CNRS), European Cattle Genetic Diversity Consortium, Faculty of Veterinary Medicine, Utrecht University [Utrecht], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Génétique Moléculaire Animale (UMR GMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), This work was also part-funded by The Wellcome Trust (grant no. 047485/Z/96/Z), and a Eurocores OMLL Programme Grant via CNRS, France., and Hubrecht Institute for Developmental Biology and Stem Cell Research

Subjects
Male, Archeology, [SDV]Life Sciences [q-bio], Animal Phylogenetics, Q1, Haplogroup, Y Chromosome, Genetics (life sciences), 2. Zero hunger, 0303 health sciences, Multidisciplinary, 630 Agriculture, 04 agricultural and veterinary sciences, Zebu, Founder Effect, Breed, humanities, Europe, Dairying, 590 Animals (Zoology), Medicine, Livestock, Research Article, Science, Zoology, Biology, QH301, 03 medical and health sciences, Genetic variation, Genetics, Animals, Cattle Farming, Y-Chromosomal Variation, Dairy, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Population Biology, business.industry, Haplotype, 0402 animal and dairy science, Genetic Variation, 040201 dairy & animal science, Biotechnology, Phylogeography, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Haplotypes, Cattle, business, Animal Genetics, Population Genetics, Founder effect
Abstract

BACKGROUND: Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS: Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS: We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries., Penedo, Lenstra mail

Published
2011
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49. Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity.

Author

Josifova, Dragana J., Monroe, Glen R., Tessadori, Federico, Graaff, Esther de, van der Zwaag2, Bert, Mehta, Sarju G., Harakalova, Magdalena, Duran, Karen J., Savelberg, Sanne M.C., Nijman, Isaäc J., Jungbluth, Heinz, Hoogenraad, Casper C., Bakkers, Jeroen, Knoers, Nine V., Firth, Helen V., Beales, Philip L., Haaften, Gijs van, and van Haelst, Mieke M.

Published
2016
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