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1. Introgressive hybridization and the evolutionary history of the herring gull complex revealed by mitochondrial and nuclear DNA

Author

Zhang Jun, Ritz Markus S, Liebers-Helbig Dorit, Sternkopf Viviane, Helbig Andreas J, and de Knijff Peter

Subjects
Evolution, QH359-425
Abstract

Abstract Background Based on extensive mitochondrial DNA (mtDNA) sequence data, we previously showed that the model of speciation among species of herring gull (Larus argentatus) complex was not that of a ring species, but most likely due more complex speciation scenario's. We also found that two species, herring gull and glaucous gull (L. hyperboreus) displayed an unexpected biphyletic distribution of their mtDNA haplotypes. It was evident that mtDNA sequence data alone were far from sufficient to obtain a more accurate and detailed insight into the demographic processes that underlie speciation of this complex, and that extensive autosomal genetic analysis was warranted. Results For this reason, the present study focuses on the reconstruction of the phylogeographic history of a limited number of gull species by means of a combined approach of mtDNA sequence data and 230 autosomal amplified fragment length polymorphism (AFLP) loci. At the species level, the mtDNA and AFLP genetic data were largely congruent. Not only for argentatus and hyperboreus, but also among a third species, great black-backed gull (L. marinus) we observed two distinct groups of mtDNA sequence haplotypes. Based on the AFLP data we were also able to detect distinct genetic subgroups among the various argentatus, hyperboreus, and marinus populations, supporting our initial hypothesis that complex demographic scenario's underlie speciation in the herring gull complex. Conclusions We present evidence that for each of these three biphyletic gull species, extensive mtDNA introgression could have taken place among the various geographically distinct subpopulations, or even among current species. Moreover, based on a large number of autosomal AFLP loci, we found evidence for distinct and complex demographic scenario's for each of the three species we studied. A more refined insight into the exact phylogeographic history within the herring gull complex is still impossible, and requires detailed autosomal sequence information, a topic of our future studies.

Published
2010
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2. Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans

Author

den Dunnen Johan T, Kloosterman Ate D, van Duijn Kate, Kersbergen Paula, Kayser Manfred, and de Knijff Peter

Subjects
Genetics, QH426-470
Abstract

Abstract Background The identification and use of Ancestry-Sensitive Markers (ASMs), i.e. genetic polymorphisms facilitating the genetic reconstruction of geographical origins of individuals, is far from straightforward. Results Here we describe the ascertainment and application of five different sets of 47 single nucleotide polymorphisms (SNPs) allowing the inference of major human groups of different continental origin. For this, we first used 74 cell lines, representing human males from six different geographical areas and screened them with the Affymetrix Mapping 10K assay. In addition to using summary statistics estimating the genetic diversity among multiple groups of individuals defined by geography or language, we also used the program STRUCTURE to detect genetically distinct subgroups. Subsequently, we used a pairwise FST ranking procedure among all pairs of genetic subgroups in order to identify a single best performing set of ASMs. Our initial results were independently confirmed by genotyping this set of ASMs in 22 individuals from Somalia, Afghanistan and Sudan and in 919 samples from the CEPH Human Genome Diversity Panel (HGDP-CEPH) Conclusion By means of our pairwise population FST ranking approach we identified a set of 47 SNPs that could serve as a panel of ASMs at a continental level.

Published
2009
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4. Large-scale migration into Britain during the Middle to Late Bronze Age

Author

Patterson, Nick, Isakov, Michael, Booth, Thomas, Büster, Lindsey, Fischer, Claire-Elise, Olalde, Iñigo, Ringbauer, Harald, Akbari, Ali, Cheronet, Olivia, Bleasdale, Madeleine, Adamski, Nicole, Altena, Eveline, Bernardos, Rebecca, Brace, Selina, Broomandkhoshbacht, Nasreen, Callan, Kimberly, Candilio, Francesca, Culleton, Brendan, Curtis, Elizabeth, Demetz, Lea, Carlson, Kellie Sara Duffett, Edwards, Ceiridwen J., Fernandes, Daniel M., Foody, M. George B., Freilich, Suzanne, Goodchild, Helen, Kearns, Aisling, Lawson, Ann Marie, Lazaridis, Iosif, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Michel, Megan, Morante, Guillermo Bravo, Oppenheimer, Jonas, Özdoğan, Kadir Toykan, Qiu, Lijun, Schattke, Constanze, Stewardson, Kristin, Workman, J. Noah, Zalzala, Fatma, Zhang, Zhao, Agustí, Bibiana, Allen, Tim, Almássy, Katalin, Amkreutz, Luc, Ash, Abigail, Baillif-Ducros, Christèle, Barclay, Alistair, Bartosiewicz, László, Baxter, Katherine, Bernert, Zsolt, Blažek, Jan, Bodružić, Mario, Boissinot, Philippe, Bonsall, Clive, Bradley, Pippa, Brittain, Marcus, Brookes, Alison, Brown, Fraser, Brown, Lisa, Brunning, Richard, Budd, Chelsea, Burmaz, Josip, Canet, Sylvain, Carnicero-Cáceres, Silvia, Čaušević-Bully, Morana, Chamberlain, Andrew, Chauvin, Sébastien, Clough, Sharon, Čondić, Natalija, Coppa, Alfredo, Craig, Oliver, Črešnar, Matija, Cummings, Vicki, Czifra, Szabolcs, Danielisová, Alžběta, Daniels, Robin, Davies, Alex, de Jersey, Philip, Deacon, Jody, Deminger, Csilla, Ditchfield, Peter W., Dizdar, Marko, Dobeš, Miroslav, Dobisíková, Miluše, Domboróczki, László, Drinkall, Gail, Đukić, Ana, Ernée, Michal, Evans, Christopher, Evans, Jane, Fernández-Götz, Manuel, Filipović, Slavica, Fitzpatrick, Andrew, Fokkens, Harry, Fowler, Chris, Fox, Allison, Gallina, Zsolt, Gamble, Michelle, González Morales, Manuel R., González-Rabanal, Borja, Green, Adrian, Gyenesei, Katalin, Habermehl, Diederick, Hajdu, Tamás, Hamilton, Derek, Harris, James, Hayden, Chris, Hendriks, Joep, Hernu, Bénédicte, Hey, Gill, Horňák, Milan, Ilon, Gábor, Istvánovits, Eszter, Jones, Andy M., Kavur, Martina Blečić, Kazek, Kevin, Kenyon, Robert A., Khreisheh, Amal, Kiss, Viktória, Kleijne, Jos, Knight, Mark, Kootker, Lisette M., Kovács, Péter F., Kozubová, Anita, Kulcsár, Gabriella, Kulcsár, Valéria, Le Pennec, Christophe, Legge, Michael, Leivers, Matt, Loe, Louise, López-Costas, Olalla, Lord, Tom, Los, Dženi, Lyall, James, Marín-Arroyo, Ana B., Mason, Philip, Matošević, Damir, Maxted, Andy, McIntyre, Lauren, McKinley, Jacqueline, McSweeney, Kathleen, Meijlink, Bernard, Mende, Balázs G., Menđušić, Marko, Metlička, Milan, Meyer, Sophie, Mihovilić, Kristina, Milasinovic, Lidija, Minnitt, Steve, Moore, Joanna, Morley, Geoff, Mullan, Graham, Musilová, Margaréta, Neil, Benjamin, Nicholls, Rebecca, Novak, Mario, Pala, Maria, Papworth, Martin, Paresys, Cécile, Patten, Ricky, Perkić, Domagoj, Pesti, Krisztina, Petit, Alba, Petriščáková, Katarína, Pichon, Coline, Pickard, Catriona, Pilling, Zoltán, Price, T. Douglas, Radović, Siniša, Redfern, Rebecca, Resutík, Branislav, Rhodes, Daniel T., Richards, Martin B., Roberts, Amy, Roefstra, Jean, Sankot, Pavel, Šefčáková, Alena, Sheridan, Alison, Skae, Sabine, Šmolíková, Miroslava, Somogyi, Krisztina, Somogyvári, Ágnes, Stephens, Mark, Szabó, Géza, Szécsényi-Nagy, Anna, Szeniczey, Tamás, Tabor, Jonathan, Tankó, Károly, Maria, Clenis Tavarez, Terry, Rachel, Teržan, Biba, Teschler-Nicola, Maria, Torres-Martínez, Jesús F., Trapp, Julien, Turle, Ross, Ujvári, Ferenc, van der Heiden, Menno, Veleminsky, Petr, Veselka, Barbara, Vytlačil, Zdeněk, Waddington, Clive, Ware, Paula, Wilkinson, Paul, Wilson, Linda, Wiseman, Rob, Young, Eilidh, Zaninović, Joško, Žitňan, Andrej, Lalueza-Fox, Carles, de Knijff, Peter, Barnes, Ian, Halkon, Peter, Thomas, Mark G., Kennett, Douglas J., Cunliffe, Barry, Lillie, Malcolm, Rohland, Nadin, Pinhasi, Ron, Armit, Ian, and Reich, David

Published
2022
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5. Deep brain stimulation of the medial forebrain bundle in treatment-resistant depression: Preliminary results showing shift and sustained antidepressant effects

Author

Gosse Jacobus Johannes Mol, Nora Runia, Roel J.T. Mocking, Dirk de Knijff, Pepijn van den Munckhof, Maarten Bot, Hilko Ardon, Dieuwertje A. de Waardt, Geert-Jan M. Rutten, P. Rick Schuurman, Damiaan A.J.P. Denys, and IsidoorO. Bergfeld

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Published
2023
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6. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain

Author

Lall, Gurdeep Matharu, Larmuseau, Maarten H. D., Wetton, Jon H., Batini, Chiara, Hallast, Pille, Huszar, Tunde I., Zadik, Daniel, Aase, Sigurd, Baker, Tina, Balaresque, Patricia, Bodmer, Walter, Børglum, Anders D., de Knijff, Peter, Dunn, Hayley, Harding, Stephen E., Løvvik, Harald, Dupuy, Berit Myhre, Pamjav, Horolma, Tillmar, Andreas O., Tomaszewski, Maciej, Tyler-Smith, Chris, Verdugo, Marta Pereira, Winney, Bruce, Vohra, Pragya, Story, Joanna, King, Turi E., and Jobling, Mark A.

Published
2021
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7. Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

Author

Arindrarto, Wibowo, Borràs, Daniel M., de Groen, Ruben A. L., van den Berg, Redmar R., Locher, Irene J., van Diessen, Saskia A. M. E., van der Holst, Rosalie, van der Meijden, Edith D., Honders, M. Willy, de Leeuw, Rick H., Verlaat, Wina, Jedema, Inge, Kroes, Wilma G. M., Knijnenburg, Jeroen, van Wezel, Tom, Vermaat, Joost S. P., Valk, Peter J. M., Janssen, Bart, de Knijff, Peter, van Bergen, Cornelis A. M., van den Akker, Erik B., Hoen, Peter A. C. ’t, Kiełbasa, Szymon M., Laros, Jeroen F. J., Griffioen, Marieke, and Veelken, Hendrik

Published
2021
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8. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Animals, Australia, Black People, Datasets as Topic, Genetic Variation, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Mutation Rate, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Phylogeny, Racial Groups, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
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

9. Study protocol of a randomized, double-blind, placebo-controlled, multi-center trial to treat antipsychotic-induced weight gain: the Metformin-Lifestyle in antipsychotic users (MELIA) trial

Author

de Boer, Nini, Guloksuz, Sinan, van Baal, Caroline, Willebrands, Leonie, Deenik, Jeroen, Vinkers, Christiaan H., Rossum, Inge Winter-van, Zinkstok, Janneke, Wilting, Ingeborg, Zantvoord, Jasper B., Backx, Frank, Swildens, Wilma E., Schouw, Marieke, Bogers, Jan, Hulshof, Folkwin, de Knijff, Rudolf, Duindam, Peter, Veereschild, Mike, Bak, Maarten, Frederix, Geert, de Haan, Lieuwe, van Os, Jim, Cahn, Wiepke, and Luykx, Jurjen J.

Published
2021
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10. The Dutch Y-chromosomal landscape

Author

Altena, Eveline, Smeding, Risha, van der Gaag, Kristiaan J., Larmuseau, Maarten H. D., Decorte, Ronny, Lao, Oscar, Kayser, Manfred, Kraaijenbrink, Thirsa, and de Knijff, Peter

Published
2020
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13. DNA-identification of the first nominate Hume's Whitethroat Sylvia althaea althaea in The Netherlands and in Finland

Author

de Knijff P and te Raa M

Subjects
cytochrome B, mtDNA, Lesser Whitethroat
Abstract

This document with public access URL https://doi.org/10.5281/zenodo.7498548 was prepared as supplementary information to the following article to appear in Dutch Birding: First European records of nominate Hume’s Whitethroat in the Netherlands in 2014 and Finland in 2020. Written by Rinse van der Vliet, Vincent van der Spek, Peter de Knijff, Laura Kvist, Petteri Lehikoinen, Aleksi Lehikoinen & William Velmala

Published
2023
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15. DNA-identification of the first Dutch Siberian northern shrike Lanius borealis sibericus from a toepad sample

Author

De Knijff, P and Raa, Marije Te

Subjects
Shrike, DNA
Abstract

This document with ZENODO URL https://doi.org/ 10.5281/zenodo.6982812 was prepared as supplementary information to the following article to appear in Dutch Birding: Siberische Noordelijke Klapekster bij Nuenen in november 1909; written by Justin J F J Jansen, Pepijn Kamminga, Martin Brandsma, Reuven Yosef & Peter de Knijff. Summary On 25 November 1909, a grey shrike Lanius was purchased by Rijksmuseum voor Natuurlijke Historie (now Naturalis Biodiversity Center) at Leiden, Zuid-Holland, Netherlands (skin RMNH.AVES1663). The bird, a first-winter female, was collected at Nuenen, Noord-Brabant, Netherlands. It was at the time identified as Great Grey Shrike L excubitor. The bird was recently re-identified as a Northern Shrike L borealis (L b borealis or L b sibericus). Here we describe all relevant technical aspects of the DNA-study that was performed in order to support this identification. For this we used a toe pad sample. We obtained a mitochondrial Cytochrome B fragment of 893 bp. which gave a 100% match with L b sibericus. This was the first record for the Netherlands, and chronologically the second for Europe.

Published
2022
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19. Skewed X-inactivation is common in the general female population

Author

Shvetsova, E, Sofronova, A, Monajemi, R, Gagalova, K, Draisma, HHM, White, SJ, Santen, GWE, Lopes, SMCDS, Heijmans, BT, Van Meurs, J, Jansen, R, Franke, L, Kielbasa, SM, Den Dunnen, JT, 't Hoen, PAC, Boomsma, DI, Pool, R, Van Dongen, J, Hottenga, JJ, Van Greevenbroek, MMJ, Da Stehouwer, C, Van der Kallen, CJH, Schalkwijk, CG, Wijmenga, C, Zhernakova, S, Tigchelaar, EF, Slagboom, PE, Beekman, M, Deelen, J, Van Heemst, D, Veldink, JH, Van den Berg, LH, Van Duijn, CM, Hofman, BA, Uitterlinden, AG, Jhamai, PM, Verbiest, M, Suchiman, HED, Verkerk, M, Van der Breggen, R, Van Rooij, J, Lakenberg, N, Mei, H, Bot, J, Zhernakova, DV, 't Hof, PV, Deelen, P, Nooren, I, Moed, M, Vermaat, M, Luijk, R, Bonder, MJ, Van Iterson, M, Van Dijk, F, Van Galen, M, Arindrarto, W, Swertz, MA, Van Zwet, EW, Isaacs, A, Francioli, LC, Menelaou, A, Pulit, SL, Palamara, PF, Elbers, CC, Neerincx, PB, Ye, K, Guryev, V, Kloosterman, WP, Abdellaoui, A, Van Leeuwen, EM, Van Oven, M, Li, M, Laros, JF, Karssen, LC, Kanterakis, A, Amin, N, Lameijer, EW, Kattenberg, M, Dijkstra, M, Byelas, H, Van Setten, J, Van Schaik, BD, Nijman, IJ, Renkens, I, Marschall, T, Schonhuth, A, Hehir-Kwa, JY, Handsaker, RE, Polak, P, Sohail, M, Vuzman, D, Hormozdiari, F, Van Enckevort, D, Koval, V, Moed, MH, Van der Velde, KJ, Rivadeneira, F, Estrada, K, Medina-Gomez, C, McCarroll, SA, De Craen, AJ, Suchiman, HE, Oostra, B, Willemsen, G, Platteel, M, Pitts, SJ, Potluri, S, Sundar, P, Cox, DR, Sunyaev, SR, Stoneking, M, De Knijff, P, Kayser, M, Li, Q, Li, Y, Du, Y, Chen, R, Cao, H, Li, N, Cao, S, Wang, J, Bovenberg, JA, Pe'er, I, Van Ommen, GJ, De Bakker, PI, Consortium, Bios, Consortium, Gonl, BIOS consortium, GoNL consortium, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Translational Immunology Groningen (TRIGR), Groningen Research Institute for Asthma and COPD (GRIAC), Stem Cell Aging Leukemia and Lymphoma (SALL), Epidemiology and Data Science, AII - Inflammatory diseases, APH - Methodology, Experimental Immunology, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, APH - Personalized Medicine, Biological Psychology, APH - Mental Health, APH - Health Behaviors & Chronic Diseases, RS: Carim - V01 Vascular complications of diabetes and metabolic syndrome, Interne Geneeskunde, RS: CARIM - R3 - Vascular biology, MUMC+: MA Reumatologie (9), MUMC+: MA Nefrologie (9), MUMC+: MA Medische Oncologie (9), MUMC+: MA Hematologie (9), MUMC+: MA Maag Darm Lever (9), MUMC+: MA Endocrinologie (9), MUMC+: HVC Pieken Maastricht Studie (9), RS: CARIM - R3.01 - Vascular complications of diabetes and the metabolic syndrome, MUMC+: MA Interne Geneeskunde (3), RS: Carim - B01 Blood proteins & engineering, RS: FHML MaCSBio, RS: CARIM - R1 - Thrombosis and haemostasis, RS: CARIM - R1.01 - Blood proteins & engineering, Biochemie, Psychiatry, VU University medical center, Pediatric surgery, Amsterdam Reproduction & Development (AR&D), Internal Medicine, Epidemiology, Genetic Identification, and Clinical Genetics

Subjects
Netherlands Twin Register (NTR), Male, 0301 basic medicine, Receptors, Cytoplasmic and Nuclear/genetics, CHROMOSOME-INACTIVATION, BIOS consortium, Receptors, Cytoplasmic and Nuclear, Septins/genetics, Population genetics, GoNL consortium, Population/genetics, Negative selection, 0302 clinical medicine, X Chromosome Inactivation, Receptors, Non-U.S. Gov't, Genetics (clinical), Netherlands, Genetics & Heredity, Genetics, education.field_of_study, Membrane Glycoproteins, Dosage compensation, DMD LOCUS, Research Support, Non-U.S. Gov't, Receptors, Peptide/genetics, Intracellular Signaling Peptides and Proteins, Peptide/genetics, Single Nucleotide, CARRIERS, TRANSLOCATION, VARIABILITY, Female, Life Sciences & Biomedicine, EXPRESSION, Biochemistry & Molecular Biology, Receptors, Peptide, Population, ADRENOLEUKODYSTROPHY, Biology, Research Support, Polymorphism, Single Nucleotide, Article, X-inactivation, DUCHENNE MUSCULAR-DYSTROPHY, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Journal Article, Humans, Polymorphism, Allele, education, Skewed X-inactivation, Gene, 0604 Genetics, Calcium-Binding Proteins/genetics, Science & Technology, CONSEQUENCES, Calcium-Binding Proteins, Membrane Glycoproteins/genetics, 030104 developmental biology, Cytoplasmic and Nuclear/genetics, PATTERNS, Intracellular Signaling Peptides and Proteins/genetics, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Septins, 030217 neurology & neurosurgery
Abstract

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants.

Published
2019
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20. A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.

Author

Thirsa Kraaijenbrink, Kristiaan J van der Gaag, Sofia B Zuniga, Yali Xue, Denise R Carvalho-Silva, Chris Tyler-Smith, Mark A Jobling, Emma J Parkin, Bing Su, Hong Shi, Chun-Jie Xiao, Wen-Ru Tang, V K Kashyap, R Trivedi, T Sitalaximi, Jheelam Banerjee, Karma Tshering of Gaselô, Nirmal M Tuladhar, Jean-Robert M L Opgenort, George L van Driem, Guido Barbujani, and Peter de Knijff

Subjects
Medicine, Science
Abstract

The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.

Published
2014
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23. Ten millennia of hepatitis B virus evolution

Author

Kocher, A, Papac, L, Barquera, R, Key, FM, Spyrou, MA, Hubler, R, Rohrlach, AB, Aron, F, Stahl, R, Wissgott, A, van Bommel, F, Pfefferkorn, M, Mittnik, A, Villalba-Mouco, V, Neumann, GU, Rivollat, M, van de Loosdrecht, MS, Majander, K, Tukhbatova, R, Musralina, L, Ghalichi, A, Penske, S, Sabin, S, Michel, M, Gretzinger, J, Nelson, EA, Ferraz, T, Nagele, K, Parker, C, Keller, M, Guevara, EK, Feldman, M, Eisenmann, S, Skourtanioti, E, Giffin, K, Gnecchi-Ruscone, GA, Friederich, S, Schimmenti, V, Khartanovich, V, Karapetian, MK, Chaplygin, MS, Kufterin, VV, Khokhlov, AA, Chizhevsky, AA, Stashenkov, DA, Kochkina, AF, Tejedor-Rodriguez, C, Garcia-Martinez de Lagran, I, Arcusa-Magallon, H, Garrido-Pena, R, Ignacio Royo-Guillen, J, Novacek, J, Rottier, S, Kacki, S, Saintot, S, Kaverzneva, E, Belinskiy, AB, Veleminsky, P, Limbursky, P, Kostka, M, Loe, L, Popescu, E, Clarke, R, Lyons, A, Mortimer, R, Sajantila, A, Chinique de Armas, Y, Hernandez Godoy, ST, Hernandez-Zaragoza, D, Pearson, J, Binder, D, Lefranc, P, Kantorovich, AR, Maslov, VE, Lai, L, Zoledziewska, M, Beckett, JF, Langova, M, Ingman, T, Garcia Atienzar, G, de Miguel Ibanez, MP, Romero, A, Sperduti, A, Beckett, S, Salter, SJ, Zilivinskaya, ED, Vasil, DV, von Heyking, K, Burger, RL, Salazar, LC, Amkreutz, L, Navruzbekov, M, Rosenstock, E, Alonso-Fernandez, C, Slavchev, V, Kalmykov, AA, Atabiev, BC, Batieva, E, Alvarez Calmet, M, Llamas, B, Schultz, M, Krauss, R, Jimenez-Echevarria, J, Francken, M, Shnaider, S, de Knijff, P, Altena, E, Van de Vijver, K, Fehren-Schmitz, L, Tung, TA, Losch, S, Dobrovolskaya, M, Makarov, N, Read, C, Van Twest, M, Sagona, C, Ramsl, PC, Akar, M, Yener, KA, Carmona Ballestero, E, Cucca, F, Mazzarello, V, Utrilla, P, Rademaker, K, Fernandez-Dominguez, E, Baird, D, Semal, P, Marquez-Morfin, L, Roksandic, M, Steiner, H, Carlos Salazar-Garcia, D, Shishlina, N, Erdal, YS, Hallgren, F, Boyadzhiev, Y, Boyadzhiev, K, Kuessner, M, Sayer, D, Onkamo, P, Skeates, R, Rojo-Guerra, M, Buzhilova, A, Khussainova, E, Djansugurova, LB, Beisenov, AZ, Samashev, Z, Massy, K, Mannino, M, Moiseyev, V, Mannermaa, K, Balanovsky, O, Deguilloux, M-F, Reinhold, S, Hansen, S, Kitov, EP, Dobes, M, Ernee, M, Meller, H, Alt, KW, Prufer, K, Warinner, C, Schiffels, S, Stockhammer, PW, Bos, K, Posth, C, Herbig, A, Haak, W, Krause, J, Kuehnert, D, Kocher, A, Papac, L, Barquera, R, Key, FM, Spyrou, MA, Hubler, R, Rohrlach, AB, Aron, F, Stahl, R, Wissgott, A, van Bommel, F, Pfefferkorn, M, Mittnik, A, Villalba-Mouco, V, Neumann, GU, Rivollat, M, van de Loosdrecht, MS, Majander, K, Tukhbatova, R, Musralina, L, Ghalichi, A, Penske, S, Sabin, S, Michel, M, Gretzinger, J, Nelson, EA, Ferraz, T, Nagele, K, Parker, C, Keller, M, Guevara, EK, Feldman, M, Eisenmann, S, Skourtanioti, E, Giffin, K, Gnecchi-Ruscone, GA, Friederich, S, Schimmenti, V, Khartanovich, V, Karapetian, MK, Chaplygin, MS, Kufterin, VV, Khokhlov, AA, Chizhevsky, AA, Stashenkov, DA, Kochkina, AF, Tejedor-Rodriguez, C, Garcia-Martinez de Lagran, I, Arcusa-Magallon, H, Garrido-Pena, R, Ignacio Royo-Guillen, J, Novacek, J, Rottier, S, Kacki, S, Saintot, S, Kaverzneva, E, Belinskiy, AB, Veleminsky, P, Limbursky, P, Kostka, M, Loe, L, Popescu, E, Clarke, R, Lyons, A, Mortimer, R, Sajantila, A, Chinique de Armas, Y, Hernandez Godoy, ST, Hernandez-Zaragoza, D, Pearson, J, Binder, D, Lefranc, P, Kantorovich, AR, Maslov, VE, Lai, L, Zoledziewska, M, Beckett, JF, Langova, M, Ingman, T, Garcia Atienzar, G, de Miguel Ibanez, MP, Romero, A, Sperduti, A, Beckett, S, Salter, SJ, Zilivinskaya, ED, Vasil, DV, von Heyking, K, Burger, RL, Salazar, LC, Amkreutz, L, Navruzbekov, M, Rosenstock, E, Alonso-Fernandez, C, Slavchev, V, Kalmykov, AA, Atabiev, BC, Batieva, E, Alvarez Calmet, M, Llamas, B, Schultz, M, Krauss, R, Jimenez-Echevarria, J, Francken, M, Shnaider, S, de Knijff, P, Altena, E, Van de Vijver, K, Fehren-Schmitz, L, Tung, TA, Losch, S, Dobrovolskaya, M, Makarov, N, Read, C, Van Twest, M, Sagona, C, Ramsl, PC, Akar, M, Yener, KA, Carmona Ballestero, E, Cucca, F, Mazzarello, V, Utrilla, P, Rademaker, K, Fernandez-Dominguez, E, Baird, D, Semal, P, Marquez-Morfin, L, Roksandic, M, Steiner, H, Carlos Salazar-Garcia, D, Shishlina, N, Erdal, YS, Hallgren, F, Boyadzhiev, Y, Boyadzhiev, K, Kuessner, M, Sayer, D, Onkamo, P, Skeates, R, Rojo-Guerra, M, Buzhilova, A, Khussainova, E, Djansugurova, LB, Beisenov, AZ, Samashev, Z, Massy, K, Mannino, M, Moiseyev, V, Mannermaa, K, Balanovsky, O, Deguilloux, M-F, Reinhold, S, Hansen, S, Kitov, EP, Dobes, M, Ernee, M, Meller, H, Alt, KW, Prufer, K, Warinner, C, Schiffels, S, Stockhammer, PW, Bos, K, Posth, C, Herbig, A, Haak, W, Krause, J, and Kuehnert, D

Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

Published
2021

24. Ten millennia of hepatitis B virus evolution

Author

Ingman, Tara, Kocher, A.; Papac, L.; Barquera, R.; Key, FM.; Spyrou, MA.; Hubler, R.; Rohrlach, AB.; Aron, F.; Stahl, R.; Wissgott, A.; van Bommel, F.; Pfefferkorn, M.; Mittnik, A.; Villalba-Mouco, V.; Neumann, GU.; Rivollat, M.; van de Loosdrecht, MS.; Majander, K.; Tukhbatova, RI.; Musralina, L.; Ghalichi, A.; Penske, S.; Sabin, S.; Michel, M.; Gretzinger, J.; Nelson, EA.; Ferraz, T.; Nagele, K.; Parker, C.; Keller, M.; Guevara, EK.; Feldman, M.; Eisenmann, S.; Skourtanioti, E.; Giffin, K.; Gnecchi-Ruscone, GA.; Friederich, S.; Schimmenti, V.; Khartanovich, V.; Karapetian, MK.; Chaplygin, MS.; Kufterin, VV.; Khokhlov, AA.; Chizhevsky, AA.; Stashenkov, DA.; Kochkina, AF.; Tejedor-Rodriguez, C.; de Lagran, IGM.; Arcusa-Magallon, H.; Garrido-Pena, R.; Royo-Guillen, JI.; Novacek, J.; Rottier, S.; Kacki, S.; Saintot, S.; Kaverzneva, E.; Belinskiy, AB.; Veleminsky, P.; Limbursky, P.; Kostka, M.; Loe, L.; Popescu, E.; Clarke, R.; Lyons, A.; Mortimer, R.; Sajantila, A.; de Armas, YC.; Godoy, STH.; Hernandez-Zaragoza, DI.; Pearson, J.; Binder, D.; Lefranc, P.; Kantorovich, AR.; Maslov, VE.; Lai, L.; Zoledziewska, M.; Beckett, JF.; Langova, M.; Atienzar, GG.; Ibanez, MPD; Romero, A.; Sperduti, A.; Beckett, S.; Salter, SJ.; Zilivinskaya, ED.; Vasil, DV.; von Heyking, K.; Burger, RL.; Salazar, LC.; Amkreutz, L.; Navruzbekov, M.; Rosenstock, E.; Alonso-Fernandez, C.; Slavchev, V.; Kalmykov, AA.; Atabiev, BC.; Batieva, E; Calmet, MA.; Llamas, B.; Schultz, M.; Krauss, R.; Jimenez-Echevarria, J.; Francken, M.; Shnaider, S.; de Knijff, P.; Altena, E.; Van de Vijver, K.; Fehren-Schmitz, L.; Tung, TA.; Losch, S.; Dobrovolskaya, M.; Makarov, N.; Read, C.; Van Twest, M.; Sagona, C.; Ramsl, PC.; Akar, M.; Yener, KA.; Ballestero, EC.; Cucca, F.; Mazzarello, V.; Utrilla, P.; Rademaker, K.; Fernandez-Dominguez, E.; Baird, D.; Semal, P.; Marquez-Morfin, L; Roksandic, M.; Steiner, H.; Salazar-Garcia, DC.; Shishlina, N. Erdal, YS.; Hallgren, F.; Boyadzhiev, Y.; Boyadzhiev, K.; Kussner, M.; Sayer, D.; Onka, Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED), Ingman, Tara, Kocher, A.; Papac, L.; Barquera, R.; Key, FM.; Spyrou, MA.; Hubler, R.; Rohrlach, AB.; Aron, F.; Stahl, R.; Wissgott, A.; van Bommel, F.; Pfefferkorn, M.; Mittnik, A.; Villalba-Mouco, V.; Neumann, GU.; Rivollat, M.; van de Loosdrecht, MS.; Majander, K.; Tukhbatova, RI.; Musralina, L.; Ghalichi, A.; Penske, S.; Sabin, S.; Michel, M.; Gretzinger, J.; Nelson, EA.; Ferraz, T.; Nagele, K.; Parker, C.; Keller, M.; Guevara, EK.; Feldman, M.; Eisenmann, S.; Skourtanioti, E.; Giffin, K.; Gnecchi-Ruscone, GA.; Friederich, S.; Schimmenti, V.; Khartanovich, V.; Karapetian, MK.; Chaplygin, MS.; Kufterin, VV.; Khokhlov, AA.; Chizhevsky, AA.; Stashenkov, DA.; Kochkina, AF.; Tejedor-Rodriguez, C.; de Lagran, IGM.; Arcusa-Magallon, H.; Garrido-Pena, R.; Royo-Guillen, JI.; Novacek, J.; Rottier, S.; Kacki, S.; Saintot, S.; Kaverzneva, E.; Belinskiy, AB.; Veleminsky, P.; Limbursky, P.; Kostka, M.; Loe, L.; Popescu, E.; Clarke, R.; Lyons, A.; Mortimer, R.; Sajantila, A.; de Armas, YC.; Godoy, STH.; Hernandez-Zaragoza, DI.; Pearson, J.; Binder, D.; Lefranc, P.; Kantorovich, AR.; Maslov, VE.; Lai, L.; Zoledziewska, M.; Beckett, JF.; Langova, M.; Atienzar, GG.; Ibanez, MPD; Romero, A.; Sperduti, A.; Beckett, S.; Salter, SJ.; Zilivinskaya, ED.; Vasil, DV.; von Heyking, K.; Burger, RL.; Salazar, LC.; Amkreutz, L.; Navruzbekov, M.; Rosenstock, E.; Alonso-Fernandez, C.; Slavchev, V.; Kalmykov, AA.; Atabiev, BC.; Batieva, E; Calmet, MA.; Llamas, B.; Schultz, M.; Krauss, R.; Jimenez-Echevarria, J.; Francken, M.; Shnaider, S.; de Knijff, P.; Altena, E.; Van de Vijver, K.; Fehren-Schmitz, L.; Tung, TA.; Losch, S.; Dobrovolskaya, M.; Makarov, N.; Read, C.; Van Twest, M.; Sagona, C.; Ramsl, PC.; Akar, M.; Yener, KA.; Ballestero, EC.; Cucca, F.; Mazzarello, V.; Utrilla, P.; Rademaker, K.; Fernandez-Dominguez, E.; Baird, D.; Semal, P.; Marquez-Morfin, L; Roksandic, M.; Steiner, H.; Salazar-Garcia, DC.; Shishlina, N. Erdal, YS.; Hallgren, F.; Boyadzhiev, Y.; Boyadzhiev, K.; Kussner, M.; Sayer, D.; Onka, and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)

Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., European Union (EU); Horizon 2020; European Research Council (ERC); Research and Innovation Program; PALEoRIDER; CoDisEASe; ARCHCAUCASUS; Seventh Framework Programme; Marie Curie Actions; Programme SASPRO; ERA.NET RUS Plus-S&T Programme; Institute of Archaeology of the Czech Academy of Sciences; Russian Foundation for Basic Research; German Research Foundation; French National Research Agency; Wenner-Gren Dissertation Fieldwork Grant; Ministry of Education and Science of the Republic of Kazakhstan; Max Planck Society; Slovak Academy of Sciences; Werner Siemens Stiftung; Paleobiochemistry; Award Praemium Academiae of the Czech Academy of Sciences

Published
2021

25. Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

Author

Arindrarto, W, Borràs, DM, de Groen, RA, van den Berg, RR, Locher, IJ, van Diessen, SAME, Holst, R, van der Meijden, ED, Honders, M W, de Leeuw, RH, Verlaat, W, Jedema, I, Kroes, WGM, Knijnenburg, J, van Wezel, T, Vermaat, JS, Valk, Peter, Janssen, B, de Knijff, P, van Bergen, C A M, van den Akker, EB, 't Hoen, PAC, Kie?basa, SM, Laros, JFJ, Griffioen, M, Veelken, H, Arindrarto, W, Borràs, DM, de Groen, RA, van den Berg, RR, Locher, IJ, van Diessen, SAME, Holst, R, van der Meijden, ED, Honders, M W, de Leeuw, RH, Verlaat, W, Jedema, I, Kroes, WGM, Knijnenburg, J, van Wezel, T, Vermaat, JS, Valk, Peter, Janssen, B, de Knijff, P, van Bergen, C A M, van den Akker, EB, 't Hoen, PAC, Kie?basa, SM, Laros, JFJ, Griffioen, M, and Veelken, H

Abstract

Acute myeloid leukemia (AML) is caused by genetic aberrations that also govern the prognosis of patients and guide risk-adapted and targeted therapy. Genetic aberrations in AML are structurally diverse and currently detected by different diagnostic assays. This study sought to establish whole transcriptome RNA sequencing as single, comprehensive, and flexible platform for AML diagnostics. We developed HAMLET (Human AML Expedited Transcriptomics) as bioinformatics pipeline for simultaneous detection of fusion genes, small variants, tandem duplications, and gene expression with all information assembled in an annotated, user-friendly output file. Whole transcriptome RNA sequencing was performed on 100 AML cases and HAMLET results were validated by reference assays and targeted resequencing. The data showed that HAMLET accurately detected all fusion genes and overexpression of EVI1 irrespective of 3q26 aberrations. In addition, small variants in 13 genes that are often mutated in AML were called with 99.2% sensitivity and 100% specificity, and tandem duplications in FLT3 and KMT2A were detected by a novel algorithm based on soft-clipped reads with 100% sensitivity and 97.1% specificity. In conclusion, HAMLET has the potential to provide accurate comprehensive diagnostic information relevant for AML classification, risk assessment and targeted therapy on a single technology platform.

Published
2021

29. Mosaic segmental uniparental isodisomy and progressive clonal selection: a common mechanism of late onset β-thalassemia major

Author

Cornelis L. Harteveld, Chiara Refaldi, Antonino Giambona, Claudia A. L. Ruivenkamp, Mariëtte J. V. Hoffer, Jeroen Pijpe, Peter De Knijff, Caterina Borgna-Pignatti, Aurelio Maggio, Maria D. Cappellini, and Piero C. Giordano

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Genomic DNA of 3 patients, born as healthy carriers and developing a late-onset severe transfusion-dependent beta-thalassemia major was studied by high-density genome wide SNP array analysis. A mosaic loss of heterozygosity for almost the entire 11p was found, not attributable to deletions but involving mosaicism for segmental paternal isodisomy of 11p. Mitotic recombination leading to mosaic segmental uniparental isodisomy on chromosome 11p in multiple tissues has been described as a molecular disease mechanism for a subset of sporadic Beckwith-Wiedemann syndrome cases. A similar mechanism also seems to be involved in causing late-onset disease in carriers of recessive mutations in other genes located in 11p, such as late-onset beta-thalassemia major and sickle cell disease. We suggest that the loss of maternally imprinted IGF-2 and H19 genes may account for the selective advantage of hematopoietic cells containing this segmental paternal isodisomy of 11p carrying the β-thalassemia mutation.

Published
2013
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30. Mitochondrial Transport from Mesenchymal Stromal Cells to Chondrocytes Increases DNA Content and Proteoglycan Deposition In Vitroin 3D Cultures

Author

Korpershoek, Jasmijn V., Rikkers, Margot, Wallis, Fleur S. A., Dijkstra, Koen, te Raa, Marije, de Knijff, Peter, Saris, Daniel B. F., and Vonk, Lucienne A.

Abstract

Objective Allogeneic mesenchymal stromal cells (MSCs) are used in the 1-stage treatment of articular cartilage defects. The aim of this study is to investigate whether transport of mitochondria exists between chondrocytes and MSCs and to investigate whether the transfer of mitochondria to chondrocytes contributes to the mechanism of action of MSCs.Design Chondrocytes and MSCs were stained with MitoTracker, and CellTrace was used to distinguish between cell types. The uptake of fluorescent mitochondria was measured in cocultures using flow cytometry. Transport was visualized using fluorescence microscopy. Microvesicles were isolated and the presence of mitochondria was assessed. Mitochondria were isolated from MSCs and transferred to chondrocytes using MitoCeption. Pellets of chondrocytes, chondrocytes with transferred MSC mitochondria, and cocultures were cultured for 28 days. DNA content and proteoglycan content were measured. Mitochondrial DNA of cultured pellets and of repair cartilage tissue was quantified.Results Mitochondrial transfer occurred bidirectionally within the first 4 hours until 16 hours of coculture. Transport took place via tunneling nanotubes, direct cell-cell contact, and extracellular vesicles. After 28 days of pellet culture, DNA content and proteoglycan deposition were higher in chondrocyte pellets to which MSC mitochondria were transferred than the control groups. No donor mitochondrial DNA was traceable in the biopsies, whereas an increase in MSC mitochondrial DNA was seen in the pellets.Conclusions These results suggest that mitochondrial transport plays a role in the chondroinductive effect of MSCs on chondrocytes in vitro.However, in vivono transferred mitochondria could be traced back after 1 year.

Published
2022
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31. Efficacy and quality of life after 6–9 years of deep brain stimulation for depression.

Author

Bergfeld, Isidoor O., Ooms, Pieter, Lok, Anja, de Rue, Lara, Vissers, Pieter, de Knijff, Dirk, Horst, Ferdinand, Beute, Guus, van den Munckhof, Pepijn, Schuurman, P. Richard, and Denys, Damiaan

Abstract

Given the invasiveness of deep brain stimulation (DBS), the effect should prove to be stable over the long-term and translate into an improvement of quality of life (QOL). To study the effectiveness and QOL up to nine years after the DBS surgery. We treated 25 adult patients with major depression with DBS of the ventral anterior limb of the internal capsule (vALIC). We followed them up naturalistically for 6–9 years after surgery (mean: 7.7 [SD:1.5] years), including a randomized crossover phase after the first year comparing sham with active DBS. Symptom severity was quantified using the Hamilton Depression Scale with response defined as a ≥50% decrease of the score compared to baseline. Quality of life was measured using the WHOQOL-BREF, assessing 5 domains (general, physical, psychological, social, environmental). Intention-to-treat response rates remained mostly stable from Year 3 to last follow-up (Year 3, 5 and 6: 40%; Year 4: 36%; Last observation: 44%). General, physical, psychological (all P < 0.001) and the environmental (P = 0.02) domain scores increased during DBS optimization and remained stable over the long term. No statistically significant changes were detected on the social domain. Patients scored significantly higher during active than sham DBS on the psychological, social and environmental domains, and trended towards a higher score on the general and physical domains. This study shows continued efficacy of vALIC DBS in depression, which translates into an improvement of QOL providing further support for DBS as a durable treatment for TRD. • Response to deep brain stimulation is maintained over 7.7 years on average. • Quality of life improves over the first year and remains stably improved. • Turning off DBS results in a reduction of quality of life. • These results supports DBS as a durable treatment for depression. [ABSTRACT FROM AUTHOR]

Published
2022
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32. The Dutch Y-chromosomal landscape

Author

Altena, E, Smeding, R, van der Gaag, KJ, Larmuseau, MHD, Decorte, R, Lao Grueso, Oscar, Kayser, Manfred, Kraaijenbrink, T, de Knijff, P, Altena, E, Smeding, R, van der Gaag, KJ, Larmuseau, MHD, Decorte, R, Lao Grueso, Oscar, Kayser, Manfred, Kraaijenbrink, T, and de Knijff, P

Published
2020

36. Abstracts

Author

Kaatsch, Hans-Jürgen, Püschel, K., Heinemann, A., Klaas, Jakob, Graß, Hildegard, Staak, Michael, Benthaus, S., Vock, R., Brinkmann, B., Temme, O., Daldrup, T., Dilger, M., Fink, T., Rittner, Ch., Thali, Michael J., Braun, M., Brueschweiler, W., Kneubuehl, B. P., Vock, P., Wirth, J., Dirnhofer, R., Bohnert, M., Berger, H., Buck, U., Pollak, S., Gotta, J. C., Erdmann, F., Riße, M., Schütz, H., Weiler, G., Pragst, F., Auwärter, V., Sporkcrt, F., Roewer, L., Willuweit, S., Kayser, M., Nagy, M., de Knijff, P., Geserick, G., Augustin, C., Betz, A., Carracedo, A., Corach, D., Dupuy, B. M., Gusmaõ, L., Henke, L., Hidding, M., Kärgel, H. J., Lessig, R., Liebeherr, E., Parson, W., Pascali, V. L., Rolf, B., Schneider, P. M., Dobosz, T., Teifel-Greding, J., Krawczak, M., Bauer, M., Patzelt, D., Kuznik, J., Bondy, B., Eisenmenger, W., Möller, H. -J., Zehner, R., Niess, C., Amendt, J., Krettek, R., Weinmann, W., Görner, M., Goerke, R., Mahler, H., Fowinkel, C., Haarhoff, K., Schmidt, P., Schmolke, C., Mußhoff, F., Menzen, M., Prohaska, C., Madea, B., Kauert, G., Gleicher, S., Drasch, G., von Meyer, L., Roider, G., Quitterer, D., Kröner, L., Toennes, S. W., Jurowich, S., Käferstein, H., Sticht, G., Gilg, T., Priemer, F., Jocham, N., Fechner, G., Ortmann, Ch., Schulte, T., Nieschalk, M., Weirich, V., Rummel, J., Rentsch, D., Wegener, R., Berehaus, G., Graß, H., Grellner, W., Rettig-Stürmer, A., Kühn-Becker, H., Georg, T., Möller, M., Wilske, J., Kemmerling, R., Sachs, H., Menting, T., Musshoff, F., Schoenemeier, S., Bürrig, K. -F., Jacob, B., Bonte, W., Maeda, H., Zhu, B. -L., Fujita, M. Q., Quan, L., Ishida, K., Taniguchi, M., Böhme, B., Rauch, E., Penning, R., Amberg, R., Blackwell, C. C., Pelz, K., Meier, V., Saternus, K. -S., Gessler, F., Böhnel, H., Bouska, I., Toupalík, P., Klir, P., Kleemann, W. J., Ast, F., Beck, U., Debertin, S., Giebe, B., Heide, S., Sperhake, J., Poets, C. F., Weis, C., Schlaud, M., Bajanowski, T., Wedekind, H., Breithardt, G., Debertin, A. S., Tönjes, H., Tschernig, T., Pabst, R., Tröger, H. D., Krill, A., Hame, M., Bouška, I., Ježková, J., Kernbach-Wighton, G., Wense, A. v. d., Kijewski, H., Goeke, M., Weber, B., Staak, M., Dettmeyer, R., Driever, F., Becker, A., Wiestler, O. D., Verhoff, M. A., Woenckhaus, J., Hauri-Bionda, R., Strehler, M., Bär, W., Ohshima, T., Takayasu, T., Kondo, T., Sato, Y., Tarbah, Fuad A., Mahler, Hellmut, Temme, Oliver, Daldrup, Thomas, Pötsch, Lucia, Emmerich, Patricia, Skopp, Gisela, Andresen, H., Schmoldt, A., Thurau, K., Vogt, S., Große-Perdekamp, M., Pufal, E., Sykutera, M., Rochholz, G., Lis, G., Sliwka, K., Zörntlein, S., Röhrich, J., Pötsch, L., Becker, J., Mattern, Rainer, Yamamoto, Yoshiko, Hayase, Tamaki, Yamamoto, Keiichi, Piette, Michel H. A., De Letter, Els A., Cordonnier, Jan, Schultes, A., Pluisch, F., Darok, M., Kollroser, M., Mannweiler, S., Babel, B., Magerl, H., Mahfoud, B., Stein, S., Iwersen-Bergmann, S., Risser, D., Hönigschnabl, S., Stichenwirth, M., Sebald, D., Kaff, A., Schneider, B., Vycudilik, W., Bauer, G., Reitz, E., Kimont, H. -G., Molnár, A., Jeszenszky, E., Benkó, A., Száz, E., Varga, T., Mayr, N. P., Schmidbauer, S., Hallfeldt, K., Bank, A., Iffland, R., Schuff, A., Fischer, T., Weingarten, Y., Alt, A., Janda, I., Wurst, F. M., Seidl, S., Seitler, C., Haag-Dawoud, Munira, Beike, J., Vennemann, B., Köhler, H., Hendreich, F. -I., Giebe, W., Reimann, I., Werner, R., Klein, A., Schulz, K., Feischer, D., Erfurt, Ch., Arnold, R., Winnefeld, K., Riepert, T., Iffland, R., Longauer, F., Kardošovå, V., Anders, S., Hildebrand, E., Schulz, F., Möbus, U., Jaroß, W., Wittig, H., Schmidt, U., Hauptmann, K., Krause, D., Prudlow, B., Rohner, T., Molz, G., Früchtnicht, W., Hoppe, B., Henßge, C., Althaus, L., Herbst, J., Preiß, U., Stein, C., Glenewinkel, F., Leinzinger, E. P., Lászik, A., Soós, M., Hubay, M., Sótonyi, P., Schliff, A., Gatternig, R., Hering, S., Edelmann, J., Plate, I., Michael, M., Kuhlisch, E., Szibor, R., von Wurmb, N., Hammer, U., Meissner, D., Kirches, E., Dietzmann, K., Pfeiffer, H., Ortmann, C., Meißner, C., Mohamed, S. A., Warnk, H., Gehlsen-Lorenzen, A., Oehmichen, M., Heidorn, F., Henkel, R., Schulz, M. M., Reichert, W., Mattern, R., Baasner, A., Banaschak, S., Schäfer, C., Benecke, M., Reibe, S., Barksdale, Larry, Sundermeier, Jon, Ratcliffe, Brett C., Lutz, S., Hohoff, C., Schürenkamp, M., Kahle, C., Fieguth, A., Ritz-Timme, S., Laumeier, I., Schütz, H. W., Schulte-Mönting, J., Chaudri, S., Welti, M., Dittmann, V., Olze, A., Schmeling, A., Reisinger, W., Klotzbach, H., Gabriel, P., Demir, T., Huckenbeck, W., Reuhl, J., Schuster, R., Maxeiner, H., Bockholdt, B., Jachau, K., Kuchheuser, W., Försterling, T., Ehrlich, E., Besselmann, M., Du Chesne, A., Albrecht, U. -V., Guan, D. W., Dreßler, J., Voigtmann, K., Müller, E., Vieler, S., Kirchner, A., Humpert, M., Breitmeier, D., Mansouri, F., Wyler, D., Marty, W., Sigrist, Th., Zollinger, U., Meyer, U., Allmen, G. v., Karger, B., Hoekstra, A., Stehmann, B., Schmidt, P. F., Peschel, O., Vollmar, C., Szeimies, U., Rothschild, M. A., Kegel, D., Klatt, A., Klatt, C., Briese, B. -H., Schyma, C., Schyma, P., Angetter, Daniela, Perdekamp, M. Große, Sun, Y., Guttenberge, R., Riede, U. -N., Poetsch, M., Seefeldt, S., Maschke, M., Lignitz, E., Zeller, M., Wehner, H. -D., Czarnetzki, A., Blin, N., Bender, K., Emmerich, P., Pádár, Zs., Egyed, B., Kemény, G., Woller, J., Füredi, S., Balogh, I., Cremer, U., Scheil, H. -G., Schiwy-Bochat, K. -H., Althoff, H., Immel, U. -D., Tatschner, Th., Lang, C., Versmold, D., Reineke, Th., Mall, G., Dahlmann, F., Büttner, A., Hubig, M., Rötzscher, K., Grundmann, C., Oritani, S., Peter, J., Popov, V., Olejnik, V., Khokhlov, V. D., Stiller, D., Romanowski, U., Kleiber, M., Klupp, N., Mortinger, H., Chadová, L., Bouška, I., Toupalik, P., Schnabel, A., Lutz, F. -U., Crivellaro, A., Strauch, H., Dan, Dermengiu, Silvia, Dermengiu, Buda, Octavian, Kandolf, R., Kaiser, R., Eis-Hübinger, A. M., Kobek, M., Jankowski, Z., Rygol, K., Kulikowska, J., Martin, H., Kolbow, K., Keil, W., Wang, Huijun, Ding, Yanqing, Huang, Guangzhao, Wu, Zhongbi, Wehner, F., Subke, J., Zdravkovic, M., Otasevic, V., Rostov, M., Karadzic, R., Kildüschov, E. M., Buromski, I. W., Plaksin, W. O., Wendland, A., Spiridonow, W. A., Sabusow, J. G., Kalinin, J. P., Heide, S., Schmidt, V., Wiegand, P., Kleiber, M., Demmler, G., Zack, F., Reischle, S., Schönpflug, M., Beier, G., Berchtenbreiter, C., Lackner, K., Jendrusch, B., Wolf, H., Buhmann, D., Summa, H., Matschke, J., Stürenburg, H. J., Junge, M., Wischhusen, F., Müldner, C., Schröder, A., Kaiser, E., Lasczkowski, G., Hofbauer, V., Eberl, N., Thomson, H., Tatschner, T., Milz, S., Gazov, E., Trübner, K., Brenner, M., Tsokos, M., Anders, S., Paulsen, F., Reith, K., Bratzke, H., Schapfeld, R., Graefe-Kirci, U., Stiller, D., Trübner, K., and Schäfer, A. Th.

Published
2000
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39. Chromosome Y microsatellites: population genetic and evolutionary aspects

Author

de Knijff, P., Kayser, M., Caglià, A., Corach, D., Fretwell, N., Gehrig, C., Graziosi, G., Heidorn, F., Herrmann, S., Herzog, B., Hidding, M., Honda, K., Jobling, M., Krawczak, M., Leim, K., Meuser, S., Meyer, E., Oesterreich, W., Pandya, A., Parson, W., Penacino, G., Perez-Lezaun, A., Piccinini, A., Prinz, M., Schmitt, C., Schneider, P. M., Szibor, R., Teifel-Greding, J., Weichhold, G., and Roewer, L.

Published
1997
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40. Evaluation of Y-chromosomal STRs: a multicenter study

Author

Kayser, M., Caglià, A., Corach, D., Fretwell, N., Gehrig, C., Graziosi, G., Heidorn, F., Herrmann, S., Herzog, B., Hidding, M., Honda, K., Jobling, M., Krawczak, M., Leim, K., Meuser, S., Meyer, E., Oesterreich, W., Pandya, A., Parson, W., Penacino, G., Perez-Lezaun, A., Piccinini, A., Prinz, M., Schmitt, C., Schneider, P. M., Szibor, R., Teifel-Greding, J., Weichhold, G., de Knijff, P., and Roewer, L.

Published
1997
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43. (Oostelijke) resedawitjes in Nederland

Author

Fokker, C., Vossen, P., de Knijff, P., Wiemers, Martin, van Swaay, C., Fokker, C., Vossen, P., de Knijff, P., Wiemers, Martin, and van Swaay, C.

Abstract

In de zomer van 2018 doken resedawitjes op in Nederland. Maar welke soort was het nu, het ‘gewone’ of het oostelijk resedawitje?

Published
2019

44. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

Author

Roewer, L., Krawczak, Michael, Willuweit, S., Nagy, M., Alves, Cintia, Amorim, Antonio, Anslinger, K., Augustin, C., Betz, Andrea, Bosch, Elena, Caglia, Alessandra, Carracedo, Angel, Corach, D., Dekairelle, A.-F., Dobosz, T., Dupuy, Berit Myhre, Furedi, S., Gehrig, C., Gusmao, Leonor, Henke, Jurgen, Henke, Lotte, Hidding, M., Hohoff, Carsten, Hoste, Bernadette, Jobling, Mark A., Kargel, H.J., de Knijff, P., Lessig, Rudiger, Liebeherr, E., Lorente, M., Martinez-Jarreta, B., Nievas, P., Nowak, M., Parson, Walther, Pascali, V.L., Penacino, G., Ploski, R., Rolf, B., Sala, A., Schmidt, U., Schmitt, C., Schneider, Peter M., Szibor, Reinhard, Teifel-Greding, J., and Kayser, M.

Subjects
Forensic genetics -- Conferences, meetings and seminars, Y chromosome -- Analysis, Haplotypes -- Analysis
Published
2001

46. A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males.

Author

Roewer, L., Kayser, M., de Knijff, P., Anslinger, K., Betz, Andrea, Caglia, Alessandra, Corach, D., Furedi, S., Henke, Lotte, Hidding, M., Kargel, H.J., Lessig, Rudiger, Nagy, M., Pascali, V.L., Parson, Walther, Rolf, B., Schmitt, C., Szibor, Reinhard, Teifel-Greding, J., and Krawczak, Michael

Subjects
Forensic genetics -- Methods, DNA testing -- Analysis, Y chromosome -- Analysis, Europeans -- Genetic aspects, Men -- Genetic aspects
Published
2000

47. The Thomas Jefferson paternity case

Author

Foster, E. A., Jobling, M. A., Taylor, P. G., Donnelly, P., de Knijff, P., Mieremet, R., Zerjal, T., and Tyler-Smith, C.

Published
1999

48. PF262 COMPREHENSIVE DIAGNOSTICS OF ACUTE MYELOID LEUKEMIA BY WHOLE TRANSCRIPTOME RNA SEQUENCING

Author

Griffioen, M., primary, Arindrarto, W., additional, Borràs, D.M., additional, Locher, I.J., additional, van Diessen, S.A., additional, van der Holst, R., additional, van der Meijden, E.D., additional, Honders, M.W., additional, de Leeuw, R.H., additional, Jedema, I., additional, Kroes, W.G., additional, Knijnenburg, J., additional, Vermaat, J.S., additional, Valk, P.J., additional, Janssen, B., additional, de Knijff, P., additional, van Bergen, C.A., additional, van den Akker, E.B., additional, ’t Hoen, P.A., additional, Kiełbasa, S.M., additional, Laros, J.F., additional, and Veelken, H., additional

Published
2019
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49. Jefferson fathered slave's last child

Author

Foster, Eugene A., Jobling, M. A., Taylor, P. G., Donnelly, P., de Knijff, P., Mieremet, Rene, Zerjal, T., and Tyler-Smith, C.

Published
1998

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