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1. CGHPRO – A comprehensive data analysis tool for array CGH

Author

Lenzner Steffen, Ropers H-Hilger, Erdogan Fikret, Chen Wei, and Ullmann Reinhard

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. Results We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the identification of odd clones. Conclusion CGHPRO is a comprehensive and easy-to-use data analysis tool for array CGH. Since all of its features are available offline, CGHPRO may be especially suitable in situations where protection of sensitive patient data is an issue. It is distributed under GNU GPL licence and runs on Linux and Windows.

Published
2005
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2. BRCA1-mediated repression of select X chromosome genes

Author

Ropers H Hilger, Liu Edison T, Nuber Ulrike A, Sotiriou Christos, Aprelikova Olga, Chandramouli Gadisetti VR, Jazaeri Amir A, Yee Cindy J, Boyd Jeff, and Barrett J Carl

Subjects
Medicine
Abstract

Abstract Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary DNA microarrays were used to compare the expression levels of X chromosome genes in 18 BRCA1-associated ovarian cancers to those of the 13 "BRCA1-like" and 14 "BRCA2-like" sporadic tumors (as defined by previously reported expression profiling). Significance was determined using parametric statistics with P < 0.005 as a cutoff. Forty of 178 total X-chromosome transcripts were differentially expressed between the BRCA1-associated tumors and sporadic cancers with a BRCA2-like molecular profile. Thirty of these 40 genes showed higher mean expression in the BRCA1-associated samples including all 11 transcripts that mapped to Xp11. In contrast, four of 178 total X chromosome transcripts showed significant differential expression between BRCA1-associated and sporadic tumors with a BRCA1-like molecular profile. All four mapped to Xp11 and showed higher mean expression in BRCA1-associated tumors. Re-expression of BRCA1 in HCC1937 BRCA1-deficient breast cancer cell resulted in the repression of 21 transcripts. Eleven of the 21 (54.5%) transcripts mapped to Xp11. However, there was no significant overlap between these Xp11 genes and those found to be differentially expressed between BRCA1-associated and sporadic ovarian cancer samples. These results demonstrate that BRCA1 mediates the repression of several X chromosome genes, many of which map to the Xp11 locus.

Published
2004
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3. Comparative study of methyl-CpG-binding domain proteins

Author

Ropers H Hilger, Roloff Tim C, and Nuber Ulrike A

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

Abstract Background Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD) can bind to single methylated CpGs and most of them are involved in transcription control. So far, five vertebrate MBD proteins have been described as MBD family members: MBD1, MBD2, MBD3, MBD4 and MECP2. Results We performed database searches for new proteins containing an MBD and identified six amino acid sequences which are different from the previously described ones. Here we present a comparison of their MBD sequences, additional protein motifs and the expression of the encoding genes. A calculated unrooted dendrogram indicates the existence of at least four different groups of MBDs within these proteins. Two of these polypeptides, KIAA1461 and KIAA1887, were only present as predicted amino acid sequences based on a partial human cDNA. We investigated their expression by Northern blot analysis and found transcripts of ~8 kb and ~5 kb respectively, in all eight normal tissues studied. Conclusions Eleven polypeptides with a MBD could be identified in mouse and man. The analysis of protein domains suggests a role in transcriptional regulation for most of them. The knowledge of additional existing MBD proteins and their expression pattern is important in the context of Rett syndrome.

Published
2003
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4. Rare diseases: human genome research is coming home

Author

Ropers, H. and van Karnebeek, C.

Abstract

After a long and largely disappointing detour, Genome Research has reidentified Rare Diseases as a major opportunity for improving health care and a clue to understanding gene and genome function. In this Special Issue of CSH Molecular Case Studies on Rare Diseases, several invited Perspectives, numerous Case Reports, and this Editorial itself address recent breakthroughs as well as unsolved problems in this wide field. These range from exciting prospects for gap-free diagnostic whole-genome sequencing to persisting problems related to identifying and distinguishing pathogenic and benign variants; and from the good news that soon, the United Kingdom will no longer be the only country to have introduced whole-genome sequencing into health care to the sobering conclusion that in many countries the clinical infrastructure for bringing Genome Medicine to the patient is still lacking. With less than 5000 genes firmly implicated in disease, the identification of at least twice as many disease genes is a major challenge, and the elucidation of their function is an even larger task. But given the renewed interest in rare diseases, their importance for health care, and the vast and growing spectrum of concepts and methods for studying them, the future of Human Genome Research is bright.

Published
2022

5. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

Author

Hu, H, Haas, S A, Chelly, J, Van Esch, H, Raynaud, M, de Brouwer, A PM, Weinert, S, Froyen, G, Frints, S GM, Laumonnier, F, Zemojtel, T, Love, M I, Richard, H, Emde, A-K, Bienek, M, Jensen, C, Hambrock, M, Fischer, U, Langnick, C, Feldkamp, M, Wissink-Lindhout, W, Lebrun, N, Castelnau, L, Rucci, J, Montjean, R, Dorseuil, O, Billuart, P, Stuhlmann, T, Shaw, M, Corbett, M A, Gardner, A, Willis-Owen, S, Tan, C, Friend, K L, Belet, S, van Roozendaal, K EP, Jimenez-Pocquet, M, Moizard, M-P, Ronce, N, Sun, R, OʼKeeffe, S, Chenna, R, van Bömmel, A, Göke, J, Hackett, A, Field, M, Christie, L, Boyle, J, Haan, E, Nelson, J, Turner, G, Baynam, G, Gillessen-Kaesbach, G, Müller, U, Steinberger, D, Budny, B, Badura-Stronka, M, Latos-Bieleńska, A, Ousager, L B, Wieacker, P, Criado, G Rodríguez, Bondeson, M-L, Annerén, G, Dufke, A, Cohen, M, Van Maldergem, L, Vincent-Delorme, C, Echenne, B, Simon-Bouy, B, Kleefstra, T, Willemsen, M, Fryns, J-P, Devriendt, K, Ullmann, R, Vingron, M, Wrogemann, K, Wienker, T F, Tzschach, A, van Bokhoven, H, Gecz, J, Jentsch, T J, Chen, W, Ropers, H-H, and Kalscheuer, V M

Published
2016
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6. Genome-wide copy number variation analysis in attention-deficit/hyperactivity disorder: association with neuropeptide Y gene dosage in an extended pedigree

Author

Lesch, K-P, Selch, S, Renner, T J, Jacob, C, Nguyen, T T, Hahn, T, Romanos, M, Walitza, S, Shoichet, S, Dempfle, A, Heine, M, Boreatti-Hümmer, A, Romanos, J, Gross-Lesch, S, Zerlaut, H, Wultsch, T, Heinzel, S, Fassnacht, M, Fallgatter, A, Allolio, B, Schäfer, H, Warnke, A, Reif, A, Ropers, H-H, and Ullmann, R

Published
2011
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8. Identification of mutations in TRAPPC9, which encodes the NIK- and IKK-[beta]-binding protein, in nonsyndromic autosomal-recessive mental retardation

Author

Mir, Asif, Kaufman, Liana, Noor, Abdul, Motazacker, Mahdi M., Jamil, Talal, Azam, Matloob, Kahrizi, Kimia, Rafiq, Muhammad Arshad, Weksberg, Rosanna, Nasr, Tanveer, Naeem, Farooq, Tzschach, Andreas, Kuss, Andreas W., Ishak, Gisele E., Doherty, Dan, Ropers, H. Hilger, Barkovich, A. James, Najmabadi, Hossein, Ayub, Muhammad, and Vincent, John B.

Subjects
Binding proteins -- Research, Gene mutations -- Analysis, Magnetic resonance imaging -- Usage, Mental retardation -- Genetic aspects, Single nucleotide polymorphisms -- Analysis, Biological sciences
Abstract

The homozygosity mapping technique is employed to determine the different mutations in TRAPPC9, which lead to the onset of nonsyndromic autosomal-recessive mental retardation in humans. The observed gene is shown to lead to the encoding of NIK- and IKK-[beta]-binding proteins, hence causing the disorder.

Published
2009

9. Homozygosity mapping in consanguineous families reveals extreme heterogeneity of non-syndromic autosomal recessive mental retardation and identifies 8 novel gene loci

Author

Najmabadi, Hossein, Motazacker, Mohammad Mahdi, Garshasbi, Masoud, Kahrizi, Kimia, Tzschach, Andreas, Chen, Wei, Behjati, Farkhondeh, Hadavi, Valeh, Nieh, Sahar Esmaeeli, Abedini, Seyedeh Sedigheh, Vazifehmand, Reza, Firouzabadi, Saghar Ghasemi, Jamali, Payman, Falah, Masoumeh, Seifati, Seyed Morteza, Grüters, Annette, Lenzner, Steffen, Jensen, Lars R., Rüschendorf, Franz, Kuss, Andreas W., and Ropers, H. Hilger

Published
2007
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10. SNP array-based homozygosity mapping reveals MCPH1 deletion in family with autosomal recessive mental retardation and mild microcephaly

Author

Garshasbi, Masoud, Motazacker, Mohammad Mahdi, Kahrizi, Kimia, Behjati, Farkhondeh, Abedini, Seyedeh Sedigheh, Nieh, Sahar Esmaeeli, Firouzabadi, Saghar Ghasemi, Becker, Christian, Rüschendorf, Franz, Nürnberg, Peter, Tzschach, Andreas, Vazifehmand, Reza, Erdogan, Fikret, Ullmann, Reinhard, Lenzner, Steffen, Kuss, Andreas W., Ropers, H. Hilger, and Najmabadi, Hossein

Published
2006
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11. Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy

Author

Mefford, Heather C., Clauin, Severine, Sharp, Andrew J., Moller, Rikke S., Ullmann, Reinhard, Kapur, Raj, Pinkel, Dan, Cooper, Gregory M., Ventura, Mario, Ropers, H. Hilger, Tommerup, Niels, Eichler, Evan E., and Bellanne-Chantelot, Christine

Subjects
Diabetes -- Genetic aspects, Diabetes -- Research, Epilepsy -- Genetic aspects, Epilepsy -- Research, Kidney diseases -- Genetic aspects, Kidney diseases -- Research, Mutation (Biology) -- Research, Biological sciences
Abstract

The first example of a recurrent genomic disorder associated with diabetes identified from samples from patients with epilepsy is described.

Published
2007

12. A Novel SLC6A8 Mutation in a Large Family with X-Linked Intellectual Disability: Clinical and Proton Magnetic Resonance Spectroscopy Data of Both Hemizygous Males and Heterozygous Females

Author

Dreha-Kulaczewski, S., primary, Kalscheuer, V., additional, Tzschach, A., additional, Hu, H., additional, Helms, G., additional, Brockmann, K., additional, Weddige, A., additional, Dechent, P., additional, Schlüter, G., additional, Krätzner, R., additional, Ropers, H.-H., additional, Gärtner, J., additional, and Zirn, B., additional

Published
2013
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15. A clinical and molecular genetic study of 112 Iranian families with primary microcephaly

Author

Darvish, H, Esmaeeli-Nieh, S, Monajemi, G B, Mohseni, M, Ghasemi-Firouzabadi, S, Abedini, S S, Bahman, I, Jamali, P, Azimi, S, Mojahedi, F, Dehghan, A, Shafeghati, Y, Jankhah, A, Falah, M, Soltani Banavandi, M J, Ghani-Kakhi, M, Garshasbi, M, Rakhshani, F, Naghavi, A, Tzschach, A, Neitzel, H, Ropers, H H, Kuss, A W, Behjati, F, Kahrizi, K, and Najmabadi, H

Published
2010
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22. CNKSR1 gene defect can cause syndromic autosomal recessive intellectual disability

Author

Kazeminasab, S., Taskiran, I., Fattahi, Z., Bazazzadegan, N., Hosseini, M., Rahimi, M., Oladnabi, M., Haddadi, M., Celik, A., Ropers, H., Najmabadi, H., and Kahrizi, K.

Abstract

The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.

Published
2018

44. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

Author

Hu, H., Haas, S. A., Chelly, J., Van Esch, H., Raynaud, M., de Brouwer, A. P. M., Weinert, S., Froyen, G., Frints, S. G. M., Laumonnier, F., Zemojtel, T., Love, M. I., Richard, H., Emde, A-K, Bienek, M., Jensen, C., Hambrock, M., Fischer, U., Langnick, C., Feldkamp, M., Wissink-Lindhout, W., Lebrun, N., Castelnau, L., Rucci, J., Montjean, R., Dorseuil, O., Billuart, P., Stuhlmann, T., Shaw, M., Corbett, M. A., Gardner, A., Willis-Owen, S., Tan, C., Friend, K. L., Belet, S., van Roozendaal, K. E. P., Jimenez-Pocquet, M., Moizard, M-P, Ronce, N., Sun, R., O'Keeffe, S., Chenna, R., Van Boemmel, A., Goeke, J., Hackett, A., Field, M., Christie, L., Boyle, J., Haan, E., Nelson, J., Turner, G., Baynam, G., Gillessen-Kaesbach, G., Mueller, U., Steinberger, D., Budny, B., Badura-Stronka, M., Latos-Bielenska, A., Ousager, L. B., Wieacker, P., Criado, G. Rodriguez, Bondeson, Marie-Louise, Annerén, Göran, Dufke, A., Cohen, M., Van Maldergem, L., Vincent-Delorme, C., Echenne, B., Simon-Bouy, B., Kleefstra, T., Willemsen, M., Fryns, J-P, Devriendt, K., Ullmann, R., Vingron, M., Wrogemann, K., Wienker, T. F., Tzschach, A., van Bokhoven, H., Gecz, J., Jentsch, T. J., Chen, W., Ropers, H-H, Kalscheuer, V. M., Hu, H., Haas, S. A., Chelly, J., Van Esch, H., Raynaud, M., de Brouwer, A. P. M., Weinert, S., Froyen, G., Frints, S. G. M., Laumonnier, F., Zemojtel, T., Love, M. I., Richard, H., Emde, A-K, Bienek, M., Jensen, C., Hambrock, M., Fischer, U., Langnick, C., Feldkamp, M., Wissink-Lindhout, W., Lebrun, N., Castelnau, L., Rucci, J., Montjean, R., Dorseuil, O., Billuart, P., Stuhlmann, T., Shaw, M., Corbett, M. A., Gardner, A., Willis-Owen, S., Tan, C., Friend, K. L., Belet, S., van Roozendaal, K. E. P., Jimenez-Pocquet, M., Moizard, M-P, Ronce, N., Sun, R., O'Keeffe, S., Chenna, R., Van Boemmel, A., Goeke, J., Hackett, A., Field, M., Christie, L., Boyle, J., Haan, E., Nelson, J., Turner, G., Baynam, G., Gillessen-Kaesbach, G., Mueller, U., Steinberger, D., Budny, B., Badura-Stronka, M., Latos-Bielenska, A., Ousager, L. B., Wieacker, P., Criado, G. Rodriguez, Bondeson, Marie-Louise, Annerén, Göran, Dufke, A., Cohen, M., Van Maldergem, L., Vincent-Delorme, C., Echenne, B., Simon-Bouy, B., Kleefstra, T., Willemsen, M., Fryns, J-P, Devriendt, K., Ullmann, R., Vingron, M., Wrogemann, K., Wienker, T. F., Tzschach, A., van Bokhoven, H., Gecz, J., Jentsch, T. J., Chen, W., Ropers, H-H, and Kalscheuer, V. M.

Abstract

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.

Published
2016
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46. Mapping translocation breakpoints by next-generation sequencing

Author

Menzel, Corinna, Tzschach, Andreas, Kalcheuer, Vera, Wei Chen, Ullmann, Reinhard, Schulz, Marcel Holger, Erdogan, Fikret, Na Li, Kijas, Zofia, Arkesteijn, Ger, Pajares, Isidora Lopez, Goetz-Sothmann, Margret, Heinrich, Uwe, Rost, Imma, Dufke, Andreas, Grasshoff, Ute, Glaeser, Birgitta, Vingron, Martin, and Ropers, H. Hilger

Subjects
Chromosome mapping -- Research, Translocation (Genetics) -- Research, Health
Abstract

The Illumina/solexa system was utilized to map and sequence the breakpoint regions on flow-sorted derivatives chromosomes from three unrelated mentally retarded patients with denovo balanced chromosomal translocations. The implementation of the method would greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations.

Published
2008

47. BOD1 Is Required for Cognitive Function in Humans and Drosophila

Author

Esmaeeli-Nieh, Sahar, primary, Fenckova, Michaela, additional, Porter, Iain M., additional, Motazacker, M. Mahdi, additional, Nijhof, Bonnie, additional, Castells-Nobau, Anna, additional, Asztalos, Zoltan, additional, Weißmann, Robert, additional, Behjati, Farkhondeh, additional, Tzschach, Andreas, additional, Felbor, Ute, additional, Scherthan, Harry, additional, Sayfati, Seyed Morteza, additional, Ropers, H. Hilger., additional, Kahrizi, Kimia, additional, Najmabadi, Hossein, additional, Swedlow, Jason R., additional, Schenck, Annette, additional, and Kuss, Andreas W., additional

Published
2016
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48. Intelligence : shared genetic basis between Mendelian disorders and a polygenic trait

Author

Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, Boomsma, Dorret I, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, and Boomsma, Dorret I

Published
2015

49. Intelligence: shared genetic basis between Mendelian disorders and a polygenic trait

Author

Onderzoeksgroep 1, Brain, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, Boomsma, Dorret I, Onderzoeksgroep 1, Brain, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, and Boomsma, Dorret I

Published
2015

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