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Regulation patterns in signaling networks of cancer
2010
BMC Systems Biology
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Formation of cellular malignancy results from the disruption of fine tuned signaling homeostasis for proliferation, accompanied by mal-functional signals for differentiation, cell cycle and apoptosis. We wanted to observe central signaling characteristics on a global view of malignant cells which have evolved to selfishness and independence in comparison to their non-malignant counterparts that fulfill well defined tasks in their sample. Results: We investigated the regulation of signaling
doi:10.1186/1752-0509-4-162
pmid:21110851
pmcid:PMC3225866
fatcat:hp6epbhr7fcyxdcx7vztyprsm4
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... rks with twenty microarray datasets from eleven different tumor types and their corresponding non-malignant tissue samples. Proteins were represented by their coding genes and regulatory distances were defined by correlating the gene-regulation between neighboring proteins in the network (high correlation = small distance). In cancer cells we observed shorter pathways, larger extension of the networks, a lower signaling frequency of central proteins and links and a higher information content of the network. Proteins of high signaling frequency were enriched with cancer mutations. These proteins showed motifs of regulatory integration in normal cells which was disrupted in tumor cells. Conclusion: Our global analysis revealed a distinct formation of signaling-regulation in cancer cells when compared to cells of normal samples. From these cancer-specific regulation patterns novel signaling motifs are proposed.
A 2-step penalized regression method for family-based next-generation sequencing association studies
2014
BMC Proceedings
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Large-scale genetic studies are often composed of related participants, and utilizing familial relationships can be cumbersome and computationally challenging. We present an approach to efficiently handle sequencing data from complex pedigrees that incorporates information from rare variants as well as common variants. Our method employs a 2-step procedure that sequentially regresses out correlation from familial relatedness and then uses the resulting phenotypic residuals in a penalized
doi:10.1186/1753-6561-8-s1-s25
pmid:25519315
pmcid:PMC4143756
fatcat:z6l77xbmtffgvbvbr6matbdal4
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... ion framework to test for associations with variants within genetic units. The operating characteristics of this approach are detailed using simulation data based on a large, multigenerational cohort.
On family-based genome-wide association studies with large pedigrees: observations and recommendations
2014
BMC Proceedings
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Family based association studies are employed less often than case-control designs in the search for diseasepredisposing genes. The optimal statistical genetic approach for complex pedigrees is unclear when evaluating both common and rare variants. We examined the empirical power and type I error rates of 2 common approaches, the measured genotype approach and family-based association testing, through simulations from a set of multigenerational pedigrees. Overall, these results suggest that
doi:10.1186/1753-6561-8-s1-s26
pmid:25519377
pmcid:PMC4143718
fatcat:3obmrvi22ncy5bp4dkurotxz7i
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... larger sample sizes will be required for family-based studies and that power was better using MGA compared to FBAT. Taking into account computational time and potential bias, a 2-step strategy is recommended with FBAT followed by MGA.
Large common deletions associate with mortality at old age
2011
Human Molecular Genetics
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Copy-number variants (CNVs) are a source of genetic variation that increasingly are associated with human disease. However, the role of CNVs in human lifespan is to date unknown. To identify CNVs that influence mortality at old age, we analyzed genome-wide CNV data in 5178 participants of Rotterdam Study (RS1) and positive findings were evaluated in 1714 participants of the second cohort of the Rotterdam Study (RS2) and in 4550 participants of Framingham Heart Study (FHS). First, we assessed
doi:10.1093/hmg/ddr340
pmid:21835882
pmcid:PMC3188993
fatcat:ycov6fiy4zhk5e3imdlxu5h7l4
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... total burden of rare (frequency <1%) and common (frequency >1%) CNVs for association with mortality during follow-up. These analyses were repeated by stratifying CNVs by type and size. Secondly, we assessed individual common CNV regions (CNVR) for association with mortality. We observed that the burden of common but not of rare CNVs influences mortality. A higher burden of large (≥500 kb) common deletions associated with 4% higher mortality [hazard ratio (HR) per CNV 1.04, 95% confidence interval (CI) 1.02 -1.07, P 5 5.82 3 10 25 ] in the 11 442 participants of RS1, RS2 and FHS. In the analysis of 312 individual common CNVRs, we identified two regions (11p15.5; 14q21.3) that associated with higher mortality in these cohorts. The 11p15.5 region (combined HR 1.59, 95% CI 1.31 -1.93, P 5 2.87 3 10 26 ) encompasses 41 genes, of which some have previously been related to longevity, whereas the 14q21.3 region (combined HR 1.57, 95% CI 1.19 -2.07, P 5 1.53 3 10 23 ) does not encompass any genes. In conclusion, the burden of large common deletions, as well as common CNVs in 11p15.5 and 14q21.3 region, associate with higher mortality.
Pattern recognition of gene expression data on signalling networks of cancer
2010
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Heidelberg, den Januar 14, 2010 ………… (Kannabiran Nandakumar) ...
doi:10.11588/heidok.00010584
fatcat:mnn7ugf4jrggfmbw4okgebgu6a
Targeted sequencing of genome wide significant loci associated with bone mineral density (BMD) reveals significant novel and rare variants: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study
2016
Human Molecular Genetics
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Bone mineral density (BMD) is a heritable phenotype that predicts fracture risk. We performed fine-mapping by targeted sequencing at WLS, MEF2C, ARHGAP1/F2 and JAG1 loci prioritized by eQTL and bioinformatic approaches among 56 BMD loci from our previous GWAS meta-analysis. Methods and Results: Targeted sequencing was conducted in 1,291 Caucasians from the Framingham Heart Study (n ¼ 925) and Cardiovascular Health Study (n ¼ 366), including 206 women and men with extreme low femoral neck (FN)
doi:10.1093/hmg/ddw289
pmid:27616567
pmcid:PMC5837042
fatcat:bsfiso7lhvcillgu22fotesqsq
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... D. A total of 4,964 sequence variants (SNVs) were observed and 80% were rare with MAF <1%. The associations between previously identified SNPs in these loci and BMD, while nominally significant in sequenced participants, were no longer significant after multiple testing corrections. Conditional analyses did not find proteincoding variants that may be responsible for GWAS signals. On the other hand, in the sequenced subjects, we identified novel associations in WLS, ARHGAP1, and 5' of MEF2C (P-values < 8x10 À 5 ; false discovery rate (FDR) q-values < 0.01) that were much more strongly associated with BMD compared to the GWAS SNPs. These associated SNVs are less-common; independent from previous GWAS signals in the same loci; and located in gene regulatory elements. Conclusions: Our findings suggest that protein-coding variants in selected GWAS loci did not contribute to GWAS signals. By performing targeted sequencing in GWAS loci, we identified less-common and rare non-coding SNVs associated with BMD independently from GWAS common SNPs, suggesting both common and less-common variants may associate with disease risks and phenotypes in the same loci.
ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology
2014
Acta Neuropathologica
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A genome-wide copy number association study of osteoporotic fractures points to the 6p25.1 locus
2013
Journal of Medical Genetics
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Osteoporosis is a systemic skeletal disease characterised by reduced bone mineral density and increased susceptibility to fracture; these traits are highly heritable. Both common and rare copy number variants (CNVs) potentially affect the function of genes and may influence disease risk. Aim To identify CNVs associated with osteoporotic bone fracture risk. Method We performed a genome-wide CNV association study in 5178 individuals from a prospective cohort in the Netherlands, including 809
doi:10.1136/jmedgenet-2013-102064
pmid:24343915
fatcat:ir33aftueresjjcrk43h3obhmy
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... porotic fracture cases, and performed in silico lookups and de novo genotyping to replicate in several independent studies. Results A rare ( population prevalence 0.14%, 95% CI 0.03% to 0.24%) 210 kb deletion located on chromosome 6p25.1 was associated with the risk of fracture (OR 32.58, 95% CI 3.95 to 1488.89; p=8.69×10 −5 ). We performed an in silico meta-analysis in four studies with CNV microarray data and the association with fracture risk was replicated (OR 3.11, 95% CI 1.01 to 8.22; p=0.02). The prevalence of this deletion showed geographic diversity, being absent in additional samples from Australia, Canada, Poland, Iceland, Denmark, and Sweden, but present in the Netherlands (0.34%), Spain (0.33%), USA (0.23%), England (0.15%), Scotland (0.10%), and Ireland (0.06%), with insufficient evidence for association with fracture risk. Conclusions These results suggest that deletions in the 6p25.1 locus may predispose to higher risk of fracture in a subset of populations of European origin; larger and geographically restricted studies will be needed to confirm this regional association. This is a first step towards the evaluation of the role of rare CNVs in osteoporosis. 122 Oei L, et al.
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture
2012
Nature Genetics
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Analyzing combinatorial regulation of transcription in mammalian cells
2011
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Nandakumar, and Matthias Eidel, for the warm atmosphere and many (not always science related) discussions. ...
uniformlydistributed-BS A big thank you goes to former and current members of the Network modeling group, specifically Gunnar Schramm, Tobias Bauer, Richa Batra, Kitiporn Plaimas, Apichat Suratanee, Kannabiran ...
doi:10.11588/heidok.00011769
fatcat:bg3v7uek2vfltpavqama7icp4e