Background: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include muta... more Background: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include mutations in IDH1, IDH2, CIC and FUBP1. Here, we have performed whole genome sequencing on three ODs to determine whether additional genetic changes contribute to tumor formation. Methods: We performed whole genome sequencing of DNA from 3 ODs grade III with 1p/19q codeletion and matched germline DNA. Targeted resequencing of identified genes was performed in an additional 32 ODs with 1p19q LOH (28/32) or partial loss of 1p (2/32), 19q (2/32). All mutations were validated by Sanger sequencing. Constructs of wildtype and mutated genes were subsequently generated (n=13), fused to GFP for visualization. Established cell lines were created to perform functional analysis. Results: Whole genome sequencing identified a total of 55 mutations in coding exons (range 8-32 mutations per tumor), including the known molecular abnormalities in IDH1 (2/3), IDH2 (1/3), CIC (2/3) and FUBP1 (1/3). Mutations in the ATRX gene were not identified. In addition to these known genes, we identified mutations in additional genes, most of which were previously not implicated in ODs. We first examined the mutation frequency of these genes in an additional 32 tumors. No additional mutations were identified. We then performed functional analysis on a subset of these mutations. For ZNF238, we observed a difference in the sub cellular localization between wildtype and mutant contructs; the wildtype protein localized to the nucleus while the mutant protein is present in the cytoplasm. In addition, stably transfected ZNF238 mutant cell line shows increased proliferation compared to wildtype. Conclusion: Our results confirm that mutations in IDH, CIC and FUBP1 are present at high frequency in oligodendrogliomas with 1p/19q loss. Functional analysis of infrequently mutated genes provide evidence that they contribute to oncogenesis. Citation Format: Lale Erdem-Eraslan, Maurice de Wit, Daphne Heijsman, Andreas Kremer, Peter J. van der Spek, Peter A.E. Sillevis Smitt, Pim J. French. Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3142. doi:10.1158/1538-7445.AM2013-3142
Ultrasound in Obstetrics & Gynecology, Sep 1, 2009
Methods and Results: Retrospective case note analysis of ultrasound and MRI diagnosed morbidly ad... more Methods and Results: Retrospective case note analysis of ultrasound and MRI diagnosed morbidly adherent placenta praevias were obtained. In the first case, an elective Cesarean section was done for major degree placenta praevia, antenatal diagnosis of morbidly adherent placenta praevia was not made. Patient had a Cesarean hysterectomy, ureteric stenting and repair of the urinary bladder. All other cases had antenatal diagnoses of morbidly adherent placenta praevias made. Colour Doppler ultrasound scan had a 100% sensitivity. In five out of six cases MRI confirmed morbidly adherent placenta praevia giving a sensitivity of 83%. Three out of seven cases (3/7) have had Cesarean hysterectomies. In four out of seven cases, uterus was preserved. Surgical haemostatic procedures undertaken include; interventional radiological procedures, bilateral internal iliac artery occlusion and B-lynch suture. Complications of internal iliac artery occlusion includes one patient suffering from popliteal arterial occlusion and subsequent vascular surgery. Conclusion: Six out of seven cases reported were antenatally diagnosed as having morbidly adherent placenta praevias by colour Doppler ultrasound and MRI. Detailed management and care plans were outlined in each case and patients and their families were briefed about the care pathways. These six cases will highlight the necessity of multidisciplinary involvement with high quality diagnostic modalities by colour Doppler ultrasound and MRI. This will have an impact on reduced maternal mortality and morbidity in this very complex and challenging clinical situation in Obstetric surgery.
Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel E... more Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors.... more Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histologic subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was done on 26 glioblastomas, 22 oligodendrogliomas, and 6 control brain samples. Our results show that Human Exon arrays can identify subgroups of gliomas based on their histologic appearance and genetic aberrations. We next used our expression data to identify differentially expressed splice variants. In two independent approaches, we identified 49 and up to 459 exons that are differentially spliced between glioblastomas and oligodendrogliomas, a subset of which (47% and 33%) were confirmed by reverse transcription-PCR (RT-PCR). In addition, exon level expression profiling also ...
Supplementary Figures 1-3 from Identification of Differentially Regulated Splice Variants and Nov... more Supplementary Figures 1-3 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Supplementary Table 3 from Identification of Differentially Regulated Splice Variants and Novel E... more Supplementary Table 3 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Background: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include muta... more Background: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include mutations in IDH1, IDH2, CIC and FUBP1. Here, we have performed whole genome sequencing on three ODs to determine whether additional genetic changes contribute to tumor formation. Methods: We performed whole genome sequencing of DNA from 3 ODs grade III with 1p/19q codeletion and matched germline DNA. Targeted resequencing of identified genes was performed in an additional 32 ODs with 1p19q LOH (28/32) or partial loss of 1p (2/32), 19q (2/32). All mutations were validated by Sanger sequencing. Constructs of wildtype and mutated genes were subsequently generated (n=13), fused to GFP for visualization. Established cell lines were created to perform functional analysis. Results: Whole genome sequencing identified a total of 55 mutations in coding exons (range 8-32 mutations per tumor), including the known molecular abnormalities in IDH1 (2/3), IDH2 (1/3), CIC (2/3) and FUBP1 (1/3). Mutations in the ATRX gene were not identified. In addition to these known genes, we identified mutations in additional genes, most of which were previously not implicated in ODs. We first examined the mutation frequency of these genes in an additional 32 tumors. No additional mutations were identified. We then performed functional analysis on a subset of these mutations. For ZNF238, we observed a difference in the sub cellular localization between wildtype and mutant contructs; the wildtype protein localized to the nucleus while the mutant protein is present in the cytoplasm. In addition, stably transfected ZNF238 mutant cell line shows increased proliferation compared to wildtype. Conclusion: Our results confirm that mutations in IDH, CIC and FUBP1 are present at high frequency in oligodendrogliomas with 1p/19q loss. Functional analysis of infrequently mutated genes provide evidence that they contribute to oncogenesis. Citation Format: Lale Erdem-Eraslan, Maurice de Wit, Daphne Heijsman, Andreas Kremer, Peter J. van der Spek, Peter A.E. Sillevis Smitt, Pim J. French. Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3142. doi:10.1158/1538-7445.AM2013-3142
Ultrasound in Obstetrics & Gynecology, Sep 1, 2009
Methods and Results: Retrospective case note analysis of ultrasound and MRI diagnosed morbidly ad... more Methods and Results: Retrospective case note analysis of ultrasound and MRI diagnosed morbidly adherent placenta praevias were obtained. In the first case, an elective Cesarean section was done for major degree placenta praevia, antenatal diagnosis of morbidly adherent placenta praevia was not made. Patient had a Cesarean hysterectomy, ureteric stenting and repair of the urinary bladder. All other cases had antenatal diagnoses of morbidly adherent placenta praevias made. Colour Doppler ultrasound scan had a 100% sensitivity. In five out of six cases MRI confirmed morbidly adherent placenta praevia giving a sensitivity of 83%. Three out of seven cases (3/7) have had Cesarean hysterectomies. In four out of seven cases, uterus was preserved. Surgical haemostatic procedures undertaken include; interventional radiological procedures, bilateral internal iliac artery occlusion and B-lynch suture. Complications of internal iliac artery occlusion includes one patient suffering from popliteal arterial occlusion and subsequent vascular surgery. Conclusion: Six out of seven cases reported were antenatally diagnosed as having morbidly adherent placenta praevias by colour Doppler ultrasound and MRI. Detailed management and care plans were outlined in each case and patients and their families were briefed about the care pathways. These six cases will highlight the necessity of multidisciplinary involvement with high quality diagnostic modalities by colour Doppler ultrasound and MRI. This will have an impact on reduced maternal mortality and morbidity in this very complex and challenging clinical situation in Obstetric surgery.
Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel E... more Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors.... more Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histologic subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was done on 26 glioblastomas, 22 oligodendrogliomas, and 6 control brain samples. Our results show that Human Exon arrays can identify subgroups of gliomas based on their histologic appearance and genetic aberrations. We next used our expression data to identify differentially expressed splice variants. In two independent approaches, we identified 49 and up to 459 exons that are differentially spliced between glioblastomas and oligodendrogliomas, a subset of which (47% and 33%) were confirmed by reverse transcription-PCR (RT-PCR). In addition, exon level expression profiling also ...
Supplementary Figures 1-3 from Identification of Differentially Regulated Splice Variants and Nov... more Supplementary Figures 1-3 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Supplementary Table 3 from Identification of Differentially Regulated Splice Variants and Novel E... more Supplementary Table 3 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
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