| 1. |
- Björn, Niclas, et al.
(författare)
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Comparison of Variant Calls from Whole Genome and Whole Exome Sequencing Data Using Matched Samples
- 2018
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Ingår i: Journal of Next Generation Sequencing & Applications. - 2469-9853. ; 5:1, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- Whole exome sequencing (WES) has been extensively used in genomic research. As sequencing costs decline it is being replaced by whole genome sequencing (WGS) in large-scale genomic studies, but more comparative information on WES and WGS datasets would be valuable. Thus, we have extensively compared variant calls obtained from WGS and WES of matched germline DNA samples from 96 lung cancer patients. WGS provided more homogeneous coverage with higher genotyping quality, and identified more variants, than WES, regardless of exome coverage depth. It also called more reference variants, reflecting its power to call rare variants, and more heterozygous variants that met applied quality criteria, indicating that WGS is less prone to allelic drop outs. However, increasing WES coverage reduced the discrepancy between the WES and WGS results. We believe that as sequencing costs further decline WGS will become the method of choice even for research confined to the exome.
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| 2. |
- Björn, Niclas, et al.
(författare)
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Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia
- 2020
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Ingår i: The Pharmacogenomics Journal. - : Nature Publishing Group. - 1470-269X .- 1473-1150. ; 20:2, s. 179-191
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Tidskriftsartikel (refereegranskat)abstract
- Chemotherapy-induced myelosuppression, including thrombocytopenia, is a recurrent problem during cancer treatments that may require dose alterations or cessations that could affect the antitumor effect of the treatment. To identify genetic markers associated with treatment-induced thrombocytopenia, we whole-exome sequenced 215 non-small cell lung cancer patients homogeneously treated with gemcitabine/carboplatin. The decrease in platelets (defined as nadir/baseline) was used to assess treatment-induced thrombocytopenia. Association between germline genetic variants and thrombocytopenia was analyzed at single-nucleotide variant (SNV) (based on the optimal false discovery rate, the severity of predicted consequence, and effect), gene, and pathway levels. These analyses identified 130 SNVs/INDELs and 25 genes associated with thrombocytopenia (P-value < 0.002). Twenty-three SNVs were validated in an independent genome-wide association study (GWAS). The top associations include rs34491125 in JMJD1C (P-value = 9.07 × 10−5), the validated variants rs10491684 in DOCK8 (P-value = 1.95 × 10−4), rs6118 in SERPINA5 (P-value = 5.83 × 10−4), and rs5877 in SERPINC1 (P-value = 1.07 × 10−3), and the genes CAPZA2 (P-value = 4.03 × 10−4) and SERPINC1 (P-value = 1.55 × 10−3). The SNVs in the top-scoring pathway “Factors involved in megakaryocyte development and platelet production” (P-value = 3.34 × 10−4) were used to construct weighted genetic risk score (wGRS) and logistic regression models that predict thrombocytopenia. The wGRS predict which patients are at high or low toxicity risk levels, for CTCAE (odds ratio (OR) = 22.35, P-value = 1.55 × 10−8), and decrease (OR = 66.82, P-value = 5.92 × 10−9). The logistic regression models predict CTCAE grades 3–4 (receiver operator characteristics (ROC) area under the curve (AUC) = 0.79), and large decrease (ROC AUC = 0.86). We identified and validated genetic variations within hematopoiesis-related pathways that provide a solid foundation for future studies using genetic markers for predicting chemotherapy-induced thrombocytopenia and personalizing treatments.
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| 3. |
- Freiholtz, David, et al.
(författare)
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SPP1/osteopontin : a driver of fibrosis and inflammation in degenerative ascending aortic aneurysm?
- 2023
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Ingår i: Journal of Molecular Medicine. - : Springer Nature. - 0946-2716 .- 1432-1440. ; 101:10, s. 1323-1333
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: Degenerative ascending aortic aneurysm (AscAA) is a silent and potentially fatal disease characterized by excessive vascular inflammation and fibrosis. We aimed to characterize the cellular and molecular signature for the fibrotic type of endothelial mesenchymal transition (EndMT) that has previously been described in degenerative AscAA. Patients undergoing elective open-heart surgery for AscAA and/or aortic valve repair were recruited. Gene expression in the intima-media of the ascending aorta was measured in 22 patients with non-dilated and 24 with dilated aortas, and candidate genes were identified. Protein expression was assessed using immunohistochemistry. Interacting distal gene enhancer regions were identified using targeted chromosome conformation capture (HiCap) in untreated and LPS-treated THP1 cells, and the associated transcription factors were analyzed. Differential expression analysis identified SPP1 (osteopontin) as a key gene in the signature of fibrotic EndMT in patients with degenerative AscAA. The aortic intima-media expression of SPP1 correlated with the expression of inflammatory markers, the level of macrophage infiltration, and the aortic diameter. HiCap analysis, followed by transcription factor binding analysis, identified ETS1 as a potential regulator of SPP1 expression under inflammatory conditions. In conclusion, the present findings suggest that SPP1 may be involved in the development of the degenerative type of AscAA. Key messages: In the original manuscript titled “SPP1/osteopontin, a driver of fibrosis and inflammation in degenerative ascending aortic aneurysm?” by David Freiholtz, Otto Bergman, Saliendra Pradhananga, Karin Lång, Flore-Anne Poujade, Carl Granath, Christian Olsson, Anders Franco-Cereceda, Pelin Sahlén, Per Eriksson, and Hanna M Björck, we present novel findings on regulatory factors on osteopontin (SPP1) expression in immune cells involved in degenerative ascending aortic aneurysms (AscAA). The central findings convey: SPP1 is a potential driver of the fibrotic endothelial-to-mesenchymal transition in AscAA.SPP1/osteopontin expression in AscAA is predominately by immune cells.ETS1 is a regulatory transcription factor of SPP1 expression in AscAA immune cells.
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| 4. |
- Pradhananga, Sailendra, et al.
(författare)
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Promoter anchored interaction landscape of THP-1 macrophages captures early immune response processes
- 2020
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Ingår i: Cellular Immunology. - : Elsevier BV. - 0008-8749 .- 1090-2163. ; 355
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Tidskriftsartikel (refereegranskat)abstract
- Macrophages are highly plastic immune cells with temporally distinct transcriptome changes upon lipopolysaccride (LPS) activation. However, to what extent transcriptome reprogramming is mediated via spatial chromatin looping is not well studied. We generated high resolution chromatin interaction maps for LPS-stimulated THP-1 macrophages (0 and 2 h) using capture Hi-C. Success of LPS stimulation was validated with transcriptome sequencing. Circa 2900 genes changed their interaction profile upon LPS stimulation and those gaining interactions were enriched for LPS response relevant processes, suggesting a substantial role for distal regulation. Immune and cardiovascular risk variants were enriched within the interacting regions, thereby providing insights into macrophage biology.
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| 5. |
- Pradhananga, Sailendra, et al.
(författare)
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The role of rare enhancer variants inbicuspid aortic valve pathology
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Bicuspid aortic valve (BAV) is a heritable congenital valve defect associated with a multitude of heart complication. BAV is a highly heritable and relatively rare disease, however in most disease cases, no coding variant can be causally linked to the disease. Given the preponderance of heritability, we sought to understand the role of non-coding rare variants in bicuspid aortic valve pathology. To this end, we generated promoters-enhancer interaction maps (HiCap), transcriptome and H3K27Ac-enhancer profiles of aortic endothelial cells derived from individuals with bicuspid or tricuspid aortic valve. Further, we sequenced the entire genome of all individuals in our study and identified the rare variants (minor allele frequency < 0.5%). Using functional and context dependent datasets, we report three-fold enrichment of non-coding rare variants in enhancer regions. Moreover, the target genes of enhancers with rare variants were relevant for valve pathology only in BAV samples. This suggests that rare non-coding variants could have significant consequences for BAV pathology
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| 6. |
- Pradhananga, Sailendra
(författare)
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Towards understanding of complex disease etiology using sequence Capture Hi-C (HiCap) and associated high throughput functional assays
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A human genome laid out in a straight line would measure 2m from end to end, but in living cells it is folded into a compact structure contained in a nuclear space with a diameter of 2µm. This compact genome is hierarchically organized and spatiotemporally regulates distinct cellular gene expression mechanisms via promoter - enhancer chromatin loops. Additionally, large scale genomic studies have identified enhancer regions enriched with complex disease risk variants but uncovering their contribution to disease pathology remains challenging. This thesis reports the genome-wide generation and analysis of regulatory and functional regions in complex disease relevant cell types. High throughput sequencing methods including whole genome/exome sequencing, capture Hi-C (HiCap), RNA sequencing, and ChIP sequencing were used to create a snapshot of the functional and genomic landscape of cell types relevant to complex diseases. Paper I present a technical comparison of variant calls generated using two genotyping technologies: whole exome and whole genome sequencing (WGS and WES). This comparison unequivocally shows that variant quality from moderately sequenced WGS variant calls is stable and concordant with deeply sequenced WES calls. Papers II and III report the assignment of target genes to cardiovascular risk SNPs using capture Hi-C (HiCap) and other functional assays and identify both known and novel biological processes related to cardiovascular pathology. Finally, paper IV reports the use of whole genome sequencing and capture Hi-C data to identify rare variants in putative enhancer regions in a patient with a congenital heart defect and reveals a number of processes and genes relevant to the pathology. In conclusion, this thesis demonstrates that combining capture Hi-C with functional high throughput sequencing methods can improve our understanding of the etiology of complex diseases. We believe that the resulting mechanistic understanding of complex disease pathologies will enable effective intervention using drugs targeting regulatory processes.
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| 7. |
- Sigurgeirsson, Benjamín, et al.
(författare)
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Genetic association of gemcitabine/carboplatin induced myelosuppression in patients with non-small cell lung cancer using whole exome sequencing
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Purpose: Chemotherapy induced myelosuppression is a recurrent problem in cancer treatment, both for the patients’ quality of life and response. Severe hematological toxicities lead to dose reduction, postponed or ceased treatment, affecting the treatment effect. Identifying genetic markers associated with toxicity is an important factor for individualized chemotherapy and might increase the overall effect of the treatment.Material and methods: Non-small cell lung cancer patients undergoing gemcitabine/carboplatin chemotherapy were included and their exomes were sequenced. Genetic variants from 212 exomes were correlated to thrombocytopenia, leukopenia, and neutropenia on single nucleotide and gene level. Results were processed through enrichment analysis and variants were validated using externally available datasets.Results: SNV analysis identified 103, 131 and 112 variants to be associated with thrombocytopenia, leukopenia and neutropenia, respectively. Gene based analysis identified 21, 54 and 31 genes to be associated with thrombocytopenia, leukopenia and neutropenia, respectively. Using external data sets 8, 26 and 9 SNVs were validated through linkage disequilibrium for thrombocytopenia, leukopenia and neutropenia, respectively.The variant rs61739531 (CADD = 25.7) in the gene MYO1G was identified to be associated with high toxicity in all forms of myelosuppression. Validated variants include rs6118 (CADD = 22.3) in SERPINA5, rs16910526 (CADD = 35.0) in CLEC7A and rs79350244 (CADD = 24.2) in DNAH2. Enrichment analysis of associated genes identified the pathways hemostasis, HIF-1 alpha transcription factor network and vitamin B12 metabolism to be involved in thrombocytopenia, leukopenia and neutropenia, respectively.Factors involved in megakaryocyte development and platelet production, was also associated with thrombocytopenia for three genes JMJD1C with the variant rs34491125 (CADD = 22.1), DOCK8 with the variant rs10491684 (CADD = 11.7) and CAPZA2 based on three variants in the gene based analysis.Conclusion: The results highlight genetic markers and relevant pathways associated with chemotherapy induced myelosuppression and form a strong foundation for further investigation into toxicity induced myelosuppression.
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| 8. |
- Svedberg, Anna, 1988-, et al.
(författare)
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Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
- 2020
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Ingår i: Lung Cancer. - : Elsevier. - 0169-5002 .- 1872-8332. ; 147, s. 106-114
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients.MATERIAL AND METHODS: Whole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia.RESULTS: Association analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients.CONCLUSION: We have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity.
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| 9. |
- Wadensten, Elisabeth, et al.
(författare)
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Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.
- 2023
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Ingår i: JCO Precision Oncology (JCO PO). - : American Society of Clinical Oncology. - 2473-4284. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored.We implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes.During the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%).Up-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.
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| 10. |
- Wadensten, Elisabeth, et al.
(författare)
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Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer
- 2023
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Ingår i: JCO Precision Oncology. - : American Society of Clinical Oncology. - 2473-4284. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored.Methods: We implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes.Results: During the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%).Conclusion: Up-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.
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