25 results on '"Eric Manderstedt"'
Search Results
2. Contribution of rare genetic variants to heart failure and cardiomyopathy in the UK Biobank
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Bengt Zöller, Eric Manderstedt, Christina Lind‐Halldén, and Christer Halldén
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Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Published
- 2023
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3. Contribution of rare and common coding variants to haematological malignancies in the UK biobank
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Bengt Zöller, Eric Manderstedt, Christina Lind-Halldén, and Christer Halldén
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Genetics ,Hematologic neoplasms ,Mutation ,Whole exome sequencing ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2023
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4. Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle‐aged and older adults: A population‐based cohort study
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Eric Manderstedt, Christina Lind‐Halldén, Christer Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, Bengt Zöller, and for the Regeneron Genetics Center
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blood coagulation ,genetic variation ,molecular epidemiology ,thrombophilia ,venous thromboembolism ,Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Abstract Background Tissue factor is the main initiator of blood coagulation, and tissue factor pathway inhibitor (TFPI) is the primary inhibitor of the initiation of blood coagulation. The genetic variation of TFPI and the relation to venous thromboembolism (VTE), that is, venous thrombosis and pulmonary embolism, remains to be clarified. This exome sequencing study aimed to determine the molecular epidemiology of the TFPI gene and the relation to VTE in a large population‐based cohort of middle‐aged and older adults. Methods The exomes of TFPI were analyzed for variants in 28,794 subjects without previous VTE (born 1923–1950, 60% women), who participated in the Malmö Diet and Cancer Study (1991–1996). Patients were followed until the first event of VTE, death, or 2018. Qualifying variants were defined as loss‐of‐function or nonbenign (PolyPhen‐2) missense variants with minor allele frequency less than 0.1%. Results No common variant was associated with VTE. Nine rare variants (two loss‐of‐function and seven nonbenign missense) were classified as qualifying and included in collapsing analysis. Prevalence of qualifying variants was 0.09%. Five individuals with VTE compared to 17 individuals without VTE carried one qualifying variant. Cox multivariate regression analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking and alcohol consumption, rs6025, rs1799963, and ancestry showed a hazard ratio of 2.9 (95% CI, 1.2–7.1) for rare qualifying variants. Conclusion Rare qualifying TFPI variants were associated with VTE, suggesting that rare variants in TFPI contribute to the development of VTE. The qualifying TFPI gene variants were very rare, suggesting a constrained gene.
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- 2022
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5. Detection of mosaics in hemophilia A by deep Ion Torrent sequencing and droplet digital PCR
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Eric Manderstedt, Rosanna Nilsson, Rolf Ljung, Christina Lind‐Halldén, Jan Astermark, and Christer Halldén
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factor VIII ,hemophilia A ,high‐throughput nucleotide sequencing ,mosaicism ,polymerase chain reaction ,Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Abstract Background The occurrence of mosaicism in hemophilia A (HA) has been investigated in several studies using different detection methods. Objectives To characterize and compare the ability of AmpliSeq/Ion Torrent sequencing and droplet digital polymerase chain reaction (ddPCR) for mosaic detection in HA. Methods Ion Torrent sequencing and ddPCR were used to analyze 20 healthy males and 16 mothers of sporadic HA patients. Results An error‐rate map over all coding positions and all positions reported as mutated in the F8‐specific mutation database was produced. The sequencing produced a mean read depth of >1500X where >97% of positions were covered by >100 reads. Higher error frequencies were observed in positions with A or T as reference allele and in positions surrounded on both sides with C or G. Seventeen of 9319 positions had a mean substitution error frequency >1%. The ability to identify low‐level mosaicism was determined primarily by read depth and error rate of each specific position. Limit of detection (LOD) was 1% require repeated testing and mononucleotide repeats with more than four repeat units need an alternative analysis strategy. Mosaicism was detected in 1 of 16 mothers and confirmed using ddPCR. Conclusions Deep sequencing using an AmpliSeq/Ion Torrent strategy allows for simultaneous identification of disease‐causing mutations in patients and mosaicism in mothers. ddPCR has high sensitivity but is hampered by the need for mutation‐specific design.
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- 2020
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6. Classic Thrombophilias and Thrombotic Risk Among Middle‐Aged and Older Adults: A Population‐Based Cohort Study
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Eric Manderstedt, Christina Lind‐Halldén, Christer Halldén, Johan Elf, Peter J. Svensson, Björn Dahlbäck, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, and Bengt Zöller
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epidemiology ,genetics ,natural anticoagulants ,thrombophilia ,venous thromboembolism ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Five classic thrombophilias have been recognized: factor V Leiden (rs6025), the prothrombin G20210A variant (rs1799963), and protein C, protein S, and antithrombin deficiencies. This study aimed to determine the thrombotic risk of classic thrombophilias in a cohort of middle‐aged and older adults. Methods and Results Factor V Leiden, prothrombin G20210A and protein‐coding variants in the PROC (protein C), PROS1 (protein S), and SERPINC1 (antithrombin) anticoagulant genes were determined in 29 387 subjects (born 1923–1950, 60% women) who participated in the Malmö Diet and Cancer study (1991–1996). The Human Gene Mutation Database was used to define 68 disease‐causing mutations. Patients were followed up from baseline until the first event of venous thromboembolism (VTE), death, or Dec 31, 2018. Carriership (n=908, 3.1%) for disease‐causing mutations in the PROC, PROS1, and SERPINC1 genes was associated with incident VTE: Hazard ratio (HR) was 1.6 (95% CI, 1.3–1.9). Variants not in Human Gene Mutation Database were not linked to VTE (HR, 1.1; 95% CI, 0.8–1.5). Heterozygosity for rs6025 and rs1799963 was associated with incident VTE: HR, 1.8 (95% CI, 1.6–2.0) and HR, 1.6 (95% CI, 1.3–2.0), respectively. The HR for carrying 1 classical thrombophilia variant was 1.7 (95% CI, 1.6–1.9). HR was 3.9 (95% CI, 3.1–5.0) for carriers of ≥2 thrombophilia variants. Conclusions The 5 classic thrombophilias are associated with a dose‐graded risk of VTE in middle‐aged and older adults. Disease‐causing variants in the PROC, PROS1, and SERPINC1 genes were more common than the rs1799963 variant but the conferred genetic risk was comparable with the rs6025 and rs1799963 variants.
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- 2022
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7. Common and Rare Variants in Genes Associated with von Willebrand Factor Level Variation: No Accumulation of Rare Variants in Swedish von Willebrand Disease Patients
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Eric Manderstedt, Christina Lind-Halldén, Stefan Lethagen, and Christer Halldén
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von willebrand factor ,von willebrand disease ,rare variant ,dna sequencing ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Genome-wide association studies (GWASs) have identified genes that affect plasma von Willebrand factor (VWF) levels. ABO showed a strong effect, whereas smaller effects were seen for VWF, STXBP5, STAB2, SCARA5, STX2, TC2N, and CLEC4M. This study screened comprehensively for both common and rare variants in these eight genes by resequencing their coding sequences in 104 Swedish von Willebrand disease (VWD) patients. The common variants previously associated with the VWF level were all accumulated in the VWD patients compared to three control populations. The strongest effect was detected for blood group O coded for by the ABO gene (71 vs. 38% of genotypes). The other seven VWF level associated alleles were enriched in the VWD population compared to control populations, but the differences were small and not significant. The sequencing detected a total of 146 variants in the eight genes. Excluding 70 variants in VWF, 76 variants remained. Of the 76 variants, 54 had allele frequencies > 0.5% and have therefore been investigated for their association with the VWF level in previous GWAS. The remaining 22 variants with frequencies
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- 2020
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8. Targeted re-sequencing of F8, F9 and VWF: Characterization of Ion Torrent data and clinical implications for mutation screening.
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Eric Manderstedt, Rosanna Nilsson, Christina Lind-Halldén, Rolf Ljung, Jan Astermark, and Christer Halldén
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Medicine ,Science - Abstract
Mutations are not identified in ~5% of hemophilia A and 10-35% of type 1 VWD patients. The bleeding tendency also varies among patients carrying the same causative mutation, potentially indicating variants in additional genes modifying the phenotype that cannot be identified by routine single-gene analysis. The F8, F9 and VWF genes were analyzed in parallel using an AmpliSeq strategy and Ion Torrent sequencing. Targeting all exonic positions showed an average read depth of >2000X and coverage close to 100% in 24 male patients with known disease-causing mutations. Discrimination between reference alleles and alternative/indel alleles was adequate at a 25% frequency threshold. In F8, F9 and VWF there was an absolute majority of all reference alleles at allele frequencies >95% and the average alternative allele and indel frequencies never reached above 10% and 15%, respectively. In VWF, 4-5 regions showed lower reference allele frequencies; in two regions covered by the pseudogene close to the 25% cut-off for reference alleles. All known mutations, including indels, gross deletions and substitutions, were identified. Additional VWF variants were identified in three hemophilia patients. The presence of additional mutations in 2 out of 16 (12%) randomly selected hemophilia patients indicates a potential mutational contribution that may affect the disease phenotype and counseling in these patients. Parallel identification of disease-causing mutations in all three genes not only confirms the deficiency, but differentiates phenotypic overlaps and allows for correct genetic counseling.
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- 2019
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9. Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients.
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Eric Manderstedt, Christina Lind-Halldén, Stefan Lethagen, and Christer Halldén
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Medicine ,Science - Abstract
von Willebrand factor (VWF) levels in healthy individuals and in patients with type 1 von Willebrand disease (VWD) are influenced by genetic variation in several genes, e.g. VWF, ABO, STXBP5 and CLEC4M. This study aims to screen comprehensively for CLEC4M variants and investigate their association with type 1 VWD in the Swedish population. In order to screen for CLEC4M variants, the CLEC4M gene region was re-sequenced and the polymorphic neck region was genotyped in 106 type 1 VWD patients from unrelated type 1 VWD families. Single nucleotide variants (SNV) and variable number tandem repeat (VNTR) allele and genotype frequencies were then compared with 294 individuals from the 1000Genomes project and 436 Swedish control individuals. Re-sequencing identified a total of 42 SNVs. Rare variants showed no accumulation in type 1 VWD patients and are not thought to contribute substantially to type 1 VWD. The only missense mutation (rs2277998, NP_001138379.1:p.Asp224Asn) had a higher frequency in type 1 VWD patients than in controls (4.9%). The VNTR genotypes 57 and 67 were observed at higher frequencies than expected in type 1 VWD patients (6.4% and 6.2%) and showed an increase in patients compared with controls (7.4% and 3.1%). Strong linkage disequilibrium in the CLEC4M region makes it difficult to distinguish between the effect of the missense mutation and the VNTR genotypes. In conclusion, heterozygous VNTR genotypes 57 and 67 of CLEC4M were highly enriched and are the most likely mechanism through which CLEC4M contributes to disease in the Swedish type 1 VWD population.
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- 2018
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10. Genetic Variation in the von Willebrand Factor Gene in Swedish von Willebrand Disease Patients
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Eric Manderstedt, Christina Lind-Halldén, Stefan Lethagen, and Christer Halldén
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dna ,molecular ,diagnosis ,sweden ,von willebrand disease ,von willebrand factor ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
von Willebrand factor (VWF) level and function are influenced by genetic variation in VWF and several other genes in von Willebrand disease type 1 (VWD1) patients. This study comprehensively screened for VWF variants and investigated the presence of ABO genotypes and common and rare VWF variants in Swedish VWD1 patients. The VWF gene was resequenced using Ion Torrent and Sanger sequencing in 126 index cases historically diagnosed with VWD. Exon 7 of the ABO gene was resequenced using Sanger sequencing. Multiplex ligation-dependent probe amplification analysis was used to investigate for copy number variants. Genotyping of 98 single nucleotide variants allowed allele frequency comparisons with public databases. Seven VWD2 mutations and 36 candidate VWD1 mutations (5 deletions, 4 nonsense, 21 missense, 1 splice, and 5 synonymous mutations) were identified. Nine mutations were found in more than one family and nine VWD1 index cases carried more than one candidate mutation. The T-allele of rs1063857 (c.2385T > C, p.Y795 = ) and blood group O were both frequent findings and contributed to disease in the Swedish VWD1 population. VWD2 mutations were found in 20 and candidate VWD1 mutations in 51 index cases out of 106 (48%). VWF mutations, a VWF haplotype, and blood group O all contributed to explain disease in Swedish VWD1 patients.
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- 2018
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11. Rare-variant collapsing analyses of arterial hypertension in the UK biobank
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Bengt Zöller, Eric Manderstedt, Christina Lind-Halldén, and Christer Halldén
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- 2023
12. Thrombotic risk determined by rare and common SERPINA1 variants in a population‐based cohort study
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Eric Manderstedt, Christer Halldén, Christina Lind‐Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Kia Manoochehri, Maria Sotiropoulos Padilla, Manasi Pradhan, Thomas D. Schleicher, Ricardo H. Ulloa, Louis Widom, Sarah E. Wolf, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Marcus B. Jones, Jason Mighty, and Lyndon J. Mitnaul
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Aged, 80 and over ,Cohort Studies ,Male ,Genotype ,Case-Control Studies ,alpha 1-Antitrypsin ,alpha 1-Antitrypsin Deficiency ,Humans ,Female ,Thrombosis ,Venous Thromboembolism ,Hematology ,Aged - Abstract
Severe alpha-1-antitrypsin deficiency (AATD), phenotype PiZZ, was associated with venous thromboembolism (VTE) in a case-control study.This study aimed to determine the genetic variation in the SERPINA1 gene and a possible thrombotic risk of these variants in a population-based cohort study.The coding sequence of SERPINA1 was analyzed for the Z (rs28929474), S (rs17580), and other qualifying variants in 28,794 subjects without previous VTE (born 1923-1950, 60% women), who participated in the Malmö Diet and Cancer study (1991-1996). Individuals were followed from baseline until the first event of VTE, death, or 2018.Resequencing the coding sequence of SERPINA1 identified 84 variants in the total study population, 21 synonymous, 62 missense, and 1 loss-of-function variant. Kaplan-Meier analysis showed that homozygosity for the Z allele increased the risk of VTE whereas heterozygosity showed no effect. The S (rs17580) variant was not associated with VTE. Thirty-one rare variants were qualifying and included in collapsing analysis using the following selection criteria, loss of function, in frame deletion or non-benign (PolyPhen-2) missense variants with minor allele frequency (MAF)0.1%. Combining the rare qualifying variants with the Z variant showed that carrying two alleles (ZZ or compound heterozygotes) showed increased risk. Cox regression analysis revealed an adjusted hazard ratio of 4.5 (95% confidence interval 2.0-10.0) for combinations of the Z variant and rare qualifying variants. One other variant (rs141620200; MAF = 0.002) showed an increased risk of VTE.The SERPINA1 ZZ genotype and compound heterozygotes for severe AATD are rare but associated with VTE in a population-based Swedish study.
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- 2022
13. Thrombotic Risk Determined by Protein C Receptor (PROCR) Variants among Middle-Aged and Older Adults: A Population-Based Cohort Study
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Eric, Manderstedt, Christer, Halldén, Christina, Lind-Halldén, Johan, Elf, Peter J, Svensson, Gunnar, Engström, Olle, Melander, Aris, Baras, Luca A, Lotta, and Bengt, Zöller
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Cohort Studies ,Male ,Risk Factors ,Endothelial Protein C Receptor ,Humans ,Female ,Thrombosis ,Venous Thromboembolism ,Hematology ,Middle Aged ,Aged ,Genome-Wide Association Study ,Protein C - Abstract
Background The protein C (PC) anticoagulant system has a key role in maintaining hemostatic balance. One missense (Ser219Gly) variant in the PC receptor (PROCR) was associated with venous thromboembolism (VTE) in genome-wide association studies. Objectives This study aimed to determine the thrombotic risk of rare and common PROCR variants in a large population-based cohort of middle-aged and older adults. Methods The exonic sequence of PROCR was analyzed for the Ser219Gly variant and other qualifying variants in 28,794 subjects (born 1923–1950, 60% women) without previous VTE, who participated in the Malmö Diet and Cancer study (1991–1996). Incidence of VTE was followed up until 2018. Qualifying variants were defined as loss-of-function or nonbenign (PolyPhen-2) missense variants with minor allele frequencies (MAFs) Results Re-sequencing identified 36 PROCR variants in the study population (26,210 non-VTE exomes and 2,584 VTE exomes), 11 synonymous, 22 missense, and three loss-of-function variants. Kaplan–Meier analysis of the known Ser219Gly variant (rs867186) showed that homozygosity for this variant increased the risk of disease, whereas heterozygosity showed no effect. Cox multivariate regression analysis revealed an adjusted hazard ratio (HR) of 1.5 (95% confidence interval [CI]: 1.1–2.0). Fifteen rare variants were classified as qualifying and were included in collapsing analysis (burden test and SKAT-O). They did not contribute to risk. However, a Arg113Cys missense variant (rs146420040; MAF = 0.004) showed an increased VTE risk (HR = 1.3; 95% CI: 1.0–1.9). Conclusion Homozygosity for the Ser219Gly variant and a previously identified functional PROCR variant (Arg113Cys) was associated with VTE. Other variants did not contribute to VTE.
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- 2022
14. Common and Rare Variants in Genes Associated with von Willebrand Factor Level Variation: No Accumulation of Rare Variants in Swedish von Willebrand Disease Patients
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Stefan Lethagen, Eric Manderstedt, Christer Halldén, and Christina Lind-Halldén
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0301 basic medicine ,lcsh:Diseases of the circulatory (Cardiovascular) system ,congenital, hereditary, and neonatal diseases and abnormalities ,Medical Biotechnology ,Population ,Genome-wide association study ,von Willebrand factor ,030204 cardiovascular system & hematology ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Von Willebrand factor ,hemic and lymphatic diseases ,ABO blood group system ,Medicinsk bioteknologi ,Genotype ,Von Willebrand disease ,medicine ,DNA sequencing ,Allele ,rare variant ,education ,Genetic association ,Genetics ,education.field_of_study ,medicine.disease ,030104 developmental biology ,lcsh:RC666-701 ,biology.protein ,Original Article ,von Willebrand disease - Abstract
Genome-wide association studies (GWASs) have identified genes that affect plasma von Willebrand factor (VWF) levels. ABO showed a strong effect, whereas smaller effects were seen for VWF, STXBP5, STAB2, SCARA5, STX2, TC2N, and CLEC4M. This study screened comprehensively for both common and rare variants in these eight genes by resequencing their coding sequences in 104 Swedish von Willebrand disease (VWD) patients. The common variants previously associated with the VWF level were all accumulated in the VWD patients compared to three control populations. The strongest effect was detected for blood group O coded for by the ABO gene (71 vs. 38% of genotypes). The other seven VWF level associated alleles were enriched in the VWD population compared to control populations, but the differences were small and not significant. The sequencing detected a total of 146 variants in the eight genes. Excluding 70 variants in VWF, 76 variants remained. Of the 76 variants, 54 had allele frequencies > 0.5% and have therefore been investigated for their association with the VWF level in previous GWAS. The remaining 22 variants with frequencies
- Published
- 2020
15. Detection of F8 int22h inversions using digital droplet PCR and mile‐post assays
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Christer Halldén, Rolf Ljung, Christina Lind-Halldén, Eric Manderstedt, and Jan Astermark
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Mutation ,Factor VIII ,Wild type ,Intron ,Locus (genetics) ,Hematology ,030204 cardiovascular system & hematology ,Biology ,Hemophilia A ,medicine.disease_cause ,Polymerase Chain Reaction ,Molecular biology ,Introns ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,law ,Genetic linkage ,Chromosome Inversion ,medicine ,Humans ,Repeated sequence ,Polymerase chain reaction ,Digital droplet pcr - Abstract
BACKGROUND: Inversions involving intron 22 (Inv22) of F8 are detected in approximately 45% of all severe hemophilia A patients. Diagnosis is complicated by the large size of the ~9.5 kb int22h repeated sequence which generates the inversions. Methods such as long-range PCR and inverse-shifting PCR are currently used diagnostically, but suffer from low PCR efficiencies and are difficult to standardize.OBJECTIVES: To design and validate a sensitive and robust assay for the detection of F8 int22h inversions.METHODS: Digital droplet PCR using mile-post assays was used to investigate archival DNA samples.RESULTS: The detection of linkage as a function of physical distance between loci was investigated using an anchor locus and mile-post loci located at 1, 6, 12 and 15 kb distances from the anchor locus. The proportion of linked molecules decreased with increasing distance between loci and showed 30-40% linked molecules for loci 12-15 kb apart. Mile-post assays specific for wild type and Inv22 type 1 and 2 chromosomes were then designed and optimized. All three assays showed high specificities and sensitivities, with coefficients of variation < 5% for all assays. Analysis of 106 patients and 20 carrier mothers showed complete concordance with previously known mutation status. The analysis demonstrated the robustness of the assays versus input DNA concentration (6 ng and higher) and level of fragmentation.CONCLUSIONS: Digital droplet PCR and mile-post assays can be used to detect F8 int22h inversions. The assay systems are technically simple to perform, highly efficient and robust. (Less)
- Published
- 2020
16. Thrombomodulin (THBD) gene variants and thrombotic risk in a population-based cohort study
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Eric Manderstedt, Christer Halldén, Christina Lind‐Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A. Lotta, and Bengt Zöller
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Cohort Studies ,Male ,Risk Factors ,Thrombomodulin ,Humans ,Female ,Thrombosis ,Hematology ,Venous Thromboembolism ,Middle Aged ,Aged ,Protein C - Abstract
The protein C anticoagulant system plays a key role in maintaining the hemostatic balance. Although several studies have identified thrombomodulin gene (THBD) variants among venous thromboembolism (VTE) patients, the role of THBD in relation to VTE in humans remains to be clarified.This study aimed to determine the thrombotic risk of rare and common THBD variants in a large population-based cohort of middle-aged and older adults.The exome sequence of THBD was analyzed for qualifying variants in 28,794 subjects (born 1923-1950, 60% women), who participated in the Malmö Diet and Cancer study (1991-1996). Patients were followed from baseline until the first event of VTE, death, or 2018. Qualifying variants were defined as loss-of-function or non-benign (PolyPhen-2) missense variants with minor allele frequency0.1%.The single common coding variant rs1042579 was not associated with incident VTE. Sixteen rare variants were classified as qualifying and included in collapsing analysis. Seven individuals with VTE compared to 24 individuals without VTE carried one qualifying variant. Cox multivariate regression analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking and alcohol consumption, rs6025, rs1799963, and the top two eigenvectors from a principal components analysis showed a hazard ratio of 3.0 (95% confidence interval 1.4-6.3) for the rare qualifying variants. The distributions of qualifying variants in THBD showed a difference for individuals with and without incident VTE indicating a possible position effect.Rare qualifying THBD variants were associated with VTE, suggesting that rare variants in THBD contribute to development of VTE.
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- 2021
17. Thrombotic Risk Determined by STAB 2 Variants in a Population-Based Cohort Study
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Eric Manderstedt, Christer Halldén, Christina Lind-Halldén, Johan Elf, Peter J. Svensson, Gunnar Engström, Olle Melander, Aris Baras, Luca A Lotta, Bengt Zöller, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Katia Karalis, Katherine Siminovitch, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Andrew Blumenfeld, Boris Boutkov, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Olga Krasheninina, Rouel Lanche, Adam J. Mansfield, Evan K. Maxwell, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Razvan Panea, Tommy Polanco, Ayesha Rasool, William Salerno, Jeffrey C. Staples, Niek Verweij, Jonas Nielsen, Tanima De, Marcus B. Jones, Jason Mighty, Michelle G. LeBlanc, and Lyndon J. Mitnaul
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Thrombotic risk ,medicine.medical_specialty ,education.field_of_study ,business.industry ,Population ,General Medicine ,medicine.disease ,Thrombosis ,Population based cohort ,Internal medicine ,Medicine ,business ,education ,Venous thromboembolism - Published
- 2021
18. Identification of F8 rearrangements in carrier and non‐carrier mothers of haemophilia A patients
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Christer Halldén, Christina Lind-Halldén, Eric Manderstedt, Rolf Ljung, and Jan Astermark
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medicine.medical_specialty ,Pediatrics ,Factor VIII ,Hematology ,business.industry ,Haemophilia A ,Mothers ,General Medicine ,Hemophilia A ,medicine.disease ,Introns ,Internal medicine ,Mutation ,Humans ,Medicine ,Medical genetics ,Female ,Identification (biology) ,business ,Genetics (clinical) - Published
- 2021
19. Next-Generation Sequencing of 17 Genes Associated with Venous Thromboembolism Reveals a Deficit of Non-Synonymous Variants in Procoagulant Genes
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Christer Halldén, Eric Manderstedt, Bengt Zöller, Christina Lind-Halldén, and Peter Svensson
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Adult ,Male ,0301 basic medicine ,medicine.medical_specialty ,Antithrombin III ,Population ,030204 cardiovascular system & hematology ,Gene mutation ,Thrombophilia ,Protein S ,Cohort Studies ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Polymorphism (computer science) ,Factor V Leiden ,medicine ,Humans ,education ,Blood Coagulation ,Gene ,Aged ,Genetics ,education.field_of_study ,Polymorphism, Genetic ,biology ,Calcium-Binding Proteins ,Factor V ,High-Throughput Nucleotide Sequencing ,Venous Thromboembolism ,Hematology ,Middle Aged ,medicine.disease ,030104 developmental biology ,Mutation ,biology.protein ,Medical genetics ,Female ,Prothrombin ,Protein C - Abstract
Background The heritability of venous thromboembolism (VTE) is only partially explained by variants in 17 previously VTE-associated genes. Objective This article screens for additional rare variants in the 17 genes and investigates the relative contributions of pro- and anticoagulant genes to VTE. Patients and Methods Ninety-six VTE patients from the population-based Malmö Thrombophilia Study were analysed using an AmpliSeq strategy and Ion Torrent sequencing and the variant data were compared with data from public databases. Results A total of 102 non-synonymous and 76 synonymous variants were identified. Forty-six non-synonymous variants were present in the human gene mutation database. Anticoagulant and procoagulant genes showed 14 and 22 rare non-synonymous variants, respectively. Individual patients showed varying numbers of risk factors; 13 patients had non-synonymous mutations in SERPINC1, PROC and PROS1 genes and 42 had factor V Leiden or prothrombin mutations generating a total of 47 patients with at least one of these risk factors. Ten common VTE-associated variants showed low level enrichments and no correlation to the other risk factors. The enrichment of previously identified risk factors was similar to previous studies. Determination of the nsyn/syn ratio (number of non-synonymous variants per non-synonymous site, nsyn, to the number of synonymous variants per synonymous site, syn) showed, as expected in patients, an increase of non-synonymous relative to synonymous anticoagulant variants compared with controls (nsyn/syn, 0.95 vs. 0.68). In contrast, non-synonymous procoagulant variants (nsyn/syn, 0.31 vs. 0.63) showed a decrease. We suggest that the deficit of non-synonymous variants in procoagulant genes is a novel mechanism contributing to VTE.
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- 2019
20. Droplet digital PCR and mile-post analysis for the detection of F8 int1h inversions
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Eric Manderstedt, Christer Halldén, Jan Astermark, Christina Lind-Halldén, and Rolf Ljung
- Subjects
polymerase chain reaction ,030204 cardiovascular system & hematology ,Biology ,Hemophilia A ,Polymerase Chain Reaction ,law.invention ,03 medical and health sciences ,Exon ,chemistry.chemical_compound ,0302 clinical medicine ,genetic linkage ,Genetic linkage ,law ,Biomedicinsk laboratorievetenskap/teknologi ,Gene duplication ,Humans ,Digital polymerase chain reaction ,Biomedical Laboratory Science/Technology ,Copy-number variation ,Gene ,Polymerase chain reaction ,sequence inversion ,Factor VIII ,Hematology ,Molecular biology ,Introns ,chemistry ,Chromosome Inversion ,Mutation ,hemophilia A ,DNA - Abstract
Background F8 int1h inversions (Inv1) are detected in 1-2% of severe hemophilia A (HA) patients. Long-range polymerase chain reaction (PCR) and inverse-shifting PCR have been used to diagnose these inversions. Objectives To design and validate a sensitive and robust assay for detection of F8 Inv1 inversions. Methods Archival DNA samples were investigated using mile-post assays and droplet digital PCR. Results Mile-post assays for Inv1 showing high specificities and sensitivities were designed and optimized. Analysis of four patients, two carrier mothers and 40 healthy controls showed concordance with known mutation status with one exception. One patient had a duplication involving exons 2-22 of the F8 gene instead of an Inv1 mutation. DNA mixtures with different proportions of wild type and Inv1 DNA correlated well with the observed relative linkage for both wild type and Inv1 assays and estimated the limit of detection of these assays to 2% of the rare chromosome. Conclusions The mile-post strategy has several inherent control systems. The absolute counting of target molecules by both assays enables determination of template quantity, detection of copy number variants and rare variants occurring in primer and probe annealing sites and estimation of DNA integrity through the observed linkage. The presented Inv1 mile-post analysis offers sensitive and robust detection and quantification of the F8 int1h inversions and other rearrangements involving intron 1 in patients and their mothers.
- Published
- 2021
21. Detection of mosaics in hemophilia A by deep Ion Torrent sequencing and droplet digital PCR
- Author
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Rosanna Nilsson, Eric Manderstedt, Christer Halldén, Christina Lind-Halldén, Rolf Ljung, and Jan Astermark
- Subjects
Genetics ,polymerase chain reaction ,Read depth ,factor VIII ,hemophilia A ,high-throughput nucleotide sequencing ,mosaicism ,Hematology ,Ion semiconductor sequencing ,Biology ,high‐throughput nucleotide sequencing ,Deep sequencing ,law.invention ,Repeated testing ,law ,Original Articles ‐ Hemostasis ,Biomedicinsk laboratorievetenskap/teknologi ,Mutation database ,In patient ,Digital polymerase chain reaction ,Diseases of the blood and blood-forming organs ,Biomedical Laboratory Science/Technology ,Original Article ,RC633-647.5 ,Polymerase chain reaction - Abstract
Background: The occurrence of mosaicism in hemophilia A (HA) has been investigated in several studies using different detection methods. Objectives: To characterize and compare the ability of AmpliSeq/Ion Torrent sequencing and droplet digital polymerase chain reaction (ddPCR) for mosaic detection in HA. Methods: Ion Torrent sequencing and ddPCR were used to analyze 20 healthy males and 16 mothers of sporadic HA patients. Results: An error-rate map over all coding positions and all positions reported as mutated in the F8-specific mutation database was produced. The sequencing produced a mean read depth of >1500X where >97% of positions were covered by >100 reads. Higher error frequencies were observed in positions with A or T as reference allele and in positions surrounded on both sides with C or G. Seventeen of 9319 positions had a mean substitution error frequency >1%. The ability to identify low-level mosaicism was determined primarily by read depth and error rate of each specific position. Limit of detection (LOD) was 1% require repeated testing and mononucleotide repeats with more than four repeat units need an alternative analysis strategy. Mosaicism was detected in 1 of 16 mothers and confirmed using ddPCR. Conclusions: Deep sequencing using an AmpliSeq/Ion Torrent strategy allows for simultaneous identification of disease-causing mutations in patients and mosaicism in mothers. ddPCR has high sensitivity but is hampered by the need for mutationspecific design.
- Published
- 2020
22. Genetic Variation in the von Willebrand Factor Gene in Swedish von Willebrand Disease Patients
- Author
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Christina Lind-Halldén, Stefan Lethagen, Eric Manderstedt, and Christer Halldén
- Subjects
lcsh:Diseases of the circulatory (Cardiovascular) system ,congenital, hereditary, and neonatal diseases and abnormalities ,diagnosis ,Population ,dna ,DNA - molecular - diagnosis - Sweden - von Willebrand disease - von Willebrand factor ,von willebrand disease ,symbols.namesake ,Von Willebrand factor ,hemic and lymphatic diseases ,ABO blood group system ,Naturvetenskap ,Genotype ,Von Willebrand disease ,medicine ,molecular ,Copy-number variation ,education ,Allele frequency ,Sanger sequencing ,Genetics ,education.field_of_study ,biology ,sweden ,medicine.disease ,von willebrand factor ,lcsh:RC666-701 ,biology.protein ,symbols ,Original Article ,Natural Sciences - Abstract
von Willebrand factor (VWF) level and function are influenced by genetic variation in VWF and several other genes in von Willebrand disease type 1 (VWD1) patients. This study comprehensively screened for VWF variants and investigated the presence of ABO genotypes and common and rare VWF variants in Swedish VWD1 patients. The VWF gene was resequenced using Ion Torrent and Sanger sequencing in 126 index cases historically diagnosed with VWD. Exon 7 of the ABO gene was resequenced using Sanger sequencing. Multiplex ligation-dependent probe amplification analysis was used to investigate for copy number variants. Genotyping of 98 single nucleotide variants allowed allele frequency comparisons with public databases. Seven VWD2 mutations and 36 candidate VWD1 mutations (5 deletions, 4 nonsense, 21 missense, 1 splice, and 5 synonymous mutations) were identified. Nine mutations were found in more than one family and nine VWD1 index cases carried more than one candidate mutation. The T-allele of rs1063857 (c.2385T > C, p.Y795 = ) and blood group O were both frequent findings and contributed to disease in the Swedish VWD1 population. VWD2 mutations were found in 20 and candidate VWD1 mutations in 51 index cases out of 106 (48%). VWF mutations, a VWF haplotype, and blood group O all contributed to explain disease in Swedish VWD1 patients.
- Published
- 2018
23. Targeted re-sequencing of F8, F9 and VWF: Characterization of Ion Torrent data and clinical implications for mutation screening
- Author
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Rosanna Nilsson, Christer Halldén, Rolf Ljung, Christina Lind-Halldén, Eric Manderstedt, and Jan Astermark
- Subjects
0301 basic medicine ,DNA Mutational Analysis ,Gene Identification and Analysis ,Artificial Gene Amplification and Extension ,030204 cardiovascular system & hematology ,Cardiovascular Medicine ,medicine.disease_cause ,Polymerase Chain Reaction ,Factor IX ,Database and Informatics Methods ,0302 clinical medicine ,Gene Frequency ,INDEL Mutation ,Medicine and Health Sciences ,Biologiska vetenskaper ,Genetics ,Mutation ,Multidisciplinary ,High-Throughput Nucleotide Sequencing ,Nonsense Mutation ,Hematology ,Biological Sciences ,Reference Standards ,Phenotype ,Cardiovascular Diseases ,Medicine ,Research Article ,Substitution Mutation ,Pseudogene ,Science ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,von Willebrand Factor ,medicine ,Humans ,Point Mutation ,Allele ,Indel ,Molecular Biology Techniques ,Allele frequency ,Gene ,Mutation Detection ,Blood Coagulation ,Molecular Biology ,Alleles ,Factor VIII ,Coagulation Disorders ,Biology and Life Sciences ,Ion semiconductor sequencing ,030104 developmental biology ,Biological Databases ,Genetic Loci ,Mutation Databases - Abstract
Mutations are not identified in ~5% of hemophilia A and 10-35% of type 1 VWD patients. The bleeding tendency also varies among patients carrying the same causative mutation, potentially indicating variants in additional genes modifying the phenotype that cannot be identified by routine single-gene analysis. The F8, F9 and VWF genes were analyzed in parallel using an AmpliSeq strategy and Ion Torrent sequencing. Targeting all exonic positions showed an average read depth of >2000X and coverage close to 100% in 24 male patients with known disease-causing mutations. Discrimination between reference alleles and alternative/indel alleles was adequate at a 25% frequency threshold. In F8, F9 and VWF there was an absolute majority of all reference alleles at allele frequencies >95% and the average alternative allele and indel frequencies never reached above 10% and 15%, respectively. In VWF, 4-5 regions showed lower reference allele frequencies; in two regions covered by the pseudogene close to the 25% cut-off for reference alleles. All known mutations, including indels, gross deletions and substitutions, were identified. Additional VWF variants were identified in three hemophilia patients. The presence of additional mutations in 2 out of 16 (12%) randomly selected hemophilia patients indicates a potential mutational contribution that may affect the disease phenotype and counseling in these patients. Parallel identification of disease-causing mutations in all three genes not only confirms the deficiency, but differentiates phenotypic overlaps and allows for correct genetic counseling.
- Published
- 2019
24. Origin of mutation in sporadic cases of severe haemophilia A in Sweden
- Author
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Anna Letelier, Eric Manderstedt, Annika Mårtensson, Stina Ivarsson, Rolf Ljung, and Christer Halldén
- Subjects
0301 basic medicine ,Genetics ,Pediatrics ,medicine.medical_specialty ,Haemophilia A ,Haplotype ,Newly diagnosed ,030204 cardiovascular system & hematology ,Biology ,medicine.disease ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,hemic and lymphatic diseases ,Mutation (genetic algorithm) ,medicine ,Severe haemophilia A ,Genetics (clinical) - Abstract
Many newly diagnosed Swedish severe haemophilia A (HA) patients are sporadic cases. Some genotypically non-carrier mothers have gone on to have two descendants with the same mutation, presumably due to mosaicism.
- Published
- 2016
25. Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients
- Author
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Christer Halldén, Christina Lind-Halldén, Stefan Lethagen, and Eric Manderstedt
- Subjects
0301 basic medicine ,Male ,Linkage disequilibrium ,Heredity ,Physiology ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,030204 cardiovascular system & hematology ,Polymerase Chain Reaction ,Geographical locations ,0302 clinical medicine ,hemic and lymphatic diseases ,Naturvetenskap ,Medicine and Health Sciences ,Missense mutation ,lcsh:Science ,Child ,Genetics ,education.field_of_study ,Multidisciplinary ,General Medicine ,Genomics ,Middle Aged ,Body Fluids ,Europe ,Variable number tandem repeat ,Genetic Mapping ,Blood ,Child, Preschool ,Female ,Anatomy ,General Agricultural and Biological Sciences ,Natural Sciences ,Research Article ,Adult ,congenital, hereditary, and neonatal diseases and abnormalities ,Genotyping ,Adolescent ,Genotype ,Population ,Single-nucleotide polymorphism ,Variant Genotypes ,Receptors, Cell Surface ,Biology ,Genome Complexity ,Research and Analysis Methods ,Polymorphism, Single Nucleotide ,von Willebrand Disease, Type 1 ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Young Adult ,Von Willebrand disease ,medicine ,Humans ,Lectins, C-Type ,European Union ,Allele ,education ,Molecular Biology Techniques ,Molecular Biology ,Alleles ,Aged ,Sweden ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,Genetic Variation ,Infant ,medicine.disease ,Introns ,Genotype frequency ,030104 developmental biology ,Haplotypes ,Genetic Loci ,lcsh:Q ,People and places ,Blood Groups ,Cell Adhesion Molecules - Abstract
von Willebrand factor (VWF) levels in healthy individuals and in patients with type 1 von Willebrand disease (VWD) are influenced by genetic variation in several genes, e.g. VWF, ABO, STXBP5 and CLEC4M. This study aims to screen comprehensively for CLEC4M variants and investigate their association with type 1 VWD in the Swedish population. In order to screen for CLEC4M variants, the CLEC4M gene region was re-sequenced and the polymorphic neck region was genotyped in 106 type 1 VWD patients from unrelated type 1 VWD families. Single nucleotide variants (SNV) and variable number tandem repeat (VNTR) allele and genotype frequencies were then compared with 294 individuals from the 1000Genomes project and 436 Swedish control individuals. Re-sequencing identified a total of 42 SNVs. Rare variants showed no accumulation in type 1 VWD patients and are not thought to contribute substantially to type 1 VWD. The only missense mutation (rs2277998, NP_001138379.1:p.Asp224Asn) had a higher frequency in type 1 VWD patients than in controls (4.9%). The VNTR genotypes 57 and 67 were observed at higher frequencies than expected in type 1 VWD patients (6.4% and 6.2%) and showed an increase in patients compared with controls (7.4% and 3.1%). Strong linkage disequilibrium in the CLEC4M region makes it difficult to distinguish between the effect of the missense mutation and the VNTR genotypes. In conclusion, heterozygous VNTR genotypes 57 and 67 of CLEC4M were highly enriched and are the most likely mechanism through which CLEC4M contributes to disease in the Swedish type 1 VWD population.
- Published
- 2018
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