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2. A Modular Genetic Approach to Newborn Screening from Spinal Muscular Atrophy to Sickle Cell Disease—Results from Six Years of Genetic Newborn Screening.

Author

Bzdok, Jessica, Czibere, Ludwig, Burggraf, Siegfried, Pauly, Natalie, Maier, Esther M., Röschinger, Wulf, Becker, Marc, and Durner, Jürgen

Subjects
SPINAL muscular atrophy, SEVERE combined immunodeficiency, SICKLE cell anemia, GENETIC testing, NEWBORN screening
Abstract

Background/Objectives: Genetic newborn screening (NBS) has already entered the phase of common practice in many countries. In Germany, spinal muscular atrophy (SMA), severe combined immunodeficiency (SCID) and sickle cell disease (SCD) are currently a mandatory part of NBS. Here, we describe the experience of six years of genetic NBS including the prevalence of those three diseases in Germany. Methods: Samples and nucleic acids were extracted from dried blood spot cards, commonly used for NBS. A qPCR assay was used to detect disease-causing variants for SMA and SCD, and the detection of T-cell receptor excision circles (TRECs) was performed for SCID screening. Results: The results of the NBS of over 1 million newborns for SMA, approximately 770,000 for SCID and over 410,000 for SCD are discussed in detail. In these newborns, we have identified 121 cases of SMA, 15 cases of SCID and syndrome-based immunodeficiencies and 77 cases of SCD or β-thalassemia. Conclusions: The flexibility of multiplex qPCR is assessed as an effective tool for incorporating different molecular genetic markers for screening. The processing of dried blood spot (DBS) filter cards for molecular genetic assays and the assays are described in detail; turn-around times and cost estimations are included to give an insight into the processes and discuss further options for optimization. The identified cases are in the range expected for the total number of screened newborns, but present a more exact view on the actual prevalences for Germany. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Quality considerations and major pitfalls for high throughput DNA-based newborn screening for severe combined immunodeficiency and spinal muscular atrophy.

Author

Bzdok, Jessica, Czibere, Ludwig, Burggraf, Siegfried, Landt, Olfert, Maier, Esther M., Röschinger, Wulf, Albert, Michael H., Hegert, Sebastian, Janzen, Nils, Becker, Marc, and Durner, Jürgen

Subjects
SEVERE combined immunodeficiency, SPINAL muscular atrophy, NEWBORN screening, T cell receptors, AUDIOMETRY, SICKLE cell anemia, T cells
Abstract

Background: Many newborn screening programs worldwide have introduced screening for diseases using DNA extracted from dried blood spots (DBS). In Germany, DNA-based assays are currently used to screen for severe combined immunodeficiency (SCID), spinal muscular atrophy (SMA), and sickle cell disease (SCD). Methods: This study analysed the impact of pre-analytic DNA carry-over in sample preparation on the outcome of DNA-based newborn screening for SCID and SMA and compared the efficacy of rapid extraction versus automated protocols. Additionally, the distribution of T cell receptor excision circles (TREC) on DBS cards, commonly used for routine newborn screening, was determined. Results: Contaminations from the punching procedure were detected in the SCID and SMA assays in all experimental setups tested. However, a careful evaluation of a cut-off allowed for a clear separation of true positive polymerase chain reaction (PCR) amplifications. Our rapid in-house extraction protocol produced similar amounts compared to automated commercial systems. Therefore, it can be used for reliable DNA-based screening. Additionally, the amount of extracted DNA significantly differs depending on the location of punching within a DBS. Conclusions: Newborn screening for SMA and SCID can be performed reliably. It is crucial to ensure that affected newborns are not overlooked. Therefore a carefully consideration of potential contaminating factors and the definition of appropriate cut-offs to minimise the risk of false results are of special concern. It is also important to note that the location of punching plays a pivotal role, and therefore an exact quantification of TREC numbers per μl may not be reliable and should therefore be avoided. [ABSTRACT FROM AUTHOR]

Published
2024
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9. High Throughput Newborn Screening for Sickle Cell Disease – Application of Two-Tiered Testing with a qPCR-Based Primary screen

Author

Janda, Joachim, primary, Hegert, Sebastian, primary, Bzdok, Jessica, additional, Tesorero, Rafael, additional, Holtkamp, Ute, additional, Burggraf, Siegfried, additional, Schuhmann, Elfriede, additional, Hörster, Friedrike, additional, Hoffmann, Georg F., additional, Janzen, Nils, additional, Okun, Jürgen G, additional, Becker, Marc, additional, and Durner, Jürgen, additional

Published
2023
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10. Newbornscreening SMA – From Pilot Project to Nationwide Screening in Germany

Author

Müller-Felber, Wolfgang, primary, Blaschek, Astrid, additional, Schwartz, Oliver, additional, Gläser, Dieter, additional, Nennstiel, Uta, additional, Brockow, Inken, additional, Wirth, Brunhilde, additional, Burggraf, Siegfried, additional, Röschinger, Wulf, additional, Becker, Marc, additional, Durner, Jürgen, additional, Eggermann, Katja, additional, Kölbel, Heike, additional, Müller, Christine, additional, Hannibal, Iris, additional, Olgemöller, Bernd, additional, Schara, Ulrike, additional, von Moers, Arpad, additional, Trollmann, Regina, additional, Johannssen, Jessika, additional, Ziegler, Andreas, additional, Cirak, Sebahattin, additional, Hahn, Andreas, additional, von der Hagen, Maja, additional, Weiss, Claudia, additional, Schreiber, Gudrun, additional, Flotats-Bastardas, Marina, additional, Hartmann, Hans, additional, Illsinger, Sabine, additional, Pechmann, Astrid, additional, Horber, Veronka, additional, Kirschner, Jan, additional, Köhler, Cornelia, additional, Winter, Benedikt, additional, Friese, Johannes, additional, and Vill, Katharina, additional

Published
2023
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16. Infants Diagnosed with Spinal Muscular Atrophy and 4 SMN2 Copies through Newborn Screening – Opportunity or Burden?

Author

Müller-Felber, Wolfgang, Vill, Katharina, Schwartz, Oliver, Gläser, Dieter, Nennstiel, Uta, Wirth, Brunhilde, Burggraf, Siegfried, Röschinger, Wulf, Becker, Marc, Durner, Jürgen, Eggermann, Katja, Müller, Christine, Hannibal, Iris, Olgemöller, Bernd, Schara, Ulrike, Blaschek, Astrid, and Kölbel, Heike

Subjects
Male, Research Report, newborn screening, Medizin, Infant, Newborn, Infant, Pilot Projects, Spinal muscular atrophy, Survival of Motor Neuron 1 Protein, Pedigree, nervous system diseases, Muscular Atrophy, Spinal, Survival of Motor Neuron 2 Protein, Neonatal Screening, survival motor neuron gene, Germany, Humans, Female, Erratum, Follow-Up Studies, SMN2
Abstract

Although the value of newborn screening (NBS) for early detection and treatment opportunity in SMA patients is generally accepted, there is still an ongoing discussion about the best strategy in children with 4 and more copies of the SMN2 gene. This gene is known to be the most important but not the only disease modifier. In our SMA-NBS pilot project in Germany comprising 278,970 infants screened between January 2018 and November 2019 were 38 positive cases with a homozygous SMN1 deletion. 40% of them had 4 or more SMN2 copies. The incidence for homozygous SMN1 deletion was 1 : 7350, which is within the known range of SMA incidence in Germany. Of the 15 SMA children with 4 SMN2 copies, one child developed physical signs of SMA by the age of 8 months. Reanalysis of the SMN2 copy number by a different test method revealed 3 copies. Two children had affected siblings with SMA Type III, who were diagnosed only after detection of the index patient in the NBS. One had a positive family history with an affected aunt (onset of disease at the age of 3 years). Three families were lost to medical follow up; two because of socioeconomic reasons and one to avoid the psychological stress associated with the appointments. Decisions on how to handle patients with 4 SMN2 copies are discussed in the light of the experience gathered from our NBS pilot SMA program.

Published
2020

17. Additional file 1 of Newborn screening for spinal muscular atrophy in Germany: clinical results after 2 years

Author

Vill, Katharina, Schwartz, Oliver, Blaschek, Astrid, Gläser, Dieter, Nennstiel, Uta, Wirth, Brunhilde, Burggraf, Siegfried, Röschinger, Wulf, Becker, Marc, Czibere, Ludwig, Durner, Jürgen, Eggermann, Katja, Olgemöller, Bernhard, Harms, Erik, Schara, Ulrike, Kölbel, Heike, and Müller-Felber, Wolfgang

Abstract

Additional file 1. Table S1: Age at first consultation at the treatment center or at collection of thesecond blood sample, discrepancy in SMN2 estimation, early-onset symptoms, and initial resultsfrom electrophysiology and CHOP INTEND. Y = years, mo = months, d = days, neg = negative,pos = positive.

Published
2021
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18. Additional file 2 of Newborn screening for spinal muscular atrophy in Germany: clinical results after 2 years

Author

Vill, Katharina, Schwartz, Oliver, Blaschek, Astrid, Gläser, Dieter, Nennstiel, Uta, Wirth, Brunhilde, Burggraf, Siegfried, Röschinger, Wulf, Becker, Marc, Czibere, Ludwig, Durner, Jürgen, Eggermann, Katja, Olgemöller, Bernhard, Harms, Erik, Schara, Ulrike, Kölbel, Heike, and Müller-Felber, Wolfgang

Abstract

Additional file 2. Table S2: Patient’s family history, ethnical background, and outcome details. = years, mo = months, d = days, neg = negative, pos = positive.

Published
2021
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19. Newborn Screening for SMA - Results After Two Years of a Large Pilot Project 

Author

Vill, Katharina, primary, Schwartz, Oliver, additional, Blaschek, Astrid, additional, Gläser, Dieter, additional, Nennstiel, Uta, additional, Wirth, Brunhilde, additional, Burggraf, Siegfried, additional, Röschinger, Wulf, additional, Becker, Marc, additional, Czibere, Ludwig, additional, Durner, Jürgen, additional, Eggermann, Katja, additional, Olgemöller, Bernhard, additional, Harms, Erik, additional, Schara, Ulrike, additional, Kölbel, Heike, additional, and Müller-Felber, Wolfgang, additional

Published
2020
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21. Fast and simple high-throughput testing of COVID 19

Author

Durner, Jürgen, primary, Burggraf, Siegfried, additional, Czibere, Ludwig, additional, Fleige, Tobias, additional, Madejska, Arleta, additional, Watts, David C., additional, Krieg-Schneider, Frank, additional, and Becker, Marc, additional

Published
2020
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29. Occurrence and role of di-myo-inositol-1,1'-phosphate in Methanococcus igneus

Author

Ciulla, Rose Anne, Burggraf, Siegfried, Stetter, Karl O., and Roberts, Mary F.

Subjects
Methanobacteriaceae -- Research, Inositol phosphates -- Physiological aspects, Salt -- Physiological aspects, Biological sciences
Abstract

2D-NMR studies reveal the production of a dimeric inositol phosphodiester, (DIP) from a marine methanogen, Methanococcus igneus, along with L-alpha-glutamate and beta-glutamate. Increase in extracellular NaCl concentrations increases the formation of the inositol compound. Turnover experiments reveal that DIP function as a compatible solute and at fixed NaCl strengths lower ammonium levels increase the accumulation of DIP. Growth temperature exhibits a significant influence on the accumulation of DIP, accumulation occurring only at temperatures beyond 80 degrees Celsius.

Published
1994

30. Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes

Author

Burggraf, Siegfried, Mayer, Thomas, Amann, Rudolf, Schadhauser, Sibylle, Woese, Carl R., and Stetter, Karl O.

Subjects
Archaeabacteria -- Research, Nucleic acid probes -- Observations, Ribosomal RNA -- Analysis, Biological sciences
Abstract

Conservation of the composition of 16S rRNA molecules within phylogenetic groupings helps differentiate phylogenetic classification of organisms. Partial sequencing of 16s rRNA genes enables confirmation of the placement of hyperthermophilic isolates within two archaeal kingdoms using probes EURY498 and CREN499. Whole-cell hybridization with fluorescence labelled oligonucleotide probes provides a clear perception of archaeal phylogeny.

Published
1994

31. 16S rRNA-targeted polymerase chain reaction and oligonucleotide hybridization to screen for Azoarcus spp., grass-associated diazotrophs

Author

Hurek, Thomas, Burggraf, Siegfried, Woese, Carl R., and Reinhold-Hurek, Barbara

Subjects
Ribosomal RNA -- Research, Polymerase chain reaction -- Analysis, Hybridization -- Analysis, Nucleic acids -- Analysis, Biological sciences
Abstract

Reverse transcription sequencing of small subunit of rRNA of three strains from different Azoarcus groups was conducted. Genus-specific primers for phylogenetic polymerase chain reactions (PCR) and oligonucleotides for the determination of amplified fragments were constructed. PCR amplification with 16S rRNA-targeted genus-specific primers and hybridization of 16s rRNA-targeted oligonucleotide, when applied to PCR-generated fragments, facilitated the discovery of the genus Azoarcus.

Published
1993

32. Pyrobaculum aerophilum sp. nov., a novel nitrate-reducing hyperthermophilic archaeum

Author

Volkl, Paul, Huber, Robert, Drobner, Elisabeth, Rachel, Reinhard, Burggraf, Siegfried, Trincone, Antonio, and Stetter, Karl O.

Subjects
Bacteria, Thermophilic -- Growth, Microbial respiration -- Analysis, Organic compounds -- Influence, Biological sciences
Abstract

A new rod-shaped hyperthermophilic archaeum, isolated from hot marine water, was found to grow best at 100 degrees centigrade and pH 7.0 by aerobic respiration and dissimilatory nitrate reduction. Its final product was revealed to be dinitrogen. The organism used organic and inorganic substances as substrates in the course of aerobic and anaerobic respirations. Elemental sulfur was found to hinder growth. The novel isolate was seen to be closely related to the genus Pyrobaculum and has been named Pyrobaculum aerophilum.

Published
1993

33. Newborn Screening for SMA - Results after Two Years of a German Pilot Project

Author

Vill, Katharina, primary, Schwartz, Oliver, additional, Blaschek, Astrid, additional, Gläser, Dieter, additional, Nennstie, Uta, additional, Wirth, Brunhilde, additional, Burggraf, Siegfried, additional, Röschinger, Wulf, additional, Becker, Marc, additional, Czibere, Ludwig, additional, Durner, Jürgen, additional, Eggermann, Katja, additional, Olgemöller, Bernhard, additional, Harms, Erik, additional, Schara, Ulrike, additional, Kölbe, Heike, additional, and Müller-Felber, Wolfgang, additional

Published
2020
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34. One Year of Newborn Screening for SMA – Results of a German Pilot Project

Author

Vill, Katharina, primary, Kölbel, Heike, additional, Schwartz, Oliver, additional, Blaschek, Astrid, additional, Olgemöller, Bernhard, additional, Harms, Erik, additional, Burggraf, Siegfried, additional, Röschinger, Wulf, additional, Durner, Jürgen, additional, Gläser, Dieter, additional, Nennstiel, Uta, additional, Wirth, Brunhilde, additional, Schara, Ulrike, additional, Jensen, Beate, additional, Becker, Marc, additional, Hohenfellner, Katharina, additional, and Müller-Felber, Wolfgang, additional

Published
2019
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35. Next generation sequencing as second-tier test in high-throughput newborn screening for nephropathic cystinosis

Author

Fleige, Tobias, primary, Burggraf, Siegfried, additional, Czibere, Ludwig, additional, Häring, Julia, additional, Glück, Birgit, additional, Keitel, Lisa Marie, additional, Landt, Olfert, additional, Harms, Erik, additional, Hohenfellner, Katharina, additional, Durner, Jürgen, additional, Röschinger, Wulf, additional, and Becker, Marc, additional

Published
2019
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36. High-throughput genetic newborn screening for spinal muscular atrophy by rapid nucleic acid extraction from dried blood spots and 384-well qPCR

Author

Czibere, Ludwig, primary, Burggraf, Siegfried, additional, Fleige, Tobias, additional, Glück, Birgit, additional, Keitel, Lisa Marie, additional, Landt, Olfert, additional, Durner, Jürgen, additional, Röschinger, Wulf, additional, Hohenfellner, Katharina, additional, Wirth, Brunhilde, additional, Müller-Felber, Wolfgang, additional, Vill, Katharina, additional, and Becker, Marc, additional

Published
2019
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37. Infants Diagnosed with Spinal Muscular Atrophy and 4 SMN2Copies through Newborn Screening – Opportunity or Burden?

Author

Müller-Felber, Wolfgang, Vill, Katharina, Schwartz, Oliver, Gläser, Dieter, Nennstiel, Uta, Wirth, Brunhilde, Burggraf, Siegfried, Röschinger, Wulf, Becker, Marc, Durner, Jürgen, Eggermann, Katja, Müller, Christine, Hannibal, Iris, Olgemöller, Bernd, Schara, Ulrike, Blaschek, Astrid, and Kölbel, Heike

Abstract

Although the value of newborn screening (NBS) for early detection and treatment opportunity in SMA patients is generally accepted, there is still an ongoing discussion about the best strategy in children with 4 and more copies of the SMN2gene. This gene is known to be the most important but not the only disease modifier. In our SMA-NBS pilot project in Germany comprising 278,970 infants screened between January 2018 and November 2019 were 38 positive cases with a homozygous SMN1deletion. 40% of them had 4 or more SMN2copies. The incidence for homozygous SMN1deletion was 1 : 7350, which is within the known range of SMA incidence in Germany. Of the 15 SMA children with 4 SMN2copies, one child developed physical signs of SMA by the age of 8 months. Reanalysis of the SMN2 copy number by a different test method revealed 3 copies. Two children had affected siblings with SMA Type III, who were diagnosed only after detection of the index patient in the NBS. One had a positive family history with an affected aunt (onset of disease at the age of 3 years). Three families were lost to medical follow up; two because of socioeconomic reasons and one to avoid the psychological stress associated with the appointments. Decisions on how to handle patients with 4 SMN2copies are discussed in the light of the experience gathered from our NBS pilot SMA program.

Published
2020
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