Erik Rozemuller - Academia.edu (original) (raw)

Uploads

Papers by Erik Rozemuller

Research paper thumbnail of 1015-LBP: Novel software and reagents for qPCR-based transplant monitoring

Human Immunology, 2014

Aim In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant mo... more Aim In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis and laboratory workflow, we have created a new assay and software suite. Methods We utilize a panel of 42 multiplexed qPCR research assays and software to comparatively genotype multiple samples on a single plate. The software presents the unique marker choices in their genomic context, allowing for knowledgeable informative assay decision making and use in post-transplant monitoring. The software enables numbers of combinations of samples to be comparatively genotyped, facilitating rapid multiple donor analyses. The results from the genotyping are stored by the software for recall during subsequent monitoring. Our software facilitates post-transplant monitoring by: allowing operators to customize their plate configuration or work with lab-defined template, performing all calculations necessary to execute the test, generating a printable protocol to assist laboratory work and generating templates to import into the qPCR machines. The software accepts standard qPCR data output for generating results. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual over time – providing a temporal view for better understanding rejection or relapse kinetics. Results This assay system provides the highest probability of finding informative markers, as compared to other commercially-available qPCR systems. The tests and software are compatible with qPCR platforms from multiple vendors. Our software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores/plots data. Conclusions This new assay system provides the most automated and platform independent qPCR-based transplant monitoring research tool available to date.

Research paper thumbnail of Rapid microchimerism analysis using multiplexed reagents and novel software

Human Immunology, 2015

Aim To overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring meth... more Aim To overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis, KimerDx has developed a new assay and software suite. Method Our reagents employ a multiplexed panel of 30 qPCR research assays and software to genotype multiple samples on a single plate and identify informative markers. The software presents the marker choices in their genomic context, allowing for informed decision-making and use in post-transplant monitoring. The genotyping results are stored by the software for recall during subsequent monitoring. Results Our software facilitates post-transplant monitoring by: allowing operators to customize their plate configuration or work with a lab-defined template, performing all calculations necessary to execute the test, generating a printable protocol to assist laboratory work and by generating templates to import into the qPCR machines. The software accepts standard qPCR data output for generating results. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual sample over time – providing a temporal view for better understanding rejection or relapse kinetics. Conclusion Our reagents and software are compatible with qPCR platforms from multiple vendors. The software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores results. B. Luiken: Employee; Company/Organization; GenDx. J. Geerlings: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx. E. Rozemuller: Stock Shareholder; Company/Organization; GenDx, KimerDx. D. Bost: Employee; Company/Organization; KimerDx BV. 6. Stock Shareholder; Company/Organization; KimerDx BV.

Research paper thumbnail of LBP07

Research paper thumbnail of Prostatic Resection in Elderly Patients

Research paper thumbnail of OR04: A Multi-Center Study Using Next-Generation Sequencing (NGS) for Hla Genotyping

Aim NGS is well-suited for HLA typing as it can deliver highly accurate and unambiguous results. ... more Aim NGS is well-suited for HLA typing as it can deliver highly accurate and unambiguous results. A simplified protocol has been developed for use with the Illumina MiSeq and has been subjected to an inter-Methods: Six laboratories, each with varying levels of NGS experience, participated in this double-blinded study. The same 16 samples were typed at HLA-A, B, C, DRB1, and DQB1 by each lab. The protocol consisted of LR-PCR, library prep, and paired-end 250 bp sequencing. Two indexing strategies were employed: (1) Locus-specific indexing by which each locus was tagged uniquely and (2) sample-specific indexing whereby all 5 loci for a sample were pooled prior to library prep. Sequence analysis was performed with Target HLA (Omixon) and NGSengine (GenDx) to assess complementarity of two analysis algorithms. Results Six sequencing runs yielded an average output of 7.8 Gb per run. The average number of sequence reads per library was 387,813. However, analysis was limited to 40K reads for...

Research paper thumbnail of Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing

The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is ra... more The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information – message annotation, reference context, full genotype, consensus sequence and novel polymorphism – and references to three categories of accessory informat...

Research paper thumbnail of 157-P

Research paper thumbnail of 158-P

Research paper thumbnail of P097

Human Immunology, 2014

Aim Next-generation sequencing (NGS) technology has great potential for the future application of... more Aim Next-generation sequencing (NGS) technology has great potential for the future application of HLA typing in routine diagnostic purposes. NGS sequencing has the advantage that it allows the sequencing of single molecule DNA sequences, meaning that the paternal and maternal alleles can be uniquely identified. As NGS can phase single molecules throughout the gene, HLA typing by means of NGS will yield typing results without ambiguities. Currently, various NGS platforms are available on the market; each platform is based on different technology and each technology has their own specific requirements in order to make them compatible for HLA typing. It is our aim to develop multiple NGS workflows that are each compatible to a specific NGS platform, such as the Illumina MiSeq, the IonTorrent PGM, and the PacBio RS Sequencer. Method Here we present our latest developments on the IonTorrent PGM platform specific workflow, which is designed for the high-resolution typing of HLA loci. The new IonTorrent workflow for HLA typing includes several consecutive steps, from the most crucial step of whole HLA locus amplification to fragmentation, adaptor ligation, suppression PCR, clonal amplification by emulsion PCR, enrichment of positive ion sphere particles and sequencing on the IonTorrent PGM platform. Results We present the application of the IonTorrent workflow for 24 samples from standardized genomic DNA reference panels. GenDx adapters are developed and applied, enabling indexing of multiple samples. The NGS data is analyzed using the NGS platform-independent NGSengine® software, developed for NGS HLA sequence analysis (GenDx). Conclusion The availability of different NGS workflows allows the end-user to choose most preferred SBT-NGS HLA typing method that fulfills their laboratory application needs and requirements. This GenDx NGS workflow for the IonTorrent PGM presented here, is a powerful method to perform HLA typing by means of NGS in a reliable, accurate and high-throughput manner. L. Krol: Employee; Company/Organization; GenDx. J. Adema: Employee; Company/Organization; GenDx. R. Kooter: Employee; Company/Organization; GenDx. F. Ruzius: Employee; Company/Organization; GenDx. E.H. Rozemuller: Employee; Company/Organization; GenDx. Stock Shareholder; Company/Organization; GenDx. L. van de Pasch: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx.

Research paper thumbnail of OR04

Research paper thumbnail of P066

Human Immunology, 2014

In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monito... more In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis and laboratory workflow, we have created a new assay and software suite. Our chemistries were chosen to be compatible with all major qPCR platforms and our software can integrate with any of those machines. We utilize a panel of multiplexed qPCR research assays and software to comparatively genotype and quantify multiple samples on a single plate. The assays are designed and validated to detect INDEL variants between individuals. These differences are used to track individuals’ genomic material in chimeric mixtures. The software analyzes output from qPCR machines and presents unique marker choices in their genomic context, allowing for knowledgeable informative assay decision making and use in post-transplant monitoring. The software enables any number of combinations of samples to be genotyped, facilitating rapid multiple donor analyses. The results from the genotyping are stored by the software for recall during subsequent monitoring. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual over time - providing a temporal view for better understanding rejection or relapse kinetics. Our software allows for customized test set up, it performs all calculations necessary to execute the test, it generates a printable protocol to assist laboratory work and it generates sample set up files to import into qPCR machines. The software accepts standard qPCR data output for generating results. This assay system provides the highest probability of finding informative markers, as compared to other commercially-available qPCR systems. The tests and software are compatible with a variety of qPCR platforms. Our software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores and plots data. J. Adema: Employee; Company/Organization; GenDx. D. Roovers: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx. E. Rozemuller: Employee; Company/Organization; GenDx, KimerDx BV. Stock Shareholder; Company/Organization; GenDx, KimerDx BV. D. Bost: Employee; Company/Organization; KimerDx BV. Stock Shareholder; Company/Organization; KimerDx BV.

Research paper thumbnail of Clinical development of a muscarinic agonist: CI-979/RU 35926

Neurobiology of Aging, 1994

Research paper thumbnail of Characterization and distribution of Mhc-DPB1 alleles in chimpanzee and rhesus macaque populations

Human Immunology, Oct 31, 1998

Research paper thumbnail of High level of chromosome 15 aneuploidy in head and neck squamous cell carcinoma lesions identified by FISH analysis: limited value of beta2-microglobulin LOH analysis

Research paper thumbnail of Ambiguous DPB1 allele combinations resolved by direct sequencing of selectively amplified alleles

Tissue Antigens, Oct 1, 1995

Research paper thumbnail of Mutation in the �2m gene is not a frequent event in head and neck squamous cell carcinomas

Research paper thumbnail of Sequencing-based typing of MICA reveals 33 alleles: a study on linkage with classical HLA genes

Immunogenetics, Jul 1, 1999

Research paper thumbnail of SBTengine�, the ultimate HLA SBT typing software

Research paper thumbnail of TAP1 and TAP2 allele frequencies in a SNaPshot: No evidence for allelic prevalence in patients with head and neck squamous-cell carcinoma compared with Dutch controls

Research paper thumbnail of HLA-DQB1 sequencing-based typing updated

Tissue Antigen, 2007

The use of direct sequencing as a typing strategy is well acknowledged. Direct sequencing identif... more The use of direct sequencing as a typing strategy is well acknowledged. Direct sequencing identifies all sequence motifs including new polymorphisms in heterozygous sequences. The earlier protocols for human leukocyte antigen HLA-DQB1 Sequencing-Based Typing (SBT) frequently encounter preferential amplification of one of the alleles that can lead to unreliable sequences or even to allelic dropout. In our new approach, the quality of the exon 2 sequences, now including both alleles to the same extend, was achieved by amplifying the HLA-DQB1*05/06 group into two groups by changing the common 3' amplification primer. In combination with exon 3 this updated HLA-DQB1 protocol provides a reliable approach for heterozygous sequencing.

Research paper thumbnail of 1015-LBP: Novel software and reagents for qPCR-based transplant monitoring

Human Immunology, 2014

Aim In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant mo... more Aim In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis and laboratory workflow, we have created a new assay and software suite. Methods We utilize a panel of 42 multiplexed qPCR research assays and software to comparatively genotype multiple samples on a single plate. The software presents the unique marker choices in their genomic context, allowing for knowledgeable informative assay decision making and use in post-transplant monitoring. The software enables numbers of combinations of samples to be comparatively genotyped, facilitating rapid multiple donor analyses. The results from the genotyping are stored by the software for recall during subsequent monitoring. Our software facilitates post-transplant monitoring by: allowing operators to customize their plate configuration or work with lab-defined template, performing all calculations necessary to execute the test, generating a printable protocol to assist laboratory work and generating templates to import into the qPCR machines. The software accepts standard qPCR data output for generating results. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual over time – providing a temporal view for better understanding rejection or relapse kinetics. Results This assay system provides the highest probability of finding informative markers, as compared to other commercially-available qPCR systems. The tests and software are compatible with qPCR platforms from multiple vendors. Our software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores/plots data. Conclusions This new assay system provides the most automated and platform independent qPCR-based transplant monitoring research tool available to date.

Research paper thumbnail of Rapid microchimerism analysis using multiplexed reagents and novel software

Human Immunology, 2015

Aim To overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring meth... more Aim To overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis, KimerDx has developed a new assay and software suite. Method Our reagents employ a multiplexed panel of 30 qPCR research assays and software to genotype multiple samples on a single plate and identify informative markers. The software presents the marker choices in their genomic context, allowing for informed decision-making and use in post-transplant monitoring. The genotyping results are stored by the software for recall during subsequent monitoring. Results Our software facilitates post-transplant monitoring by: allowing operators to customize their plate configuration or work with a lab-defined template, performing all calculations necessary to execute the test, generating a printable protocol to assist laboratory work and by generating templates to import into the qPCR machines. The software accepts standard qPCR data output for generating results. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual sample over time – providing a temporal view for better understanding rejection or relapse kinetics. Conclusion Our reagents and software are compatible with qPCR platforms from multiple vendors. The software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores results. B. Luiken: Employee; Company/Organization; GenDx. J. Geerlings: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx. E. Rozemuller: Stock Shareholder; Company/Organization; GenDx, KimerDx. D. Bost: Employee; Company/Organization; KimerDx BV. 6. Stock Shareholder; Company/Organization; KimerDx BV.

Research paper thumbnail of LBP07

Research paper thumbnail of Prostatic Resection in Elderly Patients

Research paper thumbnail of OR04: A Multi-Center Study Using Next-Generation Sequencing (NGS) for Hla Genotyping

Aim NGS is well-suited for HLA typing as it can deliver highly accurate and unambiguous results. ... more Aim NGS is well-suited for HLA typing as it can deliver highly accurate and unambiguous results. A simplified protocol has been developed for use with the Illumina MiSeq and has been subjected to an inter-Methods: Six laboratories, each with varying levels of NGS experience, participated in this double-blinded study. The same 16 samples were typed at HLA-A, B, C, DRB1, and DQB1 by each lab. The protocol consisted of LR-PCR, library prep, and paired-end 250 bp sequencing. Two indexing strategies were employed: (1) Locus-specific indexing by which each locus was tagged uniquely and (2) sample-specific indexing whereby all 5 loci for a sample were pooled prior to library prep. Sequence analysis was performed with Target HLA (Omixon) and NGSengine (GenDx) to assess complementarity of two analysis algorithms. Results Six sequencing runs yielded an average output of 7.8 Gb per run. The average number of sequence reads per library was 387,813. However, analysis was limited to 40K reads for...

Research paper thumbnail of Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing

The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is ra... more The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information – message annotation, reference context, full genotype, consensus sequence and novel polymorphism – and references to three categories of accessory informat...

Research paper thumbnail of 157-P

Research paper thumbnail of 158-P

Research paper thumbnail of P097

Human Immunology, 2014

Aim Next-generation sequencing (NGS) technology has great potential for the future application of... more Aim Next-generation sequencing (NGS) technology has great potential for the future application of HLA typing in routine diagnostic purposes. NGS sequencing has the advantage that it allows the sequencing of single molecule DNA sequences, meaning that the paternal and maternal alleles can be uniquely identified. As NGS can phase single molecules throughout the gene, HLA typing by means of NGS will yield typing results without ambiguities. Currently, various NGS platforms are available on the market; each platform is based on different technology and each technology has their own specific requirements in order to make them compatible for HLA typing. It is our aim to develop multiple NGS workflows that are each compatible to a specific NGS platform, such as the Illumina MiSeq, the IonTorrent PGM, and the PacBio RS Sequencer. Method Here we present our latest developments on the IonTorrent PGM platform specific workflow, which is designed for the high-resolution typing of HLA loci. The new IonTorrent workflow for HLA typing includes several consecutive steps, from the most crucial step of whole HLA locus amplification to fragmentation, adaptor ligation, suppression PCR, clonal amplification by emulsion PCR, enrichment of positive ion sphere particles and sequencing on the IonTorrent PGM platform. Results We present the application of the IonTorrent workflow for 24 samples from standardized genomic DNA reference panels. GenDx adapters are developed and applied, enabling indexing of multiple samples. The NGS data is analyzed using the NGS platform-independent NGSengine® software, developed for NGS HLA sequence analysis (GenDx). Conclusion The availability of different NGS workflows allows the end-user to choose most preferred SBT-NGS HLA typing method that fulfills their laboratory application needs and requirements. This GenDx NGS workflow for the IonTorrent PGM presented here, is a powerful method to perform HLA typing by means of NGS in a reliable, accurate and high-throughput manner. L. Krol: Employee; Company/Organization; GenDx. J. Adema: Employee; Company/Organization; GenDx. R. Kooter: Employee; Company/Organization; GenDx. F. Ruzius: Employee; Company/Organization; GenDx. E.H. Rozemuller: Employee; Company/Organization; GenDx. Stock Shareholder; Company/Organization; GenDx. L. van de Pasch: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx.

Research paper thumbnail of OR04

Research paper thumbnail of P066

Human Immunology, 2014

In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monito... more In an effort to overcome the sensitivity and analysis shortcomings of STR-based transplant monitoring methods, and to improve upon the current state of the art in qPCR-based chimerism analysis and laboratory workflow, we have created a new assay and software suite. Our chemistries were chosen to be compatible with all major qPCR platforms and our software can integrate with any of those machines. We utilize a panel of multiplexed qPCR research assays and software to comparatively genotype and quantify multiple samples on a single plate. The assays are designed and validated to detect INDEL variants between individuals. These differences are used to track individuals’ genomic material in chimeric mixtures. The software analyzes output from qPCR machines and presents unique marker choices in their genomic context, allowing for knowledgeable informative assay decision making and use in post-transplant monitoring. The software enables any number of combinations of samples to be genotyped, facilitating rapid multiple donor analyses. The results from the genotyping are stored by the software for recall during subsequent monitoring. Reports from a monitoring test may be generated from a single time point or using the longitudinal data collected from the individual over time - providing a temporal view for better understanding rejection or relapse kinetics. Our software allows for customized test set up, it performs all calculations necessary to execute the test, it generates a printable protocol to assist laboratory work and it generates sample set up files to import into qPCR machines. The software accepts standard qPCR data output for generating results. This assay system provides the highest probability of finding informative markers, as compared to other commercially-available qPCR systems. The tests and software are compatible with a variety of qPCR platforms. Our software solution reduces manual calculations, increases flexibility in experimental execution, generates complete protocols for use in the lab and stores and plots data. J. Adema: Employee; Company/Organization; GenDx. D. Roovers: Employee; Company/Organization; GenDx. N. Westerink: Employee; Company/Organization; GenDx. E. Rozemuller: Employee; Company/Organization; GenDx, KimerDx BV. Stock Shareholder; Company/Organization; GenDx, KimerDx BV. D. Bost: Employee; Company/Organization; KimerDx BV. Stock Shareholder; Company/Organization; KimerDx BV.

Research paper thumbnail of Clinical development of a muscarinic agonist: CI-979/RU 35926

Neurobiology of Aging, 1994

Research paper thumbnail of Characterization and distribution of Mhc-DPB1 alleles in chimpanzee and rhesus macaque populations

Human Immunology, Oct 31, 1998

Research paper thumbnail of High level of chromosome 15 aneuploidy in head and neck squamous cell carcinoma lesions identified by FISH analysis: limited value of beta2-microglobulin LOH analysis

Research paper thumbnail of Ambiguous DPB1 allele combinations resolved by direct sequencing of selectively amplified alleles

Tissue Antigens, Oct 1, 1995

Research paper thumbnail of Mutation in the �2m gene is not a frequent event in head and neck squamous cell carcinomas

Research paper thumbnail of Sequencing-based typing of MICA reveals 33 alleles: a study on linkage with classical HLA genes

Immunogenetics, Jul 1, 1999

Research paper thumbnail of SBTengine�, the ultimate HLA SBT typing software

Research paper thumbnail of TAP1 and TAP2 allele frequencies in a SNaPshot: No evidence for allelic prevalence in patients with head and neck squamous-cell carcinoma compared with Dutch controls

Research paper thumbnail of HLA-DQB1 sequencing-based typing updated

Tissue Antigen, 2007

The use of direct sequencing as a typing strategy is well acknowledged. Direct sequencing identif... more The use of direct sequencing as a typing strategy is well acknowledged. Direct sequencing identifies all sequence motifs including new polymorphisms in heterozygous sequences. The earlier protocols for human leukocyte antigen HLA-DQB1 Sequencing-Based Typing (SBT) frequently encounter preferential amplification of one of the alleles that can lead to unreliable sequences or even to allelic dropout. In our new approach, the quality of the exon 2 sequences, now including both alleles to the same extend, was achieved by amplifying the HLA-DQB1*05/06 group into two groups by changing the common 3' amplification primer. In combination with exon 3 this updated HLA-DQB1 protocol provides a reliable approach for heterozygous sequencing.