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# www.baseclear.com

## Sitemaps
[XML Sitemap](https://www.baseclear.com/sitemap_index.xml): Includes all crawlable and indexable pages.

## Posts
- [Hello world!](https://www.baseclear.com/hello-world/): Welcome to WordPress. This is your first post. Edit or delete it, then start writing!

## Pages
- [Zymo Research](https://www.baseclear.com/about-us/zymo-research/): Zymo Research offers innovative products for epigenetics, DNA/RNA purification, and several other molecular biological lab products. All products can be characterized as simple and reliable products for DNA research.
- [Quality Assurance](https://www.baseclear.com/about-us/quality-assurance/): BaseClear places quality assurance at the core of its microbial genomics services, delivering reliable DNA research and analysis that helps customers improve products and processes, support regulatory approval, and substantiate product claims.
- [General terms & conditions](https://www.baseclear.com/terms-conditions/): 1.1 Except as otherwise apparent from the context, the words and expressions capitalized in these General Terms and Conditions are defined words and expressions, which have the meaning assigned to them below:
- [Privacy policy](https://www.baseclear.com/privacy-policy/): This privacy policy sets out how BaseClear BV (“BaseClear”) uses and protects any information that you may provide to us by the use of our website and/or our services. BaseClear is committed to ensuring that your privacy is protected in doing business with us.
- [Cookie statement](https://www.baseclear.com/cookie-statement/): We make use of cookies on this website. A cookie is a simple small file that is sent along with pages from this website and stored by your browser on your hard drive from your computer. The information stored therein can be sent back to our servers on a subsequent visit.
- [Technology](https://www.baseclear.com/technology/)
- [Team](https://www.baseclear.com/about-us/team/): Our Team Meet the team
- [Contact](https://www.baseclear.com/contact/): We strive to answer your questions promptly. Complete the form, and our team will get in touch shortly.
- [About us](https://www.baseclear.com/about-us/): For more than 30 years, BaseClear has helped organizations turn biological samples into reliable, actionable insights that accelerate research, product development, manufacturing, and regulatory decisions.
- [Home](https://www.baseclear.com/): BaseClear provides genomics and quality testing solutions. We support microbial, viral, and cell applications with scientifically rigorous, regulatory-ready services that help customers accelerate development and reduce risk. 
- [Technology platforms](https://www.baseclear.com/technology/platforms/): Explore the advanced sequencing, molecular biology, automation, and data management platforms that power BaseClear's high-quality analytical and genomics services. 
- [Advanced Sequencing Solutions](https://www.baseclear.com/technology/advanced-sequencing-solutions/): From fast-track sequencing to hybrid genomics and transcriptomics, BaseClear combines cutting-edge sequencing platforms, automated workflows, and expert data analysis to deliver high-quality results when speed and insight matter most. 

## Resources
- [Multi-Locus Sequence Typing – PubMLST](https://www.baseclear.com/resource/multi-locus-sequence-typing-pubmlst/): Official overview of MLST from PubMLST, explaining the method, housekeeping genes, allele assignment, and sequence type (ST) definition.
- [MLST revisited: the gene-by-gene approach to bacterial genomics](https://www.baseclear.com/resource/mlst-revisited-the-gene-by-gene-approach-to-bacterial-genomics/): Scientific review discussing MLST in the context of modern bacterial genomics, including its role in bacterial typing and how it relates to gene-by-gene approaches and whole genome sequencing.
- [A Fast, Accurate, and Automated Workflow for Multi Locus Sequence Typing of Bacterial Isolates](https://www.baseclear.com/resource/a-fast-accurate-and-automated-workflow-for-multi-locus-sequence-typing-of-bacterial-isolates/): Application note showing MLST as a sequence-based typing method and highlighting faster, automated allele matching and sequence type assignment.
- [European Pharmacopoeia Commission. European Pharmacopoeia, tenth edition Volume 1 194-199 (EDQM, Straatsburg, July 2019)](https://www.baseclear.com/resource/european-pharmacopoeia-commission-european-pharmacopoeia-tenth-edition-volume-1-194-199-edqm-straatsburg-july-2019/): A guide to EP and global regulatory expectations for mycoplasma testing.
- [The scope of mycoplasma contamination within the biopharmaceutical industry](https://www.baseclear.com/resource/the-scope-of-mycoplasma-contamination-within-the-biopharmaceutical-industry/): Large-scale study evaluating more than 40,000 samples to assess the prevalence of mycoplasma contamination in cell cultures and biological products used in the biopharmaceutical industry.
- [Prevention and Detection of Mycoplasma Contamination in Cell Culture](https://www.baseclear.com/resource/prevention-and-detection-of-mycoplasma-contamination-in-cell-culture/): Scientific review describing the impact of mycoplasma contamination on cell physiology and metabolism, and outlining best practices for detection, prevention, and elimination in cell culture laboratories.
- [Cell line authentication: a necessity for reproducible biomedical research](https://www.baseclear.com/resource/biological-identifications-through-dna-barcodes/): Learn how cell line misidentification affects research reproducibility and why authentication is critical for reliable results.
- [Species identification in cell culture: a two-pronged molecular approach](https://www.baseclear.com/resource/species-identification-in-cell-culture-a-two-pronged-molecular-approach/): Peer-reviewed study demonstrating the use of mitochondrial DNA barcoding and COI sequencing to accurately identify cell line species and detect cross-contamination in cell culture systems.
- [Biological identifications through DNA barcodes](https://www.baseclear.com/resource/cell-line-authentication-a-necessity-for-reproducible-biomedical-research/): Landmark scientific paper introducing DNA barcoding and demonstrating how sequencing the mitochondrial cytochrome c oxidase I (COI) gene enables reliable species identification across animal taxa.
- [Resource 18](https://www.baseclear.com/resource/resource-18/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.
- [Resource 17](https://www.baseclear.com/resource/resource-17/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 16](https://www.baseclear.com/resource/resource-16/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 15](https://www.baseclear.com/resource/resource-15/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.
- [Resource 13](https://www.baseclear.com/resource/resource-13/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 14](https://www.baseclear.com/resource/resource-14/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 12](https://www.baseclear.com/resource/resource-12/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.
- [Resource 11](https://www.baseclear.com/resource/resource-11/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 10](https://www.baseclear.com/resource/resource-10/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 9](https://www.baseclear.com/resource/resource-9/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 8](https://www.baseclear.com/resource/resource-8/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 7](https://www.baseclear.com/resource/resource-7/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.
- [Resource 4](https://www.baseclear.com/resource/resource-4/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.
- [Resource 5](https://www.baseclear.com/resource/resource-5/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 6](https://www.baseclear.com/resource/resource-6/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 3](https://www.baseclear.com/resource/resource-3/): Discover trusted medical genome references that help clinicians and researchers interpret complex genetic data with confidence.
- [Resource 2](https://www.baseclear.com/resource/resource-2/): Access up-to-date genomic insights, variant databases, and medical research tools for advanced healthcare analysis.
- [Resource 1](https://www.baseclear.com/resource/resource-1/): Explore clinically curated genome resources designed to support precision diagnostics, research workflows, and personalized treatment decisions.

## Services
- [Culturomics](https://www.baseclear.com/services/food-feed-ingredients/strain-discovery/culturomics/): Combine metagenomics, culturomics, and whole genome sequencing to discover, isolate, and characterize targeted microbial strains with unique functional potential.
- [Ultima High Throughput Sequencing](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/ultima-high-throughput-sequencing/): Generate population-scale genomic data at unprecedented scale and cost efficiency through fully automated Ultima Genomics workflows and integrated sample-to-data tracking.
- [GMP-Compliant Phage DNA Sequencing](https://www.baseclear.com/services/biopharma/gmp-solutions/gmp-compliant-phage-dna-sequencing/): A flexible, end-to-end phage DNA sequencing service combining advanced NGS technology with phase-appropriate or full GMP compliance. Designed to support phage therapy development, it delivers reliable identity and purity data alongside validated workflows and documentation suitable for regulatory use.
- [GMP assay development and validation services](https://www.baseclear.com/services/biopharma/gmp-assay-development-and-validation-services/): Customer-requested, custom assay development and validation with a systematic, science- and risk-based approach to developing analytical methods that are fit for purpose and robust across the product lifecycle (Analytical Quality by Design; AQbD) in a GMP-environment
- [Competitive Product Genomics](https://www.baseclear.com/services/food-feed-ingredients/strain-discovery/competitive-product-genomics/): Gain actionable competitive intelligence by identifying the microorganisms, genetic signatures, and enzyme-producing strains present in commercial products through advanced genomics.
- [Strain Discovery](https://www.baseclear.com/services/food-feed-ingredients/strain-discovery/): Tailored culturomics with environmental sourcing and genome mining to uncover novel strains and their valuable functions.
- [Sterility Testing](https://www.baseclear.com/services/food-feed-ingredients/sterility-testing/): Analysis of microbial communities in clinical and environmental samples
- [Food Safety panel](https://www.baseclear.com/services/food-feed-ingredients/sterility-testing/food-safety-panel/): BaseClear's Food Safety Digital PCR Panel provides precise, rapid detection of foodborne pathogens, ensuring enhanced safety and compliance for the food industry with reliable, high-quality results.  
- [Viral contamination, Bovine and Porcine cells (according to 9 CFR 113.47) ​](https://www.baseclear.com/services/food-feed-ingredients/sterility-testing/viral-contamination-bovine-and-porcine-cells-according-to-9-cfr-11347/): BaseClear’s Viral Contamination Panel for Bovine and Porcine Cells (according to 9 CFR 113.47) uses digital PCR technology to provide highly sensitive, accurate, and regulatory-compliant detection of viral contamination, offering a rapid and robust alternative to traditional antibody-based methods for cell line validation. 
- [Food, Feed & Ingredients](https://www.baseclear.com/services/food-feed-ingredients/): From strain discovery and microbiome research to regulatory safety assessment, BaseClear provides food, feed, and ingredient companies with the genomic insights and scientific evidence needed to develop, validate, and commercialize innovative products with confidence.
- [Clinical Microbiomics](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/clinical-microbiomics/): GxP-aligned and GCP-supportive fecal sample microbiome sequencing for clinical trials, cohort studies, probiotic studies, and regulated microbiome research. 
- [Microbiome-Friendly Assessment ](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/microbiome-friendly-assessment/): Demonstrate microbiome friendliness with science-based microbiome analysis that provides clear evidence of how your product affects microbial diversity, composition, and ecosystem stability. 
- [Key Microbial Biomarker Detection](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/key-microbial-biomarker-detection/): Identify health- and disease-associated microbial signatures and actionable biomarkers using advanced bioinformatics, machine learning, and microbiome data analysis. 
- [Taxonomic Profiling Using Amplicon & Metagenomics Sequencing](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/taxonomic-profiling-amplicon-metagenomics/): Taxonomic Profiling is a microbiome analysis service that provides the identities and relative abundances of the microorganisms present in a sample.
- [RNA-Seq Analysis](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/rna-seq-analysis/): Generate high-quality gene expression insights using Illumina-based RNA-Seq analysis, advanced bioinformatics pipelines, and differential expression analysis for bacterial and eukaryotic samples. 
- [Functional Metagenomics Analysis](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/functional-metagenomics-analysis/): Identify the functional potential of microbial communities through advanced metagenome assembly, gene annotation, pathway analysis, and microbiome-wide statistical modeling. 
- [Regulatory Strategy & Dossier Development](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/regulatory-strategy-dossier-development/): Transform complex regulatory requirements into a clear, science-driven roadmap with integrated testing, regulatory strategy, and dossier development services designed to accelerate global market approval.
- [Project Sequencing GMP (Sanger sequencing services)](https://www.baseclear.com/services/biopharma/gmp-solutions/project-sequencing-gmp-sanger-sequencing-services/): From GMP-compliant project sequencing to fast and flexible single-run services, delivering reliable DNA sequence data tailored to your needs.
- [Mycoplasma Detection (EP 10.1 and GMP Compliant)](https://www.baseclear.com/services/biopharma/gmp-solutions/mycoplasma-detection-ep-10-1-and-gmp-compliant/): Rapid, sensitive mycoplasma detection for cell therapies, biologics, and biomanufacturing workflows, fully aligned with GMP and European Pharmacopoeia requirements (EP 10.1 chapter 2.6.7 Mycoplasmas).
- [Microbial identification using MicroSEQ® Sequencing](https://www.baseclear.com/services/biopharma/gmp-solutions/microbial-identification-using-microseq-sequencing/): Accurate and rapid bacterial and fungal identification using validated MicroSEQ® sequencing workflows and curated reference database.
- [Microbial identification using Maldi-TOF Vitek MS](https://www.baseclear.com/services/biopharma/gmp-solutions/microbial-identification-using-maldi-tof-vitek-ms/): Rapid and cost effective bacterial and yeast identification using Maldi-TOF mass spectrometry and validated VITEK®MS database workflow.
- [ISO&GMP-compliant Bacterial Whole Genome Sequencing](https://www.baseclear.com/services/biopharma/gmp-solutions/isogmp-compliant-bacterial-whole-genome-sequencing/): Illumina Whole Genome Sequencing of pure bacterial strains under ISO&GMP compliance, including variant calling against the strain’s reference genome.
- [Viral Variant Detection Analysis GMP Compliant](https://www.baseclear.com/services/biopharma/gmp-solutions/viral-variant-detection-analysis-gmp-compliant/): Identify and characterize viral genomic variants using a validated Illumina-based workflow optimized for sensitive and accurate SNP, insertion and deletion detection.
- [Adventitious Virus Testing](https://www.baseclear.com/services/biopharma/gmp-solutions/adventitious-virus-testing/): Adventitious virus testing using next‑generation sequencing provides sensitive, untargeted detection of DNA and RNA viral contaminants to strengthen risk assessment and ensure the safety of gene therapy and other biologic products.
- [Cell Line and Cell Bank Characterization Using Whole Genome Sequencing](https://www.baseclear.com/services/biopharma/gmp-solutions/cell-line-and-cell-bank-characterization-using-whole-genome-sequencing/): Characterize transgenic cell lines and cell banks with whole genome sequencing to verify genetic modifications, map integration sites, assess genetic stability, and identify genomic variants using state-of-the-art long-read and short-read sequencing technologies.
- [Quantitative Residual Host Cell DNA testing](https://www.baseclear.com/services/biopharma/gmp-solutions/quantitative-residual-host-cell-dna-testing/): Quantitation of residual host cell DNA levels using digital PCR technology to determine the host cell impurities in target samples (in-process, final product, etc.), supporting the risk assessment and regulatory compliance of biological products.
- [GMP Cell Line Species Identification via COI Sequencing](https://www.baseclear.com/services/biopharma/gmp-solutions/gmp-cell-line-species-identification-via-coi-sequencing/): Confirm the species origin of your cell lines using mitochondrial COI gene sequencing and validated DNA analysis workflows suitable for research and regulated biopharmaceutical environments. 
- [Custom qPCR assay development for complex biological matrices](https://www.baseclear.com/services/biopharma/gmp-solutions/custom-qpcr-assay-development-for-complex-biological-matrices/): We develop and optimize client-specific qPCR assays for challenging matrices in regulated and research environments, from cell & gene therapy to microbial and industrial applications.
- [Biopharma](https://www.baseclear.com/services/biopharma/): BaseClear combines advanced genomics, GMP-compliant services, and deep scientific expertise to help biopharma companies develop, characterize, and release products with confidence.
- [Multi-Locus Sequence Typing (MLST) Services](https://www.baseclear.com/services/food-feed-ingredients/sterility-testing/multi-locus-sequence-typing-mlst-services/): High-resolution, reproducible MLST analysis for bacterial strain typing across research, clinical, and industrial applications, using standardized and validated workflows. 
- [In Vitro Cytotoxicity Testing for Microbial Toxigenicity Assessment](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/in-vitro-cytotoxicity-testing-for-microbial-toxigenicity-assessment-2/): Assess the toxigenic potential of microbial strains through EFSA-aligned cytotoxicity testing, supporting regulatory safety evaluation.
- [GMP Solutions](https://www.baseclear.com/services/biopharma/gmp-solutions/): BaseClear combines GMP-compliant laboratory workflows, advanced genomics technologies, and dedicated scientific support to deliver reliable, regulatory-ready data for biopharmaceutical applications.
- [Microbiome Research](https://www.baseclear.com/services/food-feed-ingredients/microbiome-research/): Analysis of microbial communities in clinical and environmental samples.
- [Assessment of the Presence of DNA in Final Products](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/assessment-of-the-presence-of-dna-in-final-products/): Detect residual DNA from production organisms using sensitive, regulatory-aligned molecular methods.
- [Assessment of the Presence of Viable Cells in Microbial Products](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/assessment-of-the-presence-of-viable-cells-in-microbial-products/): Evaluate the presence of viable production organisms in your final product using regulatory-aligned microbiological methods.
- [Antimicrobial production Testing for Microbial Safety](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/antimicrobial-production-testing-for-microbial-safety/): Evaluate antimicrobial compound production to support regulatory safety assessment of microbial strains.
- [MIC Testing for Antimicrobial Resistance Assessment](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/mic-testing-for-antimicrobial-resistance-assessment/): Regulatory-aligned MIC testing and AMR interpretation for microbial safety assessment
- [Whole Genome Sequencing for Microbial Safety Assessment](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/whole-genome-sequencing-for-microbial-safety-assessment/): Regulatory-ready genomic characterization of microbial strains for EFSA, FDA, and global submissions.
- [Microbial Safety Assessment & Regulatory Services](https://www.baseclear.com/services/food-feed-ingredients/microbial-safety-assessment-regulatory/): Integrated strain, functional, and product-level safety assessment to support global regulatory approval.

## Team Members
- [Roel Sterken, PhD](https://www.baseclear.com/team-member/roel-sterken/)
- [Rick Kerr](https://www.baseclear.com/team-member/rick-kerr/)
- [Gert Jan van den Dungen](https://www.baseclear.com/team-member/gert-jan-van-den-dungen/)
- [Almira van den Heuvel](https://www.baseclear.com/team-member/almira-van-den-heuvel/)
- [Ruud Overbeek](https://www.baseclear.com/team-member/ruud-overbeek/)
- [Almira Gordijn](https://www.baseclear.com/team-member/almira-gordijn/)
- [Pascal Bus, PhD](https://www.baseclear.com/team-member/pascal-bus/)
- [Matthijs de Koning](https://www.baseclear.com/team-member/matthijs-de-koning/)
- [Eline Klaassens, PhD](https://www.baseclear.com/team-member/eline-klaassens/)
- [Hua Zhu, PhD](https://www.baseclear.com/team-member/hua-zhu/)
- [Diana Hanekamp, PhD](https://www.baseclear.com/team-member/diana-hanekamp/)
- [Jaitip Tipanee, PhD](https://www.baseclear.com/team-member/jaitip-tipanee/)
- [Merel Damen, PhD](https://www.baseclear.com/team-member/merel-damen/)
- [Dominika Viola-Durechova, PhD](https://www.baseclear.com/team-member/dominika-viola-durechova/)
- [Sander Mulders](https://www.baseclear.com/team-member/sander-mulders/)
- [Nathaly Lizet Lopez Garreaud](https://www.baseclear.com/team-member/nathaly-lizet-lopez-garreaud/)
- [Wouter Veneman, PhD](https://www.baseclear.com/team-member/wouter-veneman/)
- [Vlad Shtefaniuk](https://www.baseclear.com/team-member/vlad-shtefaniuk/)
- [Alex Kirov, PhD](https://www.baseclear.com/team-member/alex-kirov/)
- [Andre Nascimento](https://www.baseclear.com/team-member/andre-nascimento/)
- [Maurits Horwitz](https://www.baseclear.com/team-member/maurits-horwitz/)