Analyze it

Sample Analysis & Discovery

At Sampled, we specialize in providing customized laboratory and scientific services for clients in the public and private research sectors. From traditional qPCR-based detection platforms to high-throughput microarrays, our automated processing systems allow for fast and accurate analysis of both human and animal samples. We also provide next-generation DNA gene sequencing services that can be optimized and scaled for virtually any organism or sample size from DNA samples.

Just some of our areas of expertise include (but not limited to):

• Genomics
• Epigenomics
• Virology
• Neurology
• Oncology
• Informatics (Bioinformatics)

Genomic Services

Genome analysis, whether it be in human, animal or a variety of organisms, whole genome, exome, or custom gene panel sequencing provides access to genomic information, discovery and translational (Clinical and Research) results to support a number of studies and products. These include, biomarker discovery, metagenomics applications, and within the healthcare setting, both hereditary and acquired disease/disorder discovery and treatment options.

Genotyping is the process of identifying and investigating genetic variants in an individual by sequencing their DNA and comparing it to that of another individual or a reference sequence. Minor genetic differences can have dramatic impacts on an individual’s phenotype, from basic physical attributes to pathological changes associated with disease.

To support genomic advances in the medical and general research fields, Sampled offers pre-validated and custom genomic sequencing services and custom genotyping panels capable of analyzing hundreds or thousands of samples for specific targets as well as whole-genome studies. We also offer low-, medium-, and high-throughput gene sequencing and gene expression profiling and gene copy number analysis.

10x Genomics Certified Service Provider

We are proud to be a certified service provider for 10x Genomics and able to provide our clients with access to innovative solutions for single cell assays for Transcriptomics.

The 10x Genomics CSP program is only open to organizations who meet a high standard of technical and service requirements and are annually reviewed for each chosen application, which can include one or more of the Chromium Solutions:

• Single Cell Gene Expression
• Immune Profiling
• Genome
• Exome

Capabilities

Bioprocessing and biosample preparation, extraction, and analysis services include:

• Fully automated solutions for:
  • DNA extraction
  • Liquid-handling during PCR reaction setup
  • Genotype calling and performance metrics
  • Microarray sample processing and array development
  • Library preparation for Next Generation Sequencing (NGS)
• Integrated sample and data QC
• Various chemistries available, including TaqMan®, SNPtype™, and somatic mutation
• Custom functional assay designs and catalog array setups for BioMark™ systems
• Array design and validation for:
  • TaqMan®
  • SmartChip
  • BioMark™
• Custom assay panels for:
  • Seqstudio Illumina based Short-Long Read NextGensequencing
  • Pacbio Sequel II Long Read Sequencing

These services include assay design and wet-bench validation as well as genotyping reports at no additional cost.

Technologies

Our PCR, qPCR, DNA microarray, NGS, gene expression profiling, and copy number analysis capabilities are supported by the following high quality sequencing technologies:

• ABI 7900HT rapid real-time PCR system with 96- and 384-well compatibility and robotic loading for high-throughput analyses
• ViiATM 7 high-performance instrument for high-productivity real-time PCR processing
• ABI QuantStudio 5 for PCR-based gene expression analysis
• GeneChip and GeneTitan systems for Affymetrix genotyping products
• Illumina iScan and MiSeq systems for Illumina genotyping products
• Illumina short read sequencing: Miseq, NextSeq, Novaseq
• Pacbio Sequencer Sequel II Long Read Sequencing
• SeqStudio for targeted sequencing applications

Epigenomics

Epigenetics is the study of heritable changes in gene function or phenotype that are not attributable to DNA sequence alterations. In the medical research field, human epigenome studies are important for understanding how environmental or behavioral factors influence an individual’s genetic susceptibility to disease.

Applications of epigenetic research include:

• Characterizing the mechanisms of complex diseases such as cancer, heart disease, and diabetes
• Identifying disease-relevant regulatory elements
• Evaluating the biological role of DNA methylation in diseases

Capabilities

At Sampled, our advanced microarray and NGS platforms allow for rapid identification of epigenetic events across entire genomes. Specific services we provide include:

• Bisulfite treatment (qPCR): Bisulfite DNA treatments convert cytosine residues to uracil while leaving 5-methylcytosine residues intact. The methylation status of the treated DNA segment can then be assessed using methylation-specific qPCR or direct sequencing.
• Methylation microarrays: Medium- and high-throughput Illumina Infinium methylation arrays allow methylation sites to be interrogated at the single-CpG-site level.
• Tiling arrays: Affymetrix GeneChip Tiling arrays enable the discovery of novel transcripts and provide site mapping of protein-DNA interactions across entire genomes.
• ChIP-seq: Chromatin immunoprecipitation sequencing (ChIP-seq) of chromatin immunoprecipitated DNA enables rapid identification of DNA binding sites for transcription factors and other DNA-binding proteins involved in gene expression mediation.
• Methyl-seq: Methylation sequencing (Methyl-seq) is a fast and economical method for detecting methylation patterns and revealing epigenetic modifications across whole genomes or within specific genomic regions.
• Long Read Seq: Metagenomics studies, full-length transcripts sequencing, and genome-wide DNA modification analysis can detect epigenetic modifications across a number of applications and provide sequence data.

Technologies

Our epigenomic tools include:

• Affymetrix GeneChip® and GeneTitan® systems for high-throughput genotyping and gene expression analyses
• Illumina MiSeq, NextSeq500, and NovaSeq 6000 platforms, allowing for parallel sequencing of large sample sets
• Pacific Biosciences (PacBio) SMRT instruments (PacBio Sequel) for several research purposes including whole-genome de novo genome assembly, full-length target sequencing, metagenomics studies, full-length transcripts sequencing, and genome-wide DNA modification analysis.

Covid

Sampled contributes to ongoing COVID-19 response efforts with fast and reliable testing and processing services. Our capabilities in this area include:

Saliva Tests

We offer saliva-based COVID-19 diagnostic testing services to organizations with large-volume or ongoing COVID-19 testing needs. Benefits of our FDA/EUA-authorized¹, unsupervised saliva collection test includes:

• Low-risk, contactless sample collection
• Reduced invasiveness compared with nasal and throat swabs
• Test availability not affected by swab shortages
• Unsupervised sample collection (e.g., at home) to accommodate sick, quarantined, or high-risk patients
• Results in 24-48 hours
• High consistency with over 11,000,000 tests performed
• Virus-inactivating buffer to reduce risk of spread during sample handling
• High-accuracy PCR-based methods with multi-gene detection capabilities

Our innovative and high-throughput COVID-19 testing services allow us to process up to 100,000 saliva samples a day. This involves optimized workflows and procedures for:

• Receipt and accession
• Aliquoting
• RNA / Nucleic Acids extraction
• Sample preparation
• qPCR analysis and NGS
• Reporting of results
• -80C sample storage
• Sequencing for strain determination

Neurology

In recent years, researchers have identified several genes that influence an individual’s likelihood of developing early- or late-onset neurological disorders.  These biomarker discoveries have led to many new disorder discoveries, but also interrogate will knowns disease such as Alzheimer’s disease. Using this data, Sampled designed and developed within its laboratory the first physician-use polygenic Alzheimer’s Risk test that detects both risk-associated and protective genes related to Alzheimer’s disease development. This information can subsequently be used by a physician to guide the patient’s lifestyle choices, allowing them to take proactive steps toward improving their health and potentially preventing or delaying symptoms. The physician and patient can also discuss potential drug therapy options aimed at minimizing cognitive and functional decline if symptoms become present. 

Launched in the US in October 2021, our test includes the following features:

• Assessment of over 100,000 genetic variations associated with Alzheimer’s disease
• Easy-to-use testing procedure requiring a mouth swab or blood sample
• Unsupervised sample collection (e.g., home setting) available for elderly or vulnerable patients

Our Alzheimer’s Risk test can only be ordered by a physician, and patients are required to pay for the tests directly or through the physician. Once the test has been ordered, the testing process involves the following steps:

1. Mouth swab or blood sample is collected
2. Sample is returned to the processing laboratory
3. Results are sent to the physician to discuss with the patient

We also offer a number of Poly Genic Risk Assessments for a number of conditions such as Cancer, Autoimmunity and Virology using various genotyping methods, array, qpcr and NGS

Informatics (Bioinformatics)

Bioinformatics is a field of computational science focused on developing methods and software for acquiring, storing, analyzing, and distributing biological data, usually in the form of DNA, RNA, or protein sequences. In the medical field, bioinformatics is often used for:

• Discovering and characterizing new drugs
• Supporting research in preventative medicine, personalized medicine, and gene therapy
• Exploring genetic mechanisms of disease
• Identifying population-based disease patterns
• Analyzing and interpreting clinical or preclinical test results

Sampled maintains one of the world’s largest biorepositories and leads the research field in biobanking, bioprocessing, and analytics. Our bioinformatics services support the research community in analyzing, interpreting, and storing large sets of biological data for various medical and research purposes. Specific areas of support include:

• Maintaining the integrity of biosamples over time
• Helping researchers give context to large-scale, complex data sets
• Allowing data to be analyzed and interpreted in a biologically meaningful way
• Allowing existing data sets to be easily accessed and reused as needed