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White Papers and Videos

OEM by Qiagen Advancing with Asian Molecular Diagnostic Companies

White Paper

In this interview excerpt from Qiagen, Vice President and Head of OEM Kay Koerner discusses the volatility that molecular diagnostics manufacturers faced with their supply chain during the COVID-19 pandemic, how the pandemic affected the OEM business, developing trends in life sciences, and how the diagnostics market is evolving in the APAC region.

Using Whole-Exome Sequencing to Guide Clinical Trial Enrollment for Patients with Cancer

White Paper

Advances in precision medicine are not currently available to all patients, especially those being treated in community cancer settings. This growing gap is challenging community health­care systems to provide cost-effective, scalable, and innovative solutions for underserved patients.

This case study from Qiagen discusses how Protean BioDiagnostics partnered with Qiagen Digital Insights to develop a proprietary, multiomic, datacentric diagnostic guidance system to deploy whole-exome sequencing into clinical practice and give oncologists and practitioners access to the latest evidence-based diagnostics, therapeutics, and new clinical trials.

Manual Curation vs. Artificial Intelligence: Can Automated Variant Evidence Retrieval Replace Human Judgment?

White Paper

This white paper from Qiagen examines evidence comparing the quality of Stanford University’s Automatic Variant evidence Database (AVADA) to the manually curated Human Gene Mutation Database (HGMD) for variant annotation in clinical genomics.

CRISPRclean Stranded Total RNA Prep with rRNA Depletion

White Paper

A challenge of RNA sequencing is to efficiently eliminate abundant or uninformative sequences, such as ribosomal RNA (rRNA), to shift discovery to the lower expressing and biologically interesting transcripts. CRISPRclean Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat) uses CRISPR-based depletion with stranded RNA library preparation to specifically remove human, mouse, and rat rRNA sequences from adapter-ligated cDNA libraries. CRISPRclean Stranded Total RNA Prep with rRNA Depletion reassigns sequencing reads from abundant molecules to higher value and lower expressing transcripts in an unbiased manner without disturbing the relative transcript abundance or complexity of the library.

This white paper from Jumpcode Genomics describes an experiment that used this CRISPR-powered rRNA depletion strategy to deplete mammalian rRNA in tissue samples, improving sensitivity for the detection of lower expressing transcripts.

CRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion

White Paper

The unbiased nature of shotgun metagenomic and metatranscriptomic sequencing can be used to discover and analyze organisms co-existing in diverse biological systems, for example in wastewater surveillance, to profile viral genetic diversity across infected communities. However, much of the transcriptomic data captured in metatranscriptomic samples is uninformative, due to the abundance of ribosomal RNA (rRNA) that interferes with the efficient identification of biologically significant transcripts.

This white paper from Jumpcode Genomics describes an experiment that used a CRISPR-powered ribosomal RNA depletion strategy to improve metatranscriptomic sequencing of nasopharyngeal samples from COVID-19-positive patients.

Detection of Low-Abundance Serum Proteins Associated with Prediabetes for Predictive and Prognostic Purposes

White Paper

Methods to precisely diagnose prediabetes and diabetes by identifying associated biomarkers have been proposed to prevent or delay advanced stages of the disease; however, currently known biomarkers like the glycated proteins hemoglobin (HbA1c) and albumin are limited by poor sensitivity of detection and inaccuracy under certain clinical contexts. Additionally, the American Diabetes Association and the World Health Organization differ in their recommended healthy thresholds for fasting plasma glucose concentrations and HbA1c testing requirements. As such, there is mounting interest in identifying multiple biomarkers during the prediabetic or early diabetic stage to predict and prevent full-blown diabetic onset. 

This white paper from SomaLogic describes a need for additional biomarkers to predict the risk of developing type 2 diabetes mellitus and the application of the SomaScan Proteomic Platform to identify serum proteins associated with diabetic risk and outcome.

Detection of Low-Abundance Serum Proteins Associated with Cardiovascular Diseases for Prognostic Purposes

White Paper

Classic risk factors associated with cardiovascular disease include conditions like hypertension, hyperlipidemia, and diabetes, yet many individuals with cardiovascular disease do not present with any of the classic risk factors. There are, therefore, limitations to using risk factors alone as prognostic tools for cardiovascular disease. There is thus a need to identify biomarkers that complement existing clinically relevant indicators.

This white paper from SomaLogic describes how circulating protein biomarkers may offer a reliable tool to predict cardiovascular disease prognosis and describes how the SomaScan Proteomic Platform can identify low-abundance proteins associated with cardiovascular disease risk.

Serum Protein Signatures as a Non-Invasive Tool for Monitoring Nonalcoholic Steatohepatitis

White Paper

Nonalcoholic fatty liver disease (NAFLD) is a liver condition that affects up to 25 percent of the global population. Nonalcoholic steatohepatitis (NASH) refers to an aggressive form of NAFLD that is predicted to rise exponentially through the year 2030. Diagnosing the severity of NAFLD and NASH heavily relies on liver biopsy. Non-invasive techniques for NAFLD diagnosis and prognosis include imaging and measuring the enzymes alanine aminotransferase (ALT) and aspartate aminotransferase (AST). However, ALT and AST measurements are not sufficiently sensitive or specific, and non-invasive imaging modalities are not accurate or precise enough to differentiate between stages of steatosis or fibrosis.

This white paper from SomaLogic describes the potential of using proteomic signatures to improve non-invasive diagnosis and monitoring of liver pathology, and the potential of the SomaScan Proteomic Platform to identify such signatures.

Get the Most out of Seraseq Reproductive Health Reference Materials

White Paper

This application note from LGC SeraCare demonstrates how to use Seraseq Reproductive Health Reference Materials in pre-implantation genetic testing for aneuploidies (PGT-A) and non-invasive prenatal testing (NIPT) to compare methods, compare workflows, and train staff.

Development of a Novel Reference Material for Minimal Residual Disease Monitoring Assays

White Paper

ctDNA-based assays allow for the detection of minimal residual disease (MRD) earlier than standard clinical and imaging surveillance and could allow for treatment modification based on real-time assessment of the tumor genomic landscape. However, many challenges remain, as the analytical validation of liquid biopsy-based MRD assays requires reference materials allowing for the assessment of sensitivity and specificity at variant allele frequencies (VAFs) that can be over an order of magnitude below the typical limit of detection of standard ctDNA assays. At such low VAFs, there may be, on average, less than one copy of a somatic variant in a sample being analyzed out of billions of ctDNA fragments in a blood draw. This problem is why many MRD approaches use whole-exome sequencing data from patient tumors to design tumor-informed, personalized assays that target multiple patient-specific somatic variants, which reduces the amount of sequencing required to survey MRD while allowing the sequencing depth around the targeted variants to reach a level that is sufficient for high sensitivity and specificity.

This white paper from LGC SeraCare describes the creation of a reference material combining a tumor-derived component with a sufficiently large number of somatic mutations to accommodate the development, validation, and clinical deployment of custom, tumor-informed, ctDNA-based MRD monitoring assays.

New CentoXome: Turning Our Expertise into Your Advantage

Video

In this on-demand webinar from Centogene, Aida M. Bertoli-Avella, head of research data analysis, and Jorge Pinto Basto, senior medical director at Centogene, outline the main challenges of rare disease diagnostics, highlight the features of the New CentoXome whole-exome sequencing test, and describe successes of the test in clinical cases.

Unraveling a Clinically Relevant Uniparental Disomy with NEW CentoXome

White Paper

This white paper from Centogene presents a case study in which a physician employed the New CentoXome whole-exome sequencing test to diagnose osteopetrosis type 4 caused by uniparental disomy in a 6-month-old patient.

ARUP Laboratories Reduces Turnaround Time on Panel Analysis by 30 Percent with GenomOncology

White Paper

The GenomOncology (GO) Precision Oncology API Suite extends the knowledge of GenomOncology’s Precision Oncology Platform by integrating directly with in-house systems and workflows, providing users an extensive database of annotations and treatment options that can be utilized to enhance patient care. The GO Precision Oncology API Suite is utilized at numerous institutions across the United States, including the CAP-, ISO 15189-, and CLIA-certified diagnostic lab, ARUP Laboratories (ARUP).

Interested in learning more about how ARUP utilizes GenomOncology’s precision oncology solutions? Then read our latest case study to gain insight into how:

  • ARUP selected and implemented the GO Precision Oncology API Suite in 2019 due to the depth of annotation sources within the solution, its overall flexibility, and its ability to be easily integrated into ARUP’s current workflows and processes. 
  • ARUP reduced its turnaround time on panel analysis and variant annotation by nearly 30%, enabling its Clinical Variant Scientist team to analyze more cases and spend less time documenting variant classification information. 
  • ARUP has chosen to extend its use of the GO Precision Oncology Suite by integrating the GO Clinical Trial and Therapy Matching APIs into its current workflows to strengthen its patient care offerings.

The Benefits of PGT-A, PGT-M, and Expanded Carrier Screening in IVF Research

Video

In this webinar from Thermo Fisher Scientific, Murat Çetinkaya and Volkan Baltaci discuss the advantages of preimplantation genetic testing for aneuploidy (PGT-A), testing for monogenetic/single-gene disorders (PGT-M), and carrier screening in in vitro fertilization (IVF) research, as well as molecular technologies improving workflows in IVF and how IVF research labs are benefiting from advanced NGS technologies.

The Increasing Use of Carrier Screening in Fertility Clinics

Video

Genetic disorders previously associated with specific ethnic groups now occur at increasing frequency in broader populations. Based on assumptions about prevalence, traditional carrier screening only targets single gene disorders according to ancestry or family history and may not accurately reflect changing frequencies. Expanded carrier screening (ECS) by next-generation sequencing (NGS) enables rapid carrier screening research and genetic analysis across a broader range of disorders, crossing ancestries and geographic regions with an accurate, scalable, cost-effective solution.

This on-demand webinar from Thermo Fisher Scientific discusses probabilities of genetic variants, the benefits and challenges of carrier screening and screening technologies, why screening is advantageous in family planning, who should be offered screening, and what should be screened for.