Dr. Alcaraz will discuss improving IVF research outcomes with Reproseq and PGD-SEQ.

Multi-gene hereditary cancer panels increased the possibility to identify individuals with cancer predisposing gene variants. The purpose of this study was to investigate the prevalence of pathogenic variants in genes implicated in hereditary cancer predisposition in BRCA1/2 negative patients. A cohort of 204 non-BRCA woman affected by breast / ovarian cancer were retested using a multigene custom panel of 27 cancer-associated genes. Twenty-six different deleterious germline variants were identified in ten genes (prevalence 12,74%). In particular, ten pathogenic variants were detected in CHEK2, two in BRIP1 and RAD51, six in monoallelic MUTYH, while one in RAD51D, PTEN, TP53, ATM, APC and NBN. The highest mutation prevalence was observed in the CHEK2 gene (38.5%), followed by MUTYH (15,8%), BRIP1 and RAD51 (7.7%). While in the remaining genes, the mutation prevalence was 3.84%. Additionally, 43 patients (21,07%) were found to carry a VUS detected in 16 different genes. Our findings demonstrate the utility of expanded panel testing in woman with personal history of ovarian and/or breast cancer, particularly for identification of hereditary cancer syndromes.

Next-generation sequencing (NGS) has become an increasingly useful tool in myeloid research, providing the ability to evaluate multiple molecular targets simultaneously. Despite the broad information provided by NGS, workflow complexity and long lead times have proven to be significant barriers for research laboratories interested in leveraging this technology. The Ion Torrent Genexus System addresses these challenges directly, as a turn key solution which can yield results in as little as one day. Paired with the Oncomine Myeloid Research Assay, users can interrogate relevant biomarkers for myeloid malignancies quickly and efficiently, eliminating the need for multiple testing platforms.

With declining birth rate in many societies, reproductive healthcare has become a rising issue in both Western and Eastern countries. Next-generation sequencing (NGS) has witnessed expedited applications in enhancing well-beings of couples with reproductive needs due to its low cost and improved accuracy and coverage. Leveraging the advances in NGS, we have developed the first NMPA-approved third-generation IVF PGT-A testing kit that could detect aneuploidies prior to implantation during IVF cycle. We conducted a large-scale multicenter randomized clinical trial with 1792 couples enrolled and 7602 embryos tested with PGT-A at the stage of blastocysts. The average aneuploidy rate across all six participating institutes was 39.2%, of which chromosome 13, 16, 18, 21 and 22 were those with highest frequency for chromosome numerical abnormality. PGT-A screening significantly improved clinical outcomes for IVF-treated patients. The success rate of IVF pregnancy was improved from 45% to 72% and miscarriage rate was reduced from 32% to 6.9%.

Above all, we believe NGS has the potential to make a difference in the field of reproductive care by reducing the chance of miscarriages, decreasing risk of genetic disorders and lowering financial and psychological burdens for carrier families.

Dr. Tulio will discuss SARS-COV-2 variants evolution and vaccines in Africa.

GENETRON S5 - Development of tumor molecular pathology diagnosis platform One step technology Lung 8 Kit - Significance of high throughput NGS in clinical tumor mutation detection Genetron NGS solutions for clinical molecular pathology

Alongside Dr. Ivana Antonucci, Rosella Ferrante will discuss multi-gene hereditary cancer panels increased the possibility to identify individuals with cancer predisposing gene variants. The purpose of this study was to investigate the prevalence of pathogenic variants in genes implicated in hereditary cancer predisposition in BRCA1/2 negative patients. A cohort of 204 non-BRCA woman affected by breast / ovarian cancer were retested using a multigene custom panel of 27 cancer-associated genes. Twenty-six different deleterious germline variants were identified in ten genes (prevalence 12,74%). In particular, ten pathogenic variants were detected in CHEK2, two in BRIP1 and RAD51, six in monoallelic MUTYH, while one in RAD51D, PTEN, TP53, ATM, APC and NBN. The highest mutation prevalence was observed in the CHEK2 gene (38.5%), followed by MUTYH (15,8%), BRIP1 and RAD51 (7.7%). While in the remaining genes, the mutation prevalence was 3.84%. Additionally, 43 patients (21,07%) were found to carry a VUS detected in 16 different genes. Our findings demonstrate the utility of expanded panel testing in woman with personal history of ovarian and/or breast cancer, particularly for identification of hereditary cancer syndromes.

Laboratories can proactively participate in the fight against SARS-CoV-2. In this context, we have established a SARS-CoV-2 testing and genome sequencing workflow that can detect and sequence positive cases within 48 hours for effective contact tracing. This fast, easy-to-use integrated workflow combines RT-PCR and the Ion AmpliSeq™ SARS-CoV-2 Insight Research Assay. At the same time, we also use the Oncomine™ Precision Assay to study genomic alterations in lung cancer biopsies. In summary, labs can simultaneously run assays for virus variant identification and genomic cancer research using the Ion Torrent™ Genexus™ Integrated Sequencer.

Join us as our Associate Director of Product Management, Andrew Hutchison, discusses using the Genexus Purification System for a complete specimen to report NGS workflow.

Dr. Roger C. Levesque will discuss ecogenomics whole genome SARS-CoV-2 wastewater AmpliSeq multi sample Analysis.

Next-generation sequencing (NGS) has become an ever increasingly utilized tool by testing laboratories looking to run inherited disease panels.  NGS allows for minimal sample input, reduced time to results and an abundance of data.  Onboarding these tests however can challenge laboratories when it comes to the Analytical Validation (AV). In this webinar we will do an overview of some of the regulations for clinical testing.  We will dive into the most stringent validation standards and explore data analysis within the scope of an analytical validation for inherited disease applications.  An experienced AV Project Manager will share their experiences and insight into the AV journey and what is involved with successful AV consulting support.

In this work, we first unravel the differences in class-switching and repartition of naïve B cells across responders and non-responders to MTX in RA using a cutting-edge B cell repertoire analysis. These data are then further used to develop the first immunology-based prediction model for response to MTX in RA based on an innovative machine learning approach.

Ion AmpliSeq On-Demand panels bring practical pack sizes and a optimized gene catalog to custom next-generation sequencing (NGS) panels, so you can iterate panel design for human disease research with efficiency and convenience. Uncover the 7 facts about targeted next generation sequencing using Ion AmpliSeq On-Demand Gene Panels in this short presentation.

Dr. Pea will discuss Empowering Custom Design of Targeted Gene Panels With AmpliSeq Designer.

Shawn Prince, Senior Field Application Scientist with QIAGEN Digital Insights, will discuss an industrial-scale analysis service for SARS-CoV-2 whole genome sequencing (WGS) data.

In this discussion, Luca Quagliata, PhD will discuss Thermo Fisher Scientific’s commitment to support clinical laboratories across the EU in preparation for the transition to IVDR.

Uma Ramasubramanian will discuss Genexus Software - A Comprehensive, Easy to Use Interface Enabling Setup, tracking, and analysis for NGS.

Next-generation sequencing (NGS) has become an ever increasingly utilized tool by testing laboratories looking to run inherited disease panels.  NGS allows for minimal sample input, reduced time to results and an abundance of data.  Onboarding these tests however can challenge laboratories when it comes to the Analytical Validation (AV). In this webinar we will do an overview of some of the regulations for clinical testing.  We will dive into the most stringent validation standards and explore data analysis within the scope of an analytical validation for inherited disease applications.  An experienced AV Project Manager will share their experiences and insight into the AV journey and what is involved with successful AV consulting support.

NGS-based assays for the rapid and cost-effective molecular diagnosis of inherited disorders are becoming a routine part of clinical care. While larger, multigene panels offer higher diagnostic yields, there is a concurrent increase in the rate of inconclusive results, illuminating the importance of high-quality and confident variant interpretation.

In this webinar, we introduce a genomic variant analysis, interpretation and reporting solution that major labs and population health programs around the world currently use as part of their clinical NGS testing programs. QCI Interpret is clinical decision support software that accelerates variant interpretation and reporting by automating curation workflows, dynamically computing variant classifications according to professional guidelines, and generating customized, patient-specific reports with trusted and transparent evidence.

To illustrate the efficiency and accuracy QCI Interpret, we will present two use-cases to show how an automated workflow can be easily developed and optimized for cardiovascular disease and hereditary cancer applications.

In this webinar, you will learn:

• How QCI Interpret reduces test turnaround time and accelerates throughput

• How QCI Interpret dynamically and transparently computes variant classifications using all criteria of the ACMG/AMP published guidelines for the assessment of variants in genes associated with inherited diseases

• How QCI Interpret enables genetic testing labs to leverage the knowledge equivalent of having performed 100,000 tests on day one of implementation

Join us as our Business Development Manager (Reproductive Health), Michael Richardson, discusses Ion Torrent NGS Applications in Reproductive Health Research.

Newborn screening is of great importance in public health systems and the different programs in place include an increasing number of genetic targets, with the constraint of reducing to the minimum the time to get analysis results. In this presentation, we will discuss examples of targeted next-generation sequencing workflows based on the gold standard AmpliSeq™ technology, for the study of genes involved in immunodeficiencies including severe combined immunodeficiencies, and of a core set of newborn screening genes.

For Research Use Only. Not for use in diagnostic procedures.

Research shows MYCN amplification may contribute to poor clinical outcome in childhood neuroblastoma. In this study we analysed the effects of MYCN deletion in neuroblastoma cells by RNA-seq analysis using the Ion Torrent™ Next-Generation Sequencing Systems. This study expands on the current knowledge of how MYCN protein control the biology of neuroblastoma cells. Together our data support direct MYC inhibition as a promising strategy for the treatment of MYCN-driven tumours.

Molecular Diagnostics of Infectious Diseases, in particular for viral infections evolved enormously over the last decades in both volume, level of automation as well as turnaround time. The initial focus was on detection for clinical diagnosis, inclusivity of genotypic variants and on quantitative assessment of viral load during treatment or upon organ transplantation. The role of genotypic characterization of viral pathogens in clinical care was limited and mainly applied antiviral resistance determination in the treatment of eg HIV or HBV infections, or for epidemiological reasons such as typing of Influenza virus. Next Generation Sequencing has opened up possibilities for identification of unknown pathogens but also for rapid whole genome characterization of pathogens. Requirements and technological advances for diagnostic and clinical application NGS will be discussed.

The Ion torrent™ Genexus System promises to make NGS available to almost any molecular laboratory. The hands-off, set-up-and-go workflow integrates and automates nucleic acid extraction and purification, library preparation, sequencing, analysis & reporting under a single software ecosystem. With only 10 minutes hands-on time over two touchpoints the Genexus System can help improve the productivity of any testing center whilst being amenable to facilities that have not before considered NGS. Whilst other NGS technologies, as well as the traditional way of sending out/outsourcing samples, can take weeks to obtain results, the Genexus System can go from a biological specimen to a report in just one day. In addition, the system can analyze individual samples cost-effectively—reducing the need for batching, and empowering laboratories to deliver results faster than ever. Oncology research is still hampered by the availability of material to test, with a large proportion of samples having very small amounts of tissue and/or being of inferior quality. Most NGS technologies require large amounts of sample, leading to more than one out of four samples being unusable for sequencing. Employing Ion Torrent™ AmpliSeq technology Oncomine Assays running on the Genexus System require only 10 ng of DNA/RNA per library, resulting in more than 95% of samples producing sequencing results.

Advances in next generation sequencing have improved our understanding of the complexity and molecular heterogeneity of acute myeloid leukemia (AML). The continued development of molecularly targeted therapies is changing the paradigm of AML treatment in the upfront and relapse settings. Critical, as we move toward an era of more impactful precision oncology in AML, is our ability to perform rapid and timely next generation sequencing (within 24-48 hours) to identify druggable molecular targets in AML. Early understanding of the disease’s genetic makeup will allow us to provide the best care and clinical outcomes for our AML patients, while also maximizing utilization of hospital resources. 

Founded in 2014, MAKO Medical is a College of American Pathologists (CAP) accredited laboratory that operates more than 70,000 square feet of laboratory space across two North Carolina facilities. The Henderson facility was expanded in 2020 in response to COVID-19, MAKO expanded its capabilities to address the growing need testing, increasing the lab’s capacity from 50,000 to 150,000 tests per day.  In response to efforts made to establish a national network to identify and monitor new viral variants, the Center For Disease Control established the NS3 (National SARS-CoV-2 Strain Surveillance) program, of which, MAKO was selected as a strategic partner.  Here, we discuss considerations in implementing a large-scale NGS-based genomic surveillance laboratory capable of routinely processing up to 6000 samples a day collected from across the United States. 

Worldwide prevalence of infertility is reported between 10-15% amounting to more than 50 million couples. Approximately one-third of infertility is attributed to the female partner, one-third attributed to the male partner and one-third is caused by a combination of problems in both partners or, is unexplained. The physiology of fertility and reproduction is complex and multiple genes influence the process starting from gonadal development and maturation, production of gametes, fertilization, embryo implantation and growth, uterine factors, fetal development to childbirth. Polymorphisms or variants in any of these functional genes associated with different reproductive metabolic and development pathways can result in reproductive failure or infertility. The advent of Next Generation Sequencing (NGS) technology allows not only deep investigation of multiple genes but provides an opportunity to create customized genomic panels. We developed our comprehensive infertility genomic panel covering all aspects of fertility and reproduction functions with integration of full gene sequencing design and mutation hot spot design.

Our clinical validation demonstrated several infertility and pregnancy correlations with multiple gene variants in Indian population. Based on the phenotype and genotype correlations, comprehensive Genomic Fertility Analysis (GFATM) software developed by our lab provides infertility risks, pharmacogenomic implications and personalized management options for both male and female partners. The session will show case a few case studies demonstrating clinical utility of the male (GeneAndroTM) and female (GeneFeminaTM) genomic panels developed by our lab for Indian population.

The Genexus system that is fully automatic NGS facilitated a genomic surveillance of the virus. We have analyzed about 150 cases using the Genexus system. Fully automatic NGS is effective when you want to identify the virus type and confirm the genotype matching at an early stage because anyone can do NGS at any time. In the case of a nosocomial infection, it is possible to identify the infection route at an early stage by performing a sequence as soon as possible, we could review the infection prevention measures at an early stage.

Being a WHO-recognised, National Influenza Centre (NIC), ICMR-NIV, Pune, established the SARS-CoV-2 test protocols for India.

NIC has established Ion Gene Studio S5 Plus platform for continuously monitoring evolution of SARS-CoV-2. The first 3 cases of SAR-CoV-2 in India were detected at NIC towards end of January 2020 and genetic characterization revealed two different introductions representing Wuhan strain L clade and S clade, respectively. G clade was introduced by travellers and Indians returning from Italy in March 2020. Further, as a part of nation-wide genomic surveillance, geographic distribution of SARS-CoV-2 clades and variants circulating in different parts of India between January and December 2020 was studied for evolutionary trends. Temporal data of the SARS-CoV-2 genomes revealed switch to G/GR/GH clades.

With the emergence of the Alpha variant of SARS-CoV-2 in mid-December 2020, the Indian SARS-COV-2 genome surveillance consortium (INSACOG) was established with ICMR-NIV as one of the Regional Genome Sequencing Laboratories in the country. Between December 23, 2020 and January 14, 2021, samples from 385 UK returnees were assessed and 140 were identified as alpha variants. Under INSACOG, till September 30, 2021, 60,043 samples were sequenced from travellers and community. Among VOCs, Delta variant was found to be predominant in circulation. Genomic sequencing of SARS CoV-2 cases in the eastern part of Maharashtra, in February 2021, attributed the upsurge in cases to the emergence of B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3. Thus, our study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra and India. Subsequently, the WHO declared Delta as a VOC. Overall, our studies show the vital role of genomic surveillance for early detection of variants having public health implications.

 Syndromic testing is popular for the detection infectious agents diseases in both human and animal samples. This type of testing generally requires testing for each individual target, however, targeted NGS is suited to this type of testing because of the large number of primer sets that can be incorporated into a single panel. The purpose of this study was to develop and validate a targeted next- generation sequencing (NGS) assay for vector-borne pathogens as part of a larger panel for canine/feline syndromic research testing. Test feasibility and analytical specificity were evaluated with type strains or positive samples from dogs. We compared the analytical sensitivity of the method to the Ct values obtained by qPCR testing. Sensitivity and specificity were assessed with a set of known positive and negative samples, based on qPCR testing. Positive and negative percent agreements and Cohen’s kappa were calculated. For each sample, pathogen target regions were amplified and DNA libraries were sequenced on the Ion Torrent S5 system. Primer sets were specific for the intended targets, and the method detected 17 different pathogens. Analytical sensitivity was equivalent to a qPCR Ct value of approximately 35-36. Cohen’s kappa was 0.804, which indicates almost perfect agreement between the qPCR assay and the targeted NGS assay. The positive percent agreement was 92% and the missed qPCR positives were due to failure to detect pathogens in samples with high Ct values. The negative percent agreement was 88%, and targeted NGS was able to detect multiple pathogens in a sample with a single test, including samples missed by qPCR. Using a targeted NGS method reduces costs associated with NGS sequencing and allows for a 2-3 day turn-around time, making this a viable method for detecting vector-borne agents in canine whole blood samples.