APJ Virtual Genetic Solutions Tour 2020

The utility of Polygenic Risk Scores (PRS) is gaining researchers' attention for identifying individual genetic risk and disease risk prediction in Alzheimer's Disease (AD) at both the early and pre-symptomatic stages of the disease. genoSCORE™ combines Cytox's proprietary technologies variaTECT™, a proprietary single nucleotide polymorphism (SNP) profiling array built on the Axiom platform from Thermo Fisher Scientific, with the SNPfitR™ analytical and interpretive software incorporating algorithms developed in partnership with Cardiff University, to give a PRS that identifies any individual's genetic risk of developing AD from blood or saliva-extracted DNA. This can help in patient stratification for clinical trial research to develop targeted treatments for AD.
 
Learning Objectives:

Select the highest risk APOE3/E4 subjects mostly likely to develop AD

Identify highest/low risk APOE3/E3 subjects for inclusion/exclusion in clinical studies

 

Genomic imbalances or copy number variations (CNVs) are a major cause of pregnancy losses, fetal anomalies identified during prenatal period, congenital defects in newborn, dysmorphology and developmental delay in infants, autism spectrum disorders and mental retardation. Routine karyotyping at 550 band resolution is limited to identifying aneuploidy and large structural anomalies such as chromosomal inversions, deletions and duplications larger than 5 Mb through microscopy and image analysis. Fluorescent in situ hybridization (FISH) testing can useful in detection of smaller genomic imbalances only when the clinical diagnosis is clear and narrowed down to a single condition. CytoMicroarrays can overcome these problems and can identify sub-microscopic microdeletions and duplications of >25 KB size in addition to offering differential diagnosis. Several international bodies including ACMG recommend CytoMicroarray as first tier test for congenital anomalies, developmental delay and autism disorders. The SNP backbone of the cytomicroarray facilitates identification of LOH (Loss of heterozygosity) and UPD (Uni parental disomy) along with CNVs. Limitations of CytoMicroarray include inability to detect CNVs of >25Kb, low level mosaicism of <20% and balanced translocations. The lecture presents 2yr lab experience with a set of case results to demonstrate sensitivity of Cytomicroarray in identification of genomic imbalances along with phenotypic correlation.

Theragen Bio. (TheragenEtex Subsidiary company) has been conducted the genome-wide research and the genome-based genetic testing services. From 2007, researchers of Theragen Bio. are collaborating with the genome sequencing projects and genome-wide association study projects. Through those researches, we found a novel Korean variants and associated diseases. Based on the research results, Theragen Bio developed the genetic testing service using OpenArray platform of Quantstudio 12K. Quantstudio revealed the fast, accurate genotype results and researcher friendly softwares enhanced the further developments of genetic testing service. However, the increase of GWAS results gave us some limitation of the service marker selection and high cost. In the reason, we considered Microarray Axiom platforms, because the platform has the robustness and flexibility. Asian PMRA array has several merits for our service, we make a choice of using the chip contents. Theragen PMRA chip was added 50,000 SNP loci to Asian PMRA array as the baseline microarray contents. Customized 50,000 SNPs are including 5,000 commercial markers that used in the theragen genetic testing service, 5,000 research finding markers of theragen, and 10,000 rare and hereditary cancer mutation markers, and 30,000 Korean genome specific rare markers. Finally, Theragen PMRA chip is possible to use the genetic testing service of predictive SNPs and diagnostic mutations, Asian population genome-wide association study and meta-analysis, and functional candidate marker researches. Theragen PMRA chip is applied to Hellogene, GeneStyle genetic testing service, GWAS of clinical and academic collaboration. In future, we will use this chip to the newborn screening, CNV research, pharmacogenomics, rare disease diagnostics, and so on. In addition, the chip contents will be optimized by the experiences of each SNP genotype qualities.

Genetic diseases are known occur due to various types of mutations in the human genome. The molecular assays to diagnose these diseases have been developed based on the type of mutation commonly seen in each disease. Advances in the field molecular genetics have now made it possible to sequence whole exome or whole genome of an individual through next generation sequencing. Whole exome sequencing is already being used in clinical practice for diagnosis of rare disorders. It is now possible to sequence multiple genes responsible for a phenotype at much lower cost using these technologies. Hence the question arises whether the traditional methods based on capillary electrophoresis are still relevant or not? And the answer is a big YES. Although next generation sequencing can provide an answer in most of the cases, there are certain situations in molecular diagnostics where Sanger sequencing can provide efficient and cost effective solutions. Diseases showing genetic homogeneity for mutations, like sickle cell anemia, achondroplasia etc, common mutations in populations and those caused due of mutations in single genes of small size, e.g Beta thalassemia, are better tested using sanger sequencing of specific exons.

Sanger sequencing is very important for familial segregation study, prenatal diagnosis and family screening following identification of a variant in next generation sequencing based assay. Fragment analysis following fluorescent primer based PCR is very helpful in initial screening of patients with Duchenne muscular dystrophy or Spinal muscular atrophy, wherein the common genetic mechanism is a deletion/duplication of one or several exon/s. Triplet repeat disorder testing for diseases like Spinocerebellar ataxias, Fragile X syndrome etc, relies heavily on capillary electrophoresis for detection of repeat expansion. Various examples of relevance of capillary electrophoresis in today’s era of molecular diagnosis of genetic diseases will be discussed in the presentation.

Shantanu will be providing an overview about how predictive genomics is a powerful capability to help predict disease risk and understand drug response in order to improve health outcomes and manage costs. He will be talking about some of the large population scale genotyping efforts implemented on the Applied Biosystems Axiom Microarray platform which have led to personalized health outcomes. This includes the prestigious UK Biobank and the Finngen projects in which genotyping data from customized Axiom microarrays were integrated with biobank data and electronic health records to create a national precision medicine asset of lasting value. Shantanu will also be speaking about how the Axiom microarray platform has been used to drive pharmacogenomics initiatives for clinical research.

Molecular breeding can significantly reduce the cost and time required to deliver improved plant and animal species for agricultural use. Advancements in genomic technologies are accelerating these breeding programs by enabling higher-throughput genotyping across large populations than ever before. Applied Biosystems AgriSeqTM targeted genotyping by sequencing (GBS) solutions are our latest innovation that helps our customers economically deliver high-throughput plant and animal genotypes.

The AgriSeq targeted GBS solution utilizes a highly efficient multiplexed PCR chemistry where hundreds to thousands of markers can be targeted and uniformly amplified in a single reaction. The amplicon libraries can then be barcoded and pooled for simultaneous sequencing of hundreds of samples on the Ion Torrent suite of next-generation sequencing (NGS) instruments. One of the powers of this technology is its capability to support multiple types of markers including single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs), insertions and deletions (InDels), and other structural variants (e.g. inversions, duplications). At a cost of pennies or less per genotype, AgriSeq targeted GBS is capable of generating up to 2.6 million genotypes per day from high-quality NGS data. Whether you’re looking to achieve more accurate marker-assisted breeding selection, or to improve your livestock parentage discrimination and trait monitoring, our solutions can help advance your plant and animal breeding programs.

The talk will detail how AgriSeq™ targeted GBS is successfully being used as a high throughput, customizable and cost-effective genotyping solution in aquaculture, animal and plant breeding studies, parentage testing and genetic purity.

Most bladder cancer (BC) cases are non-muscle-invasive BC (NIBMC), which is rarely lethal. However, nearly one-fifth of NMIBC cases progress to muscle-invasive BC (MIBC), which shows a 5-year overall survival rate of 50%.

Cytology is widely conducted for diagnosis of urothelial bladder cancer; however, its sensitivity is still low. Recent studies show that liquid biopsies can reflect tumor genomic profiles. I aim to investigate whether plasma or urine is more suitable for detecting tumor‐derived DNA in patients with early‐stage urothelial bladder cancer. Targeted sequencing of 71 genes was carried out using a total of 150 samples including primary tumor, urine supernatant, urine precipitation, plasma and buffy coat from 25 patients with bladder cancer and five patients with cystitis and benign tumor. I compared mutation profiles between each sample, identified tumor‐identical mutations and compared tumor diagnostic sensitivities between urine and conventional cytology. I would like to present the data that urine is an ideal liquid biopsy for detecting tumor‐derived DNA and more precisely reflects tumor mutational profiles than plasma. Genomic analysis of urine is clinically useful for diagnosis of superficial bladder cancer at early stage.

The study of human development and diseases relies on analysis of samples obtained and manipulated ex vivo. It is critical in such studies to know the provenance and confirm that the identity of these materials is correct. Analysis of highly variable short tandem repeats (STRs), provides a simple, inexpensive and highly specific genetic “fingerprint” of a human sample.  In this study, we describe a complete workflow for cell line authentication, chimeric receptor T-cell (CAR-T) and induced pluripotent stem cell (iPSC) sample matching.  Analysis of serial dilutions of purified genomic DNA from isolated human cell lines identified the correct alleles from as little as 0.1ng of purified DNA.  Samples immobilized onto Copan NUCLEIC Cards were correctly identified when a suspension of 5-10 x 105 cells were dried onto the cards.  Contaminating HeLa alleles could be detected in mixture when they were present in as little as 1% of genomic DNA from this population.  Blinded samples of donor and iPSCs, as well as manipulated CAR-T cells, were correctly matched in every case tested. Together, these results describe a facile and consolidated workflow for establishing the provenance, authenticity and identity of ex vivo-obtained human samples.

Common buckwheat (Fagopyrum esculentum Moench; 2n = 2x =16) is an outcrossing pseudocereal widely cultivated in the temperate zone. Buckwheat is fast-growing and is tolerant of cool climates and high elevations. The seeds of buckwheat contain a high level of starch and high quality of protein with a well-balanced amino acid profile without gluten. The genetic improvement of this minor yet important crop has achieved only limited success, mainly due to its heteromorphic self-incompatible (SI) system. Our challenge is to elucidate the characteristic heteromorphic SI system and genetically improve the agricultural traits of buckwheat.

We previously developed a self-compatible (SC) common buckwheat line by an interspecific cross between F. esculentum (SI species) and F. homotropicum (SC species). Here, we identified the genetic loci of the SI/SC trait and pre-harvest sprouting (PHS) tolerance, which is an important trait in buckwheat using three F2 populations (crosses A to C) derived from SI × SC lines. To construct genetic maps and performed quantitative trait loci (QTL) analysis efficiently, we developed the Ion AmpliSeq custom panel. Using this custom panel, we detected a single genetic locus which tightly linked with SI/SC trait. QTL analysis detected two, four, and two QTLs for PHS tolerance in crosses A, B, and C, respectively. We also detected some QTLs for maturity time.

Microsatellite instability (MSI) is a hypermutation phenotype that results from impaired DNA mismatch repair (MMR). The presence of high levels of MSI (MSI-H) is potentially predictive of Lynch syndrome, a hereditary condition associated with increased cancer risk across a variety of tumor types, including colorectal, gastric, and endometrial cancers. Additionally, MSI-H tumors are known to be more sensitive to immune checkpoint inhibitor treatment than microsatellite stable (MSS) tumors.

Traditional MSI analysis methods have limitations. IHC staining for DNA MMR enzyme reactivity is semiquantitative at best and relies on subjective interpretation that varies from person to person, while commonly used molecular MSI assays have insufficient markers for applications across multiple tumor types and cumbersome data analysis. The new Applied Biosystems™ TrueMark™ MSI Assay helps overcome these limitations with an expanded 13-microsatellite marker panel for accurate MSI analysis of multiple cancer sample types beyond just colorectal cancer. This 15-plex fluorescent PCR fragment analysis assay is performed via a standard capillary electrophoresis workflow with low DNA input. The included software offers automated calling and does not require running tumor and matched normal tissue.

To demonstrate the utility of the TrueMark MSI Assay, we performed a retrospective study using FFPE research samples derived from colon, gastric, and endometrial cancers. The assay produced high concordance with IHC and fewer ambiguous results relative to an alternative, commercially available MSI assay due to the expanded marker set. The combination of our expanded panel and automated analysis software constitutes an important tool for studying MSI.

Use of Ampliseq™ panels to study SARS-CoV-2and the host response to infection

Soren Alexandersen^1,2,3

¹ Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia;

² Deakin University, Geelong, VIC 3220, Australia;

³ Barwon Health, University Hospital Geelong, Geelong, VIC 3220 Australia

Ampliseq™ panels and next generation sequencing (NGS) on the Ion Torrent platform of diagnostic samples from infected individuals were used to study severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and to look at the host response to infection. We present selected results of near-full length SARS-CoV-2 virus genomic sequences assembled from such samples as well as show preliminary data on analysis of the expression of inflammatory genes. Future studies are planned to look even closer at the host immune response by using additional panels including the available Ampliseq™ Oncomine Immune Response, BCR and TCR panels. We also very briefly present very recent and exciting data on analysis of SARS-CoV-2 subgenomic RNAs by close analysis of NGS reads.

Coronavirus research cannot wait.  

As we know researchers around the world are diligently working to gain a better understanding of the novel coronavirus with the goal of rapidly identifying future treatment options and possible vaccine targets. With a comprehensive portfolio of genetic analysis products, Thermo Fisher Scientific is your trusted partner for virus discovery, pathogen detection, epidemiological surveillance, vaccine development, and host genetics to advance your research.   

This is the second part of the genetics analysis solutions presentation focusing on vaccine research as well as host genetics and population genomics studies. This talk will explain why immune repertoire Sequencing with NGS is not only an important tool for vaccine development but also can be utilized to predict disease severity. This presentation will provide case studies example of microarray genotyping is used to identify vulnerable population as well as to study host genetic factors associated with potential risk and susceptibility to SARS-CoV-2.  

NGS technology has grown leaps and bounds in reproductive genetics field. Infertility is on the rise and with the mushrooming of so many IVF clinics in our country and increasing number of IVF cases there is a great demand of add on technologies which will improve IVF outcome. Aneuploidies in the Preimplantation embryos have been already proved and chromosomal abnormalities impacts the IVF outcome by causing repeated IVF failures/ repeated miscarriages. Earlier FISH technology was only available to analyse limited number of chromosomes and many RCT’S did not publish favourable outcome. Comprehensive chromosome screening (CCS) with greater precision and accuracy is now possible on NGS which seems to improve IVF outcome. However, there are many controversies still on whom to apply PGT and whom not to. Personal experience is what counts and availability of such a par technology should not be made devoid from patients. Clinical benefits of offering PGT are many and should be carefully assessed. Chromosomal abnormalities follow a straight forward diagnosis either on embryo level or postnatal. Postnatally – couple carriers of any balanced translocation can be candidates of repeated abortions due to the unbalanced form of chromosomal translocation. In such cases PGT SR can be offered to overcome the reproductive issues. Additionally traditional FISH based method studies only the translocation chromosome leaving behind the other chromosomes non tested. However PGT SR provides CCS which improves pregnancy outcomes.

Single gene diseases were also traditionally carried out by PCR and then sangers sequencing for PGT M. With the availability of genome wide linkage analysis and the development of NGS PANELS for diseases, it has now become possible to perform PGT M for known genetic defects thereby reducing technical challenges and improving accuracy.

NGS based reproductive genetic tests provides a complete solution from Preimplantation level, prenatal level to postnatal genec diagnosis.

Background: Preimplantation genetic testing for aneuploidy (PGT-A) and structural rearrangement (PGT-SR) have been widely used within indications of previous miscarriages, repeated implantation failures, and balanced translocation carriers. The purpose of this survey is to investigate factors associated with yield of transferrable embryos having copy number = 2.

Method: The 124 couples with male or female balanced translocation carriers were enrolled between Sep 2019 to May 2020. Mean female age and number of tested embryos were 36.40±3.90 years and 5.87±3.83 counts, respectively. All sequencing libraries were amplified by Ion SingleSeq Kit from ReproSeq and the data were produced by Ion 530 chip with at least 200,000 uniquely mapped sequencing reads.

Results: The overall rate of transferrable embryo with copy number = 2 is about 20% but the rate of couples with at least 1 embryo having normal copy number is 64.5%. The factors of female age < 40 years and trophectoderm biopsy mostly presented beneficial effects on increased rate of transferrable embryos. Male translocation carriers and counts of tested embryos showed limited associations with yield of embryos having copy number = 2.

Conclusion: The couples with male or female balanced translocation carriers may have a difficulty of having transferrable embryo but the issue may be improved by trophectoderm biopsy and increased counts of tested embryos.

Lung cancer management has changed over the last few years with several actionable targets being recognised and mandated in the optimal management of these patients. The biomarker ordering practices have also changed with multidisciplinary communication becoming the key to successful strategies.

We present our experience in a tertiary care cancer setup. The transition from sequential testing to ordering multigene panels had taken place few years ago. The single gene panel was done using several strategies that included RT PCR for EGFR, Immunohistochemistry for ALK and ROS1 by FISH. With the Next Generation Sequencing (NGS) being included in the diagnostic armamentarium, the feasibility of testing several genes in one go has become a reality with significant reductions in cost and turnaround time. The advantages also including making the assays more comprehensive including mutations and fusions.

However, though theoretically, NGS offered a potential advantage, there were several operational challenges. The oncologists order the tests as per standard guidelines but whether it is to be taken up for NGS testing or single gene testing as alluded to earlier needs to be ascertained by the pathologist based on the availability of tissue, balancing the turn around time and cost. Visual indicators during the cycle of events that lead to preparation of paraffin embedded blocks has helped optimise the precious lung cancer tissue.

A coordinated effort between medical oncologists, pathologists radiologists, molecular biologists and histotechnologists helps address these issues and reap the benefits of NGS testing and management of lung cancers.

Genetic carrier screening is a method to help couples discover whether they are at risk of passing on serious genetic disorders to their children. When carried out before conception or early in pregnancy, carrier screening provides prospective parents with the information they need to make informed reproductive decisions that lead to the best possible outcomes for their families. Until recently, however, carrier screening has been restricted to a limited number of single-gene tests offered mainly to higher-risk individuals or populations based on race, ethnicity, or ancestry. With genetic analysis tools, such as Next Generation Sequencing and Microarray technology, hundreds of disorders can be screened at once using a single sample, allowing more comprehensive and universal carrier screening referred to as expanded carrier screening (ECS). Here, I will discuss the advantages and  implementation of pan-ethnic expanded carrier screening in a commercial laboratory in Malaysia.

Immune checkpoint blockade is promising for treating non-small-cell lung cancer (NSCLC). We used multipanel markers to predict the response to immune checkpoint inhibitors (ICIs) by characterizing gene expression signatures or individual genes in patients who showed durable clinical benefit to ICIs. Twenty-one patients with NSCLC treated with single-agent anti-programmed cell death protein (PD)-1 antibody were analyzed and their clinicopathological characteristics and response to ICIs were characterized. Nine (43%) showed a durable clinical benefit (DCB), while the remaining 12 (57%) patients showed non-durable benefit (NDB). The M1 and peripheral T cell signatures showed the best performance for discriminating DCB from NDB (sensitivity, specificity, accuracy = 0.89, 1.0, 0.95, respectively). Progression-free survival (PFS) was significantly longer in patients with high M1 signature or high peripheral T cell signature scores. CD137 and PSMB9 mRNA expression was higher in the DCB group than in the NDB group. Patients with high PSMB9 expression showed longer PFS. M1 signature, peripheral T cell signature and high mRNA expression level of CD137 and PSMB9 showed better predictive performance than known biomarkers, such as PD-L1 immunohistochemistry, tumor mutation burden, or tumor-infiltrating lymphocytes.

The Philippine government, thru the Philippine Carabao Center (PCC), has undertaken a genetic improvement program of dairy buffaloes. Selection of semen donor bulls is based on the performance of daughters. Performance data and pedigree information came from animals in institutional herds managed by the Center. Riverine dairy breeds present locally came from Bulgaria, Brazil, USA and Italy. Present constraints are the limited number of animals maintained in institutional herds where performance data is regularly collected, limited space for bulls undergoing progeny testing, accuracies of progeny test bulls are low due to the small number of daughters with lactation records, and progeny testing is slow and expensive. Even with the above constraints, phenotypic and genetic trends were still positive.

With the availability of a buffalo SNP chip, genomic information was now used in the diary buffalo breeding program. The reference population consisted of females, with up to three lactation records, coming from three riverine breeds that are all Murrah-based. Single-step genomic evaluation was utilized to generate breeding values. The additional SNP information provided by the genotyped animals increased the accuracy of prediction in ssGLUP compared to pBLUP. Young bulls are now being selected for milk yield based on their breeding values coming from pedigree, performance data and genomic information. Use of genomic selection still resulted in genetic gain, mainly due to the reduction of the generation interval (from ~8 years to 3.5 years). It also resulted in the decrease of long term costs with the reduction of the number of bulls maintained since there are no more waiting bulls.

NGS is still perceived as a complex, hard to implement and validate method that requires highly experienced people. Outsourcing next-generation sequencing (NGS) testing could be an option to overcome these limitations but it might end up being very expensive, and stringent sample requirements often lead to results being of poor quality and inconclusive. Recent clinical research studies show this issue effects approximately 20% of patients, excluding samples not submitted because they failed to meet sample quantity criteria.  A Multi-centric evaluation of performance of the Genexus Integrated Sequencer and Oncomine Precision Assay in detecting variants from FFPE and plasma samples of different type of tumors across four external customer laboratory sites will be discussed and concordance, success rate and reproducibility of results on different class of biomarkers will be presented. The results highlight how is possible to adopt in any molecular laboratory a complete and reliable molecular profiling solution for the testing of variants relevant for cancer management in an automated and fast manner.

Long-term succession of microbial communities in bulk soil is ecosystem dependent. We have learnt this by studying microbial communities from different ecosystems using Sanger Sequencing of their 16S rRNA genes. In sand dunes, communities undergo continuous maintenance (overlap) accompanied by a concomitant replacement (turnover) during 77,000 years of ecosystem development or as the soil ages. While microbial diversity increases with soil developmental age during natural succession, it has a non-linear correlation with the intensity of disturbance in agricultural soils. Upon restoration of disturbed soils, transitional microbial communities are formed that differ significantly from those in disturbed and native soils. In fact, land-use history has a stronger impact on soil microbial communities than aboveground vegetation or soil properties. Further, research from glacial retreats in New Zealand suggests that succession of microbial communities is closely aligned with ecosystem development, pedogenesis and vegetative succession. We are now investigating soils from Lonar crater to understand whether this ecosystem dependence in general bulk soils is also reflected in the compaction zones at the crater.

High production ability has been used for primary selection in dairy breeding schemes. In particular, milk yield, fat yield, and protein yield are the most important economic traits for dairy cattle selection. To date, genetic improvement of these economic traits has been performed successfully based on traditional best linear unbiased prediction (BLUP), and the breeding values of economic traits have been applied with selection indices in Korean dairy breeding systems. The BLUP used in combination with individual records and estimated breeding value (EBV) has resulted in considerable genetic progress in the dairy industry. In recent years, however, genomic information in the form of commercial single-nucleotide polymorphic (SNP) marker panels from various companies (i.e., Illumina, San Diego, CA, USA; Neogen-GeneSeek, Lincoln, NE, USA; and Affymetrix, Santa Clara, CA, USA) have become available for genetic evaluations, as a consequence of improvements in genotyping technology and statistical methods after introduction by Meuwissen et al in 2001. Accordingly, genomic prediction using genotypic data has been widely applied for various livestock.

Genomic selection (GS) involves selection of bulls based on genomic breeding values, which are derived from the combination of EBVs and direct breeding values (DGVs) based on SNPs using several blending formulae or single-step methods (e.g., ss-GBLUP (single-step genomic Best Linear Unbiased Prediction) and single-step super hybrid model.

The advantages of GS are simplicity and resistance to preselection bias and more reliable prediction than traditional BLUP. When GS schemes are applied in the field, the use of young bulls should be the most effective in terms of reliability. For example, in young Holstein bulls in the United States, reliabilities for predicted transmitting abilities for milk yield based on genomic information ranged from 73% to 79%.

The most important thing in GS is reference population that has both phenotype and genomic information. The larger the reference population size, the higher the accuracy of the GS. However, the total dairy population in Korea is small with about 400,000 heads, so there is a limit to growing the reference population. In Korea, it is difficult to expect the effects of GS as much as countries with large reference size. The other important thing in GS is using genetic information that including how many significant makers. Previous studies have shown that using custom array with significant markers for dairy cow is more effective than using conventional commercial array (e.g., Illumina bovine 50k array).

The objective of using custom array (Axiom myDesign Array plate) were to increase genomic accuracy while overcoming the small population size by including significant markers for Korean dairy cattle in the custom array.

Here I review the applications of Ion Torrent NGS technology in the field of microbiome research and some recent publications about it. With Ion Torrent 16S rRNA next generation sequencing, there are two common methods. The first one is custom targeted sequencing for one or two hypervariable regions, and the second method is Ion 16S Metagenomics kit sequencing for seven hypervariable regions (V2, 3, 4, 6, 7, 8 and 9). The Ion 16S Metagenomics kit is designed for rapid and comprehensive analyses for bacterial community research.

With these two methods, the products of PCR amplicons can be sequenced Ion Torrent NGS system (Ion GeneStudio S5 System) and analyzed using metagenomics workflow in the Ion Reporter software (Cloud computing service or local server). Microbiome researches based on Ion Torrent NGS using these methods have been introduced in various publications including intestinal, skin, oral microbiomes with humans or other animals, and forensic investigations.

Thermo Fisher has also released another very new and interesting kit for species-level microbiome profiling of microbial diversity in the human gut microbiome. This Ion AmpliSeq Microbiome Health Research Kit targets 8 out of the 9 hypervariable regions for increased resolution, and specific amplicons for 73 key bacterial species with immuno-oncology as well as autoimmune diseases and gut-related disorders. This new kit can be a very useful solution between simple 16S rRNA gene amplicon-based sequencing and very expensive and complicated shotgun metagenome sequencing.

Next generation genomics technology is playing a significant role in improving the outcomes of genomic tools used in livestock farming, cultivation of crops, selection of quality seeds with improved traits etc. Molecular markers are now key components of crop improvement programs, and are applied to identify cultivars, analyze genetic diversity, construct linkage maps and identify quantitative trait loci (QTL). Applied Biosystems AxiomTM Microarray offers several advantages such as custom design capabilities with fastest turn-around time, zero SNP dropouts and highly automated genotyping analysis which are key to successful deployment of livestock and crop breeding projects. This presentation introduces the Axiom microarray platform and its key features followed by technology advantages with respect to the custom design process. The presentation will also feature successful implementation of Axiom microarray technology that has enabled scientists attain their objectives for breeding programs.

Learn about how the new Ion Torrent Genexus System is addressing key challenges to next-generation sequencing (NGS) implementation, like hands-on time, time-to-result, user expertise, and affordability. 

Ion Torrent Genexus System in combination with the new Oncomine Precision Assay, represents a new-generation solution for genomic profiling of cancer samples and enables a broad spectrum of labs, even without previous expertise, to provide fast genomic profiling. We will also discuss the importance of detecting both novel fusions and known fusions via FusionSync detection technology.  

Introducing Oncomine Myeloid assay on Genexus to simplify and accelerate myeloid profiling where users can simultaneously interrogate all relevant DNA mutations and fusion transcripts for research on myeloid malignancies.  The single-day turnaround time allowing you to provide a full myeloid NGS profile at the same time as other molecular test results. 

Dr. Timothy J. Triche MD, PhD, Co-Director of Center for Personalized Medicine at Children’s Hospital Los Angeles​ (CHLA), shares how he and his team used sequencing data generated with the Ion AmpliSeq SARS-CoV-2 Research Panel to analyze phylogenetic relationships among a cluster of six SARS-CoV-2-positive samples. By identifying two distinct lineages between the two sets, the team was able to conclude that the source of transmission wasn’t shared. Comparative analysis showed that, not unexpectedly, the mother and son had nearly identical strains of the virus that originated in Utah, with links to Europe, while the four health care workers had strains only distantly related to each other and to the family. This confirmed that there was no transmission between the patient family and the health care workers. Further, the health care workers acquired the virus from community spread and not from the patient and family member.

The Ion AmpliSeq SARS-CoV-2 Research Panel is a targeted NGS solution that enables interrogation of the complete SARS-CoV-2 genome for epidemiological research. This nucleic acid-to-analysis solution includes the assay and an intuitive and powerful set of analysis tools in the Torrent Suite SARS-CoV-2 Research Plug-in package, enabling hypothesis-neutral analysis and a dramatically simplified workflow.

Coronavirus research cannot wait.  

As we know researchers around the world are diligently working to gain a better understanding of the novel coronavirus with the goal of rapidly identifying future treatment options and possible vaccine targets. With a comprehensive portfolio of genetic anaylsis products, Thermo Fisher Scientific is your trusted partner for virus discovery, pathogen detection, epidemiological surveillance, vaccine development, and host genetics to advance your research.   

This is the first part of the genetics analysis solutions presentation focusing on virus discovery, pathogen detection and epidemiological surveillance application areas. This talk will present to you the emerging applications for SARS-CoV-2 research with specific case studies such as using how rapid NGS results were important for contact tracking and tracing, understand of Zoonatic transmission and wastewater-based epidemiology of SARS-CoV-2.