Podcasts about Genotyping

Baby-making is more complicated than it might seem, and any couple struggling to conceive and achieve a successful pregnancy is faced with a confusing maze of fertility optimization measures.This is where whole genome personal genotyping can be very helpful. Your genes obviously have everything to do with fertility, and your genes are unique. Personal genotyping can illuminate what you might be doing wrong in the fertility optimization department. It empowers you and your partner to practice precision Biohacking by identifying the medicine, supplements, therapies, and lifestyle changes you need to bring a beautiful baby into the world.This deep-dive presentation will elucidate 17 problematic fertility genes you may have, how to find them, which conditions they are associated with, and give you a jumping-off point for addressing them...2:45 Important disclaimer: your genes don't have to be your destiny4:00 How to search your genome8:11 Single gene disorders10:18 On procrastination12:57 Polygenetic complexes17:22 MTHFR21:38 SLC19A122:04 DHFR23:25 MTR and MTT26:30 TCN27:00 PAI/SERPINE131:37 PEMT32:38 APEO34:18 FVL and F235:30 NOS37:05 GST/GPX42:04 PON43:20 VDR44:50 Male factor infertility51:40 Stress management hacks57:55 Folic Acid - The New Smoking?59:25 Niacin/Vitamin B31:00:30 Acupuncture1:04:50 Conclusion and inspirationRead: Decode Your Genome with Personal Genotyping for Precision Fertility Optimization

In this episode, Naim Alkhouri, Mike Betel, Michelle Long and Jeff McIntyre join Jörn Schattenberg and Roger Green to look back at The Liver Meeting 2024. This conversation considers how the anticipated approval of a second MASH drug without biopsy might affect clinical trials and discusses two recent publications on patient genotyping and patient clusters. The conversation starts with Roger asking the group whether the presence of two approved MASH medications that do not require biopsy will make recruiting clinical trials that require them more challenging. The group doubts this will not add a significant new challenge to already-challenging trial recruitment. Naim comments that while this is a concern, it is already factored into trial schedules and that, given the number of patients available for trial, this should be highly manageable. Michelle discusses the importance of risk stratification in overall trial enrollment and this issue. Jeff and Mike agree that while this is a concern, it is part of a broader concern about the use of biopsy and should not in itself be a primary focus in terms of trial design at this point in time. Naim introduces two other topics he considers worthy of consideration: the impact of synergy between resmetirom and GLP-1 agonists and the importance of different genetic polymorphisms in predicting the impact of drugs on specific patients. On synergy, he comments that MAESTRO-NASH data suggests that the presence of a GLP-1 does not affect the impact of resmetirom on fibrosis level. On the second point, he notes that several papers looked at major genotypes like PNPLA3 and HD17N13 and specifically cites a late-breaker from Arun Sanyal indicating that g-allele status may impact MASH independent of weight or insulin. Michelle mentions a recent paper in Nature identifying distinct clusters of patients based on how their SLDs progress over time, with a two-cluster solution indicating patients with concomitant diabetes and obesity vs. those without these two concomitant diseases. Roger shares a key point from each paper on treatment in the US. Data in the PNPLA3 paper might suggest that the course of disease in Hispanics, who have high levels of g-allele abnormalities, might be different from other ethnic groups with far lower abnormality rates. He also notes that the faster disease progression in the non-metabolic cluster highlights the importance of learning more about Lean MASH and how to treat it, since faster progression of disease suggests later diagnosis and higher morbidity, mortality and treatment costs levels.

In this episode, my guest Dr Kasia Kines and I explore the Epstein-Barr virus (EBV), a common yet often misunderstood virus that affects a significant portion of the global population. Dr. Kasia Kines is an Amazon best-selling author of the Epstein-Barr Virus Solution, a Doctor of Clinical Nutrition from MUIH (Maryland University of Integrative Health), a graduate of the first doctoral functional nutrition program created by Dr. Liz Lipski, PhD and CEO of Holistic Nutrition Naturally LLC and EBV Educational Institute. Join us as we discuss how EBV is contracted, its symptoms including chronic fatigue, the various factors that can trigger its reactivation, how it can trigger endometriosis and impacts fertility. Dr Kines provide insights and actionable tips to help you manage your health in relation to EBV.   A NUMBER OF ACTIONABLE TIPS WERE DISCUSSED INCLUDING: Recognising personal stressors that may trigger EBV reactivation. Understanding the environmental factors contributing to EBV complications. Importance of proper testing for conditions like Hashimoto's thyroiditis related to EBV. EPISODE HIGHLIGHTS: Understanding Epstein-Barr Virus (EBV): Kasia explains that EBV is a herpes virus affecting 90-95% of the global population and is contracted through various means, including saliva and blood. Triggers for EBV Reactivation: Stress is identified as the primary reactivating trigger for EBV, with personal and environmental factors playing significant roles in its impact on health and fertility. Dioxins and Endometriosis: Kasia discusses how dioxins, which are implicated in endometriosis, can reactivate EBV, highlighting the importance of being aware of environmental toxins. Testing for Autoimmune Conditions: The conversation emphasises the need for proper testing for conditions like Hashimoto's thyroiditis, which often goes unrecognized in women with low thyroid symptoms. Chronic Fatigue and EBV: Kasia shares insights on the connection between chronic fatigue syndrome and EBV, noting that many individuals experience a decline in their health after an initial EBV infection. Importance of Holistic Approaches: The discussion touches on the need for a comprehensive understanding of health that includes emotional, environmental, and physiological factors affecting recovery from EBV. RESOURCES MENTIONED: Epstein-Barr Virus Solution Book: A comprehensive best-selling book by Dr Kines Recent Study on Heavy Metals in Tampons: Highlights concerning findings about contaminants in feminine hygiene products: https://publichealth.berkeley.edu/news-media/research-highlights/first-study-to-measure-toxic-metals-in-tampons-shows-arsenic-and-lead Shearston et al. (2024). Tampons as a source of exposure to metal(oids): https://doi.org/10.1016/j.envint.2024.108849  FURTHER READING: Wang et al., (2024). Evodiamine suppresses endometriosis development induced by early EBV exposure through inhibition of ERβ. Doi: 10.3389/fphar.2024.1426660. PMID: 39148548; PMCID: PMC11324466. Grabarek et al. (2023). Detection and Genotyping of Human Papillomavirus (HPV16/18), Epstein–Barr Virus (EBV), and Human Cytomegalovirus (HCMV) in Endometrial Endometroid and Ovarian Cancers. https://www.mdpi.com/2076-0817/12/3/397# >>Endo Fertility Podcast Goodie Bag

In September 2022, a cell-free DNA assay using next-generation sequencing and quantitative counting tech for fetal antigen status determination became clinically available in the USA. This allowed maternal screening for fetal RBC genotypes for RH negative patients. This test was recognized by thre ACOG in March 2024 as one option to “triage” anti-D immunoglobulin in RH negative women. But can this technology be trusted in alloimmunized patients? In women with antibodies against foreign antibodies, this cell free DNA fetal screening option MUST get it right. We now have that data. In this episode, we will summarize remarkable results, published ahead of print on July 25, 2024 in the Green Journal. This study is a win for science and prenatal care. Listen in for details (BillontoOne, Inc is not a sponsor for this podcast).

Personal genotyping is a Biohacking gamechanger. It gives you an ocean of actionable data about yourself - what kind of diet is ideal for you, how much coffee you should be drinking, how much Vitamin D you need to supplement, which vices you can flirt with and which you must absolutely avoid, if you should do endurance or power training in the gym, etc. And it lets you know which kind of life-ruining genetic conditions you might need a prevention plan for to enjoy a long life of beauty, joy, and meaning.Personal genotyping gets complicated fast, so I recently read the book on personal genotyping, Outsmart Your Genes by Dr. Brandon Colby, and I learned some things about the common mistakes health-conscious, prevention-minded people make when it comes to personal genotyping. These are high-stakes mistakes with perhaps the ultimate consequence if you end up misinformed by the genotyping results you get.Read Review

To watch this as a video Download it and play it from the Downloads section in the Castbox app on your device.Personal genotyping is a Biohacking gamechanger. It gives you an ocean of actionable data about yourself - what kind of diet is ideal for you, how much coffee you should be drinking, how much Vitamin D you need to supplement, which vices you can flirt with and which you must absolutely avoid, if you should do endurance or power training in the gym, etc. And it lets you know which kind of life-ruining genetic conditions you might need a prevention plan for to enjoy a long life of beauty, joy, and meaning.Personal genotyping gets complicated fast, so I recently read the book on personal genotyping, Outsmart Your Genes by Dr. Brandon Colby, and I learned some things about the common mistakes health-conscious, prevention-minded people make when it comes to personal genotyping. These are high-stakes mistakes with perhaps the ultimate consequence if you end up misinformed by the genotyping results you get.Read Review

Proving that our podcast tagline, “Medicine Moves Fast” is true… this episode highlights something that is, once again,

In this episode, the team from the Atrium Health System discuss their award-winning submission to the ASHP Best Practices.  They will share how their program implemented a novel pharmacist-led DPYD testing program with CDS integration and demonstrated pre-treatment testing with genotype-guided fluoropyrimidine dosing improves patient safety by mitigating severe toxicities and hospitalizations in DPYD variant carriers. The information presented during the podcast reflects solely the opinions of the presenter. The information and materials are not, and are not intended as, a comprehensive source of drug information on this topic. The contents of the podcast have not been reviewed by ASHP, and should neither be interpreted as the official policies of ASHP, nor an endorsement of any product(s), nor should they be considered as a substitute for the professional judgment of the pharmacist or physician.

Zack Bateson is the Research Manager at the National Ag Genotyping Center based in Fargo, North Dakota. You heard a little bit about the work the National Genotyping Center is doing in episode five with Dr. Brian Jenks. In this episode we dive deeper into the services they offer to provide DNA testing for farmers and agronomists. Bateson got his start in DNA-based testing working in wildlife biology with prairie chickens and lizards, but says all of the skills can be applied to any organisms including variety detection, herbicide resistance, and soil pathogens, which is where he focuses today. “Growers can send us kochia and we can genotype them for the resistance to group 14. Then they're able to have a discussion with either their agronomists or other consultants to see whether it can be another actionable spraying opportunity or if there's something else that they can do about these resistant weeds.” - Zach BatesonThe National Ag Genotyping Center is a private nonprofit diagnostic lab that provides genetic testing to identify pathogens, pests and genetic traits such as resistance to herbicides. This valuable information can help growers determine next steps in treatment of fields without having to rely solely on potentially costly trial and error practices. Alongside these established practices they are also developing identification testing for different causes of root rot.“The work involved is simpler for a person to do, especially with robotics, we can not only do tens of samples per day, but we can extract from hundreds of samples per day. We can test for multiple genetic markers throughout the day, so we're talking hundreds and almost thousands of data points that can be processed and reported out.” - Zach BatesonThis Week on Growing Pulse Crops:Meet Zack Bateson, the Research Manager at the National Ag Genotyping Center based in Fargo, North DakotaExplore the work done at the National Ag Genotyping Center and the value they provide growers in North Dakota. Discover the support and research being developed at the National Ag Genotyping Center and the future projects they expect to participate inGrowing Pulse Crops is produced by Dr. Audrey Kalil and hosted by Tim Hammerich of the Future of Agriculture Podcast.

This week, Adam Woods talks about the beef trade, Darren Carty on the opening of the BIC scheme and Aidan Brennan for his opinion around the genotyping and tagging delays.

Charles O'Donnell, Louise Hickey and Aisling O'Brien bring you the biggest stories of the week in Irish agriculture from Agriland, which this week includes:  ·      Genotyping programme changes after passport delays·      Reactors, restrictions and costs all rise for TB programme ·      665 herds identified for illegal burning·      ‘The dairy cow can't pay for everything'·      TD hits out at septic tank grant rolloutDon't forget to rate, review and follow The Farming Week, Agriland's weekly review of Irish agriculture and visit Agriland.ie for more. 

In this episode of Acquisitions Anonymous, Michael and Heather discuss an investment opportunity in a genomic testing , specializing in DNA sequencing and genotyping for mice. Despite their initial unfamiliarity with the technical details, they recognize the company's significant role in pharmaceutical research. They are impressed by its financial performance, noting substantial growth in revenue and EBITDA, along with high margins. The conversation also explores potential barriers to entry, the impact of technological advancements, and the type of buyer suitable for such a specialized business. They conclude that the company's high margins, growth potential, and strategic importance in healthcare and pharmaceuticals make it an attractive investment opportunity, albeit one requiring a buyer to quickly grasp the complexities of the field.Today's deal comes from Axial.  Axial is a trusted deal-sourcing platform serving professional acquirers in the American lower middle market.Thanks to this week's sponsors!Acquisition Lab and their team have been longtime supporters of the pod.Created by Walker Diebel author of Buy Then Build: How to Outsmart the Startup Game, is an accelerator with a highly vetted cohort-based educational and support community for people serious about buying a business.Acquisition Lab exists to help people buy a business and navigate all the complexities of the process, as well as provide a trusted framework, tools, and resources to support you from search to close.If you are serious about buying a business, check out acquisitionlab.com or email the Lab's director Chelsea Wood, chelsea@buythenbuild.com.-------------CloudBookkeeping offers adaptable solutions to businesses that want to focus on growth with a “client service first” approach. They offer a full suite of accounting services, including sophisticated reporting, QuickBooks software solutions, and full-service payroll options. Do you love Acquanon and want to see our smiling faces? Subscribe to our Youtube channel. Do you enjoy our content? Rate our show! Follow us on Twitter @acquanon Learnings about small business acquisitions and operations.

Dr. Corey Watson is an Associate Professor at the University of Louisville. His work focuses on characterising and cataloguing antibody genetic diversity in human and mouse to better understand disease susceptibility and clinical health outcomes. Dr. William Lees is a researcher at University of London. His work focuses on developing Adaptive Immune Receptor (AIR) reference sets for diverse species and the annotation of experimental sequence data. In this episode we talk about the recent work by the Germline Database Working Group of the AIRR-Community. The accuracy of V and J gene segment assignment improves with the quality of the reference germline set. The accurate assignment is critical for characterization of somatic hypermutation. We discuss the challenges in creating a database to hold all relevant and potentially relevant germline information, especially in the light of increased discovery rate through technological advances and improved analysis pipelines. We also reflect on the complexity in handling personalised germline reference sets. The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding. Comments are welcome to the inbox of onairr@airr-community.org  or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.  Website of the AIRR-C Germline Database Working Group https://www.antibodysociety.org/the-airr-community/airr-working-groups/germline_database/  Papers mentioned Collins, Andrew M., Mats Ohlin, Martin Corcoran, James M. Heather, Duncan Ralph, Mansun Law, Jesus Martínez-Barnetche, et al. 2023. “AIRR-C Human IG Reference Sets: Curated Sets of Immunoglobulin Heavy and Light Chain Germline Genes.” BioRxiv. https://doi.org/10.1101/2023.09.01.555348  Rodriguez, Oscar L., Yana Safonova, Catherine A. Silver, Kaitlyn Shields, William S. Gibson, Justin T. Kos, David Tieri, et al. 2023. “Genetic Variation in the Immunoglobulin Heavy Chain Locus Shapes the Human Antibody Repertoire.” Nature Communications 14 (1). https://doi.org/10.1038/s41467-023-40070-x  Lees, William D., Scott Christley, Ayelet Peres, Justin T. Kos, Brian Corrie, Duncan Ralph, Felix Breden, et al. 2023. “AIRR Community Curation and Standardised Representation for Immunoglobulin and T Cell Receptor Germline Sets.” Immunoinformatics (Amsterdam, Netherlands) 10 (100025): 100025. https://doi.org/10.1016/j.immuno.2023.100025  Jackson, Katherine J. L., Justin T. Kos, William Lees, William S. Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, et al. 2022. “A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice.” Frontiers in Immunology 13. https://doi.org/10.3389/fimmu.2022.888555  Ford, Easton E., David Tieri, Oscar L. Rodriguez, Nancy J. Francoeur, Juan Soto, Justin T. Kos, Ayelet Peres, et al. 2023. “FLAIRR-Seq: A Method for Single-Molecule Resolution of near Full-Length Antibody H Chain Repertoires.” The Journal of Immunology 210 (10): 1607–19. https://doi.org/10.4049/jimmunol.2200825  Omer, Aviv, Ayelet Peres, Oscar L. Rodriguez, Corey T. Watson, William Lees, Pazit Polak, Andrew M. Collins, and Gur Yaari. 2022. “T Cell Receptor Beta Germline Variability Is Revealed by Inference from Repertoire Data.” Genome Medicine 14 (1). https://doi.org/10.1186/s13073-021-01008-4  Rodriguez, Oscar L., Catherine A. Silver, Kaitlyn Shields, Melissa L. Smith, and Corey T. Watson. 2022. “Targeted Long-Read Sequencing Facilitates Phased Diploid Assembly and Genotyping of the Human T Cell Receptor Alpha, Delta, and Beta Loci.” Cell Genomics 2 (12): 100228. https://doi.org/10.1016/j.xgen.2022.100228  Tools mentioned TIgGER (Immcantation) https://tigger.readthedocs.io/en/stable  IgDiscover https://github.com/NBISweden/IgDiscover  Partis https://github.com/psathyrella/partis MiXCR https://mixcr.com

On this episode Lauren, Claire and Eoin where joined by Mark Waters from ICBF (Irish Cattle Breeding Federation).They have a conversation about the National Genotyping Programme.  The National Genotyping Programme is a collaborative initiative designed to enable Ireland to take the first step in achieving a fully genotyped national herd. The programme has been developed based on a cost-sharing model between the Department of Agriculture, Food & the Marine, the beef & dairy industry & participating farmers.Genotyping the national herd will provide a huge opportunity for the Dairy and Beef industry to increase its sustainability credentials on a global scale. Ireland will become the first country in the world to provide a DNA-verified traceability system. It will lead to an acceleration in the rates of gain of our national breeding indexes (e.g. EBI, Eurostar and DBI), which will enhance farm sustainability and reduce carbon emissions.To find out more; https://www.icbf.com/The Sod Pod; https://ie.timacagro.com/podcast-the-sod-pod/

David Coen from Sheep Ireland is on this week's OviCast to talk about progress in breeding in the hill sector. David discusses the impact hill genetics has on the national flock, SIS scheme and ram eligibility.  We discuss the work by the 17 breeding groups over the past year to get rams genotyped and the impact this has had on developing flock books. Finally we finish up with David discussing how breeders can build on this going forwards to improve genetic improvement in hill flocks. Some links discussed in this week's episode to search for potential rams or to sign up to Sheep Ireland are:Ram Search:https://appsh.sheep.ie/ram-searchRam sales/catalogues:https://www.sheep.ie/?page_id=29Sign up online form:https://forms.office.com/pages/responsepage.aspx?id=AH5m37xZikKh2Tgra-Oid02OFzIK2SJKuUbHvUCuGqJURVpMT1ZLRU02RkxPTDdGTkhFRFNKNFpLTS4uFor more episodes from the OviCast podcast, visit the show page at:https://www.teagasc.ie/animals/sheep/ovicast-sheep-podcast

In this episode, Renslow Sherer, MD, discusses managing virologic failure in a person living with HIV who is heavily treatment experienced, including:Guideline recommendations for selecting a new ART regimenOptions for patients with multidrug-resistant HIV from existing drug classes and novel mechanisms of action with no cross-resistanceData from TMB-301 and TMB-311 for ibalizumab, BRIGHTE for fostemsavir, and CAPELLA for lenacapavir on the use of these agents for people living with HIV who are heavily treatment experienced with multidrug-resistant HIVPresenter:Renslow Sherer, MDDirectorInternational HIV Training CenterProfessor of MedicineSection of Infectious Diseases and Global HealthDepartment of MedicineUniversity of ChicagoChicago, IllinoisTo download the slides:https://bit.ly/3OcqxIETo view the full online program:https://bit.ly/3ZjSFhg

In this episode, Renslow Sherer, MD, discusses managing a first ART failure in the setting of COVID-19, including:Guideline recommendations for resistance testingGuideline recommendations for selecting a new ART regimenData on retained efficacy of NRTIs in second-line regimens in the EARNEST and NADIA studiesConsideration of drug‒drug interactions between ART and COVID-19 treatmentPresenter: Renslow Sherer, MDDirector International HIV Training Center Professor of Medicine Section of Infectious Diseases and Global Health Department of Medicine University of Chicago Chicago, Illinois To download the slides: https://bit.ly/3OcqxIE To view the full online program: https://bit.ly/3ZjSFhg

On this week's show, Adam Woods talks about genotyping and SCEP, Darren Carty on the EU's nature restoration law and Aidan Brennan looks forward to Moorepark 2023.

Gearóid Slattery from ICBF joins Catherine Egan on this week's Beef Edge podcast to discuss the National Genotyping Programme.   The National Genotyping Programme is a collaborative initiative enabling Ireland to take the first step in achieving a fully genotyped national herd. The scale of the programme is a world first and sees Ireland placed firmly at the forefront when it comes to national sustainability efforts. The NGP has been developed based on a cost-sharing model between the programme partners, consisting of the Department of Agriculture, Food & the Marine (DAFM), Dairy Industry Ireland (DII), Meat Industry Ireland (MII) and participating farmers.  The first year of the programme will be funded by the Brexit Adjustment Reserve (BAR).  For the remaining four years, the genotyping costs of €18 per sample will be divided equally between the three Programme Partners; 1. DAFM, 2. DII & MII and 3. Participating farmers (i.e. €6 contribution per programme partners). Genotyping the national herd will provide a huge opportunity for both the dairy and beef industry to increase its sustainability credentials on a global scale. Ireland will become the first country in the world to provide a DNA-verified traceability system.  It will lead to an acceleration in the rates of gain of our national breeding indexes (e.g. EBI, Eurostar & DBI), which will enhance farm sustainability and reduce carbon emissions. The closing date for applications for dairy herds is 14th July 2023. The closing date for beef herds is yet to be announced. For more episodes from the Beef Edge podcast, visit the show page at:https://www.teagasc.ie/thebeefedge         Produced on behalf of Teagasc by LastCastMedia.com 

On this week's episode of the Dairy Edge, Mark Waters, Co-ordinator of the DNA Registration Project at ICBF joins Stuart Child to discuss the National Genotyping scheme that was launched recently by the Minister for Agriculture. Mark starts by telling us exactly what genotyping is and what it has to offer both farmers and the industry as a whole.  He says that it is hard to overstate the value of genotyping and that the big thing will be the rate of gain that will be achievable. This has the potential to allow for more palatable actions with regard to climate change targets compared to some of the actions that are currently being suggested, such as a large scale reduction in animal numbers . Mark then explains how farmers can sign up for the scheme, what they have to do in 2023 and what is expected from 2024 onwards when the DNA registration process will start in earnest. Finally, Mark highlights that the purpose of the scheme is to genotype the existing herd to allow for the DNA registration process to become a reality and that people are committing to this when signing up.  It is imperative that people take samples and return them in a timely manner to facilitate preparation for the DNA registration next spring.     For more episodes from the Dairy Edge podcast go to the show page at: https://www.teagasc.ie/animals/dairy/the-dairy-edge-podcast/ The Dairy Edge is a co-production with LastCastMedia.com

On this week's podcast we discuss the weanling trade, the ash dieback debacle and the new €83m genotyping scheme.

This week, we talk to Adam on selling bulls, Darren on the impact of Islamic festivals on lamb prices and Aidan on the new national genotyping programme. Adam also chats to Michael Murray from ESB Networks on the possible dangers during the silage season.

Aisling O'Brien & Francess McDonnell bring you the biggest stories of the week in Irish agriculture, which this week include: - Rewetting controversy continues in Dáil and on the streets - Minister formally announces €43m genotyping programme - Almost 130,000 farmers apply for BISS and other schemes - Green TD calls for live exports to end - Vet issues appeal after 8 calves killed by slurry fumes - Bogs to be developed for recreation activities Rate, review and follow The Farming Week, Agriland's weekly review of Irish agriculture and visit Agriland.ie for more. --- Send in a voice message: https://podcasters.spotify.com/pod/show/the-farming-week/message

We introduce our new co-host, Mr. Jeremy Sherrill! In an interview with Bioinformatician Dr. Abeer Madouly, we discuss the evolving role of race, ethnicity, and ancestry in the field of immunogenetics. Dr. Madouly discusses how and why they are used in HLA genotyping now and in the future. We also answer a question from listener regarding CHS testing in our newest segment, The Tea.

This week we chat to Adam Woods on the new genotyping scheme, Darren Carty on the new Young Farmer scheme and Siobhan Walsh gives her thoughts on how specialised livestock farmers can mix it up with tillage farmers.

In this week's episode we'll discuss how azacytidine therapy influences the contributions of mutated HSC clones to hematopoiesis in MDS and CMML, learn more about the risk of venous thromboembolism in patients with adult-type diffuse glioma, and discuss the importance of 1p32 deletions as an independent and adverse prognostic factor in myeloma.

(01:11)Dr. Hasadsri, could you provide us with an overview of what carrier screening is?(02:28)Can you really expand on why these tests are important?(05:25)So in your experience, who could benefit from carrier screening and when should that testing be performed?(06:45)Can you just share how does a healthcare provider order carrier screening and then secondarily what sample types are accepted?(08:05)Can you share what are some of the unique features of our testing that sets the Mayo Clinic Laboratories apart?(10:36)So the last question I have is could you just summarize the benefits of doing carrier screening at Mayo?

David Coen from Sheep Ireland joins Ciarán Lynch on this week's OviCast to explain genotyping rams.  David outlines the benefits of genotyping rams and the kind of information it can provide from scrapie genotypes to parentage verification to genomic evaluations.  David and Ciarán also discuss the processes and costs involved for producers.  David then explains the ram genotype task in the Proposed DAFM Sheep Improvement Scheme highlighting the criteria for both lowland and hill flocks.  Finally, in relation to hill flocks, David discusses how genotyping could lay the foundation for breed improvement programmes within hill breeds.  For more episodes from the OviCast podcast, visit the show page at:https://www.teagasc.ie/animals/sheep/ovicast-sheep-podcast

NBA great Alonzo Mourning returned home from the Sydney Olympics after winning the gold medal feeling ill. He surprisingly was diagnosed shortly after with kidney disease. Scientists have discovered his type of kidney disease is linked to having genetic variants of the APOL1 gene – ones that 13% of people with African ancestry carry. Dr. Ogo Egbuna leads clinical development for the team researching APOL1-mediated kidney disease at Vertex where they're investigating a small molecule therapy to target its underlying cause.Produced by Bloomberg Media Studios and Vertex Pharmaceuticals.  Featured guests:Alonzo Mourning is a retired NBA player, the Vice President, Player Programs for the Miami Heat, an advocate for kidney disease research, and a beneficiary of a kidney transplant.David Friedman is an Associate Professor of Medicine, Harvard Medical School and a Principal Investigator and Nephrologist at Beth Israel Deaconess Medical Center. He's researched and consulted for Vertex Pharmaceuticals.Janice Lea  is a Professor of Medicine and Clinical Director of Nephrology at Emory University School of Medicine.Ogo Egbuna is Vice President, Clinical Development at Vertex Pharmaceuticals Read more about Vertex's approach to targeting kidney disease.Produced by Bloomberg Media Studios and Vertex Pharmaceuticals.  

The buzz around the potential of Precision Medicine continues as new technologies, more powerful computing and our ability to store, share and interpret Big Data increases.  On this podcast Steve Coldicott and Scott Buckler chat about all aspects of the industry with patients, healthcare industry and research professionals about creating personalised medicines for each and every one of us. Genotyping and artificial intelligence are together starting to predict the progression of glaucoma in individual patients, sparing them from suboptimal treatments and side effects. Recent research efforts are exploring modifiable risk factors such as caffeine consumption.  During this episode, Dr Anthony Khawaja chats with Scott Buckler about the need for precision management in glaucoma.   For more content, and to see many episodes of this podcast in video form, please visit out website: https://precisionmedicineforum.com/

We chat to Adam Woods on why he thinks genotyping is the key to dairy beef success. Declan Marren talks about the key takeaways from the Thrive Open Day in Cashel and we pose key questions on the new nitrate rules to Aidan Brennan.

Host Jeremy C. Park talks with Antonio Taylor, Director of Technical Services for Transnetyx and Marketing Chair for SIM Memphis, who discusses the power of working with youth and introducing and encouraging them to pursue STEM-related professions and possibilities. During the interview, Antonio spotlights his role at Transnetyx, a Memphis, Tennessee area-based business that launched the world's first fully automated genotyping system for detecting transgenic, knockout, knock-in, SNP, and CRISPR mutations in animal research models. Transnetyx's mission is to provide the most efficient path to discovery for researchers across the globe, in order to pave the way for research to advance and deeper understandings to emerge.Antonio then highlights SIM Memphis, which is the Memphis Chapter of the Society for Information Management, a professional society of local IT leaders. He spotlights their efforts around mentoring and working with youth and youth-driven organizations, including Memphis-Shelby County Schools, DeSoto County Schools, Memphis Public Library, and Boys and Girls Clubs of Greater Memphis, in order to promote academic excellence and student success and to introduce and encourage the pursuit of IT and STEM-related professions and possibilities. He wraps up discussing their SIM Strategy Series for Executives, which is Memphis' premier single-day event designed exclusively for the IT executive community being held on October 26, 2022 at the Hilton Memphis Hotel.Visit https://chapter.simnet.org/memphis/home to learn more about SIM Memphis, and https://www.transnetyx.com to learn more about Transnetyx.

In this episode, John D. Baxter, MD, explores recommendations and data on the use of proviral DNA genotyping to inform antiretroviral therapy (ART) choice for patients who are treatment experienced.Listen as he gives his perspectives on:US Department of Health and Human Services guideline recommendations on the use of proviral DNA genotypingUS Department of Health and Human Services guideline recommendations and supporting data on switching ART with viral suppression and underlying drug resistanceStudy 380-4030 on outcomes with bictegravir- and dolutegravir-based ART in patients with preexisting nucleos(t)ide reverse-transcriptase inhibitor resistanceThe BRAAVE 2020 study on switching to bictegravir/emtricitabine/tenofovir alafenamide in Black persons with HIV, some of whom had baseline ART resistanceBetween-class ART switches with underlying resistanceSusceptibility of tenofovir disoproxil fumarate and abacavir with thymidine analogue mutationsPresenter:John D. Baxter, MDProfessor of MedicineDivision of Infectious DiseasesDepartment of PathologyCooper Medical School of Rowan UniversityHead, Division of Infectious DiseasesCooper University Health CareCamden, New JerseyFollow along with the slides at:https://bit.ly/3HmkSLcSee the entire program at: https://bit.ly/3fOl0XX

Is sequencing the SARS-CoV-2 genome useful for patient care? What about institutional infection control? And if clinical labs decide to perform SARS-CoV-2 sequencing, how should they do it? How should they report the results? And will they get paid? Until recently, sequencing of SARS-CoV-2 genomes has mainly been done in public health or research laboratories. Now, there is increasing interest in sequencing the viral genome in healthcare settings for uses in patient care and infection control. We'll be talking about a new guideline that can help clinical labs and institutions decide whether to perform SARS-CoV-2 sequencing. Guest: Dr. Alex Greninger Dr. Francesca Lee Links: Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: an IDSA/ASM Consensus Review Document https://journals.asm.org/doi/10.1128/JCM.01659-21

Host: Matt Birnholz, MD Guest: Mark H. Stoler, MD Now that vaccinated women have entered the screening population, we are seeing HPV 16 and 18 decreasing. These changes in HPV genotype prevalence may have a significant impact on the clinical management of cervical cancer, and an HPV test with extended genotyping may change the way we screen for cervical cancer as well. Joining Dr. Matt Birnholz to discuss the role of HPV extended genotyping in cervical cancer screening and the importance of identifying HPV 31 is Dr. Mark Stoler, Professor of Pathology and Clinical Gynecology at the University of Virginia Health System.

In this episode of MODPATH CHAT, our guests Dr. Natalia Buza and Dr. Pei Hui from the department of Pathology at Yale University share their approach to the application of DNA genotyping to the diagnosis and prognostication of Hydatidiform moles and Gestational trophoblastic tumors. Genotyping is now the gold standard in the confirmation and subtyping of sporadic hydatidiform moles. DNA genotyping is critical to the separation of gestational trophoblastic neoplasia from non-gestational counterparts/mimics of either germ cell or somatic origin. Modern Pathology, 34, 1658–1672 (2021). https://www.nature.com/articles/s41379-021-00831-9. See acast.com/privacy for privacy and opt-out information.

In this week's episode, we'll start by reviewing an intriguing study that, while not randomized, calls into question whether less-intensive induction therapies provide a survival or quality of life benefit in older patients with AML. Next, we will review the somewhat surprising findings from human and mouse model studies demonstrating that platelets downregulate T cell activity during sepsis, a finding that is associated with reduced survival. We will close with a report on a targeted genotyping approach that could reduce diagnostic and treatment delays in patients with primary CNS lymphoma.

With the rams sales season kicking into high gear, Dr Alan Bohan from Sheep Ireland joins Ciarán Lynch on this week's OviCast to discuss how genotyping has improved the genetic information available to breeders and farmers alike. Alan discusses the increase in the number of animals genotyped this year and explains the process and costs involved in genotyping. He then discusses the benefits of genotyping animals from parentage verification to scrapie genotyping. Genotyping also provides a genomic evaluation which improves the accuracy of the index and Alan explains why this is a major benefit to farmers. Finally, he discusses this year's Sheep Ireland multi-breed sale and the use of the ram search tool to find rams and pedigree breeders in your own locality. For more episodes from the OviCast podcast, visit the show page at: https://www.teagasc.ie/animals/sheep/ovicast-sheep-podcast

Host: Lee P. Shulman, MD, FACMG, FACOG Guest: Anna-Barbara Moscicki, MD Updated cervical cancer screening guidelines were published by both the American Society for Colposcopy and Cervical Pathology (ASCCP) and the American Cancer Society (ACS). Dr. Lee Shulman leads a discussion with Dr. Anna-Barbara Moscicki on the recent guidelines, the range of cervical cancer screening tests, and the impact on risk stratification and patient management.

CME credits: 0.25 Valid until: 14-07-2022 Claim your CME credit at https://reachmd.com/programs/cme/riding-wave-change-cervical-cancer-screening-managing-patients-light-risk-using-extended-genotyping/12697/ Updated cervical cancer screening guidelines were published by both the American Society for Colposcopy and Cervical Pathology (ASCCP) and the American Cancer Society (ACS). Dr. Lee Shulman leads a discussion with Dr. Anna-Barbara Moscicki on the recent guidelines, the range of cervical cancer screening tests, and the impact on risk stratification and patient management.

CME credits: 0.25 Valid until: 14-07-2022 Claim your CME credit at https://reachmd.com/programs/cme/riding-wave-change-cervical-cancer-screening-managing-patients-light-risk-using-extended-genotyping/12697/ Updated cervical cancer screening guidelines were published by both the American Society for Colposcopy and Cervical Pathology (ASCCP) and the American Cancer Society (ACS). Dr. Lee Shulman leads a discussion with Dr. Anna-Barbara Moscicki on the recent guidelines, the range of cervical cancer screening tests, and the impact on risk stratification and patient management.

Genotyping for COVID-19 variants surveillance is explored with the Director of the UC Davis Genome Center and the director of the Healthy Davis Together project.

Despite guidance in a 2015 publication from international experts in immunohematology and transfusion medicine, many clinicians and laboratorians have yet to integrate RHD genotyping into routine practice when a patient’s RhD serologic typing is weaker than expected. In this interview, international immunohematology expert Sue Johnson shows us how we can do better!

Read the article on Wiley Online Library: https://onlinelibrary.wiley.com/doi/10.1111/trf.16100

An awesome interview with Lauren McKnight from the Garvan Institute on all things genetic sequencing, profiling and genotyping.  Covering the following key point: Investigate the use of technologies to determine inheritance patterns in a population using, for example: (ACSBL064, ACSBL085) - DNA sequencing and profiling (ACSBL086) Thanks to STEM Reactor for sponsoring this podcast. They provide everything you need to do biotechnology at school, check them out at www.stemreactor.com.au

In this episode, Dr. Joseph Eron and Dr. Jason Halperin discuss caring for complex HIV cases, including patients with underlying resistance or comorbidities.Presenters:Joseph J. Eron, Jr., MDProfessor of Medicine and EpidemiologyUniversity of North Carolina School of MedicineDirector, AIDS Clinical Trials UnitUniversity of North CarolinaChapel Hill, North CarolinaJason Halperin, MD, MPHAssistant Professor of MedicineDepartment of Infectious DiseasesTulane UniversityInfectious Disease PhysicianCrescentCareNew Orleans, LouisianaContent based on an online CME program supported by an independent educational grant from ViiV Healthcare.Link to full program:https://bit.ly/34fVILZ

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.11.335323v1?rss=1 Authors: Choi, K., He, H., Gatti, D. M., Philip, V. M., Raghupathy, N., Munger, S. C., Chesler, E. J., Churchill, G. A. Abstract: Transcriptome profiling by RNA sequencing (RNA-Seq) of genetically segregating populations is widely used to investigate the regulatory programme of gene expression and its downstream phenotypic consequences. We address analytical challenges of RNA-Seq experiments in multi-parent populations (MPPs) that are derived from two or more inbred founder strains. Genotyping arrays or low-coverage DNA sequencing are commonly used to detect founder strain variants and to reconstruct the founder haplotype mosaic of MPP individuals. We propose and evaluate a new method, Genome reconstruction by RNA-Seq (GBRS), that simultaneously reconstructs individual diploid genomes and quantifies total and allele-specific expression directly from RNA-Seq data. We demonstrate that there is sufficient information in the genetic variants revealed in RNA-Seq data to reconstruct MPP haplotypes. Unlike existing RNA-seq-based genotyping methods, GBRS exploits multi-way allele-specific expression and jointly use closely neighboring variants. GBRS haplotype reconstructions have accuracy comparable to array-based reconstructions. GBRS provides RNA-Seq quantification that is tailored to individual genomes and does not suffer from biases that can arise when using reference genome alignment. GBRS also provides a quality control for detecting sample mix-ups and can improve power to detect expression quantitative trait loci. GBRS software is freely available at https://github.com/churchill-lab/gbrs. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.16.252635v1?rss=1 Authors: Mo, S., Li, J., Li, B., Yu, R., Nie, S., Zhang, Z., Kashif, M., He, S., Liao, J., Jiang, Q., Shen, P., Yan, B., Jiang, C. Abstract: Motivation Sulfate reduction is an important process in the sulfur cycle. However, the relationship between this process and the genotype of microorganisms involved in subtropical mangrove ecosystems is poorly understood. Genotyping can identify and is crucial for sulfate reduction in mangrove ecosystems with high sulfur concentrations. A professional and efficient gene integration database of sulfur metabolism has not been established yet. Results This work aimed to evaluate sulfate reduction by microorganisms in mangroves by using a sulfur metabolism gene integrative database (SMDB) that was mainly constructed to analyze the sulfur cycle (sub) gene families quickly and accurately. The database achieved high coverage, fast retrieval, and low false positives. Relative enrichment of sulfate adenylyltransferase indicated that environmental factors select for a partial dissimilatory sulfate reduction process. Furthermore, the sulfate reduction community compensates by producing certain sulfate-reduction genes in response to high-sulfur environments in mangrove sediments. Taxonomic assignment of dissimilatory sulfate-reduction genes revealed that Crenarchaeota and Halobacterota are completely responsible for this process. Sulfite reductase can help the community cope with the toxic sulfite produced by these Archaea phyla. Collectively, these findings suggested that Halobacterota and Crenarchaeota play essential roles in dissimilatory sulfate reduction. Availability and implementation SMDB is freely available under http://smdb.gxu.edu.cn/ and https://github.com/taylor19891213/sulfur-metabolism-gene-database. Supplementary information Supplementary data are available at Bioinformatics online. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.18.209882v1?rss=1 Authors: Islam, M., Abdullah,, Zubaida, B., Shafqat, N., Masood, R., Khan, U., Waseem, S., Waheed, M. T., Haider, W., Tahir, J., Ahmed, I., Naeem, M., Ahmad, H. Abstract: Wheat (Triticum aestivum) is the most important staple food in Pakistan. Knowledge of its genetic diversity is critical for designing effective crop breeding programs. Here we report agro-morphological and yield data for 112 genotypes (including 7 duplicates) of wheat (Triticum aestivum) cultivars, advance lines, landraces and wild relatives, collected from several research institutes and breeders across Pakistan. We also report genotyping-by-sequencing (GBS) data for a selected sub-set of 52 genotypes. Sequencing was performed using Illumina HiSeq 2500 platform using the PE150 run. Data generated per sample ranged from 1.01 to 2.5 Gb; 90% of the short reads exhibited quality scores above 99.9%. TGACv1 wheat genome was used as a reference to map short reads from individual genotypes and to filter single nucleotide polymorphic loci (SNPs). On average, 364,074{+/-}54479 SNPs per genotype were recorded. The sequencing data has been submitted to the SRA database of NCBI (accession number SRP179096). The agro-morphological and yield data, along with the sequence data and SNPs will be invaluable resources for wheat breeding programs in future. Copy rights belong to original authors. Visit the link for more info

Welcome to the NeurologyLive Mind Moments podcast. Tune in to hear leaders in neurology sound off on topics that impact your clinical practice.     In this episode, we’re joined by Dr. Daniel Claassen, an associate professor of neurology in the Department of Cognitive and Behavioral Neurology and Movement Disorders at Vanderbilt University. Dr. Claassen discussed the recent work he and colleagues did in assessing the feasibility of conducting clinical trials using therapies that target single nucleotide polymorphisms, or SNPs, in patients with Huntington disease.      Thanks for listening to the NeurologyLive Mind Moments podcast. For more neurology news and expert-driven content, visit neurologylive.com (http://neurologylive.com/) . REFERENCE Claassen DO, Corey-Bloom J, Dorsey ER, et al. Genotyping single nucleotide polymorphisms for allele-selective therapy in Huntington disease. Neurology. 2020;6(3):e430. doi: 10.1212/NXG.0000000000000430

Dr. Daniel Claassen discusses his paper,  "Genotyping Single Nucleotide Polymorphisms for Allele-Selective Therapy in Huntington Disease". Show References: Paper: https://ng.neurology.org/content/6/3/e430 Podcast: https://neurology.libsyn.com/website

Using precision genotyping for identifying resistance mechanisms in advanced lung cancer can help guide treatment decisions and prolong the benefit... The post Genotyping in lung cancer and multi-cancer detection appeared first on VJOncology.

Using precision genotyping for identifying resistance mechanisms in advanced lung cancer can help guide treatment decisions and prolong the benefit... The post Genotyping in lung cancer and multi-cancer detection appeared first on VJOncology.

We recently had the opportunity to interview Rebecca Millecamps, a Marketing Manager at Fujirebio, a global leader in the field of in vitro diagnostics (IVD). In 2019, Novosanis and Fujirebio, signed a worldwide, non-exclusive agreement for the distribution of  Colli-Pee®, Novosanis’ urine collection device for use with Fujirebio’s INNO-LiPA HPV genotyping Extra II assay. This partnership enables detection and full genotyping of Human Papillomavirus (HPV) in first-void urine (first 20 mL of urine) collected with Colli-Pee®. In this podcast, Rebecca discusses how urine testing will impact HPV testing, what the benefits are of performing HPV genotyping in urine samples and the future for urine testing for HPV compared to cervical samples. 

Farm Talk Segment 1 - Zach Bateson - National Ag Genotyping Center

Farm Talk Segment 5 - Zach Bateson - National Ag Genotyping Center

This webinar will present the recent advancements in custom SNP panel design using whole genome analysis and review various genotyping technologies, optimized for different agricultural use cases. During this session you’ll learn: • Why understanding your diversity is key to efficient and applicable genotyping• Which various genotyping methods should be applied for different species and […] The post Seed World Innovation Webinar Series: Next Generation Genotyping – Better breeding predictions at a lower cost appeared first on Seed World.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.04.28.061184v1?rss=1 Authors: Grydeland, H., Sederevicius, D., Wang, Y., Bartres-Faz, D., Bertram, L., Dobricic, V., Düzel, S., Ebmeier, K. P., Lindenberger, U., Nyberg, L., Pudas, S., Sexton, C. E., Sole-Padulles, C., Walhovd, K. B., Fjell, A. M. Abstract: Objective: To test the hypothesis that worse self-reported sleep relates to reduced hippocampal integrity as indexed by increased intra-hippocampal water diffusion, and that this relationship is stronger in the presence of {beta}-amyloid (A{beta}) accumulation, a marker of Alzheimer's disease (AD) pathology. Methods: Two-hundred and fifty-one participants, aged 19-81 years, completed the Pittsburgh Sleep Quality Index, and 2 diffusion tensor imaging sessions, on average 3 years apart, allowing estimates of decline in hippocampal microstructural integrity as indexed by increased mean diffusivity (MD). We used the delayed recall from the California Verbal Learning Test to measure memory change. 18F-Flutemetamol PET, in 108 participants above 44 years of age, yielded 23 A{beta} positive cases. Genotyping enabled controlling for APOE {varepsilon}4 status, and polygenic scores for sleep efficiency and AD. Results: Worse global sleep quality and sleep efficiency related to more rapid reduction in hippocampal microstructural integrity over time. Focusing on sleep efficiency, this relationship was stronger in presence of cortical A{beta} accumulation. Sleep efficiency also related to memory decline indirectly via hippocampal integrity decline. The results were not explained by genetic risk for sleep efficiency and AD. Conclusions: Poor self-reported sleep efficiency related to decline in hippocampal integrity, especially in the presence of A{beta} accumulation. Poor sleep and hippocampal microstructural decline may partly explain memory decline in older adults with A{beta} pathology. The relationships were not explained by genetic risk, and poor self-reported sleep efficiency might constitute a risk factor for AD, although the causal mechanisms driving the of observed associations are unknown. Copy rights belong to original authors. Visit the link for more info

Dr. Jan Dutz speaks with JCMS Editor-in-chief Dr Kirk Barber about the article Dutz co-authored in the Nov/Dec 2019 edition of the Journal of Cutaneous Medicine and Surgery. The article focuses on how East Asians exposed to the urate-lowering drug allopurinol have a predilection for severe cutaneous drug reactions such as drug-induced hypersensitivity syndrome or drug reaction with eosinophilia and systemic symptoms and Stevens-Johnson syndrome/toxic epidermal necrolysis. Dr Barber and Dr Dutz discuss why screening of patients of East Asian descent for the presence of HLA-B*58:01 prior to allopurinol initiation has been a Canadian missed opportunity. And what more can be done to encourage wider use of this inexpensive screening test.Dr. Jan Dutz is Professor and Head of the Department of Dermatology and Skin Science at UBC. He is also a Senior Scientist with the British Columbia Children's Hospital Research Institute.Theme music by Lee RosevereProduced by David McGuffin - Explore Podcast Productions 

Dr. Jan Dutz speaks with JCMS Editor-in-chief Dr Kirk Barber about the article Dutz co-authored in the Nov/Dec 2019 edition of the Journal of Cutaneous Medicine and Surgery. The article focuses on how East Asians exposed to the urate-lowering drug allopurinol have a predilection for severe cutaneous drug reactions such as drug-induced hypersensitivity syndrome or drug reaction with eosinophilia and systemic symptoms and Stevens-Johnson syndrome/toxic epidermal necrolysis. Dr Barber and Dr Dutz discuss why screening of patients of East Asian descent for the presence of HLA-B*58:01 prior to allopurinol initiation has been a Canadian missed opportunity. And what more can be done to encourage wider use of this inexpensive screening test. Dr. Jan Dutz is Professor and Head of the Department of Dermatology and Skin Science at UBC. He is also a Senior Scientist with the British Columbia Children’s Hospital Research Institute. Theme music by Lee Rosevere Produced by David McGuffin - Explore Podcast Productions  

Sergey Musienko is the founder and CEO of Atlas Biomed. They provide genetic sequencing and microbiome tests to monitor your health. Sergey is a graduate of the singularity university ran by Ray Kurzweil where he first started working on the idea for Atlas Biomed. They are now one of the leading sources of data and insights into health for the curious and health-conscious human. I have used their tests myself and can highly recommend the insights and the user interface of the website is simply fantastic. There is a tonne of complicated data that they boil down into a really accessible and interesting format. They provide all the key information for how to actively increase your health and life-span with cutting edge science. Insights The importance of genetics in getting to know an individual’s health. How efforts are being made to make medicine proactive rather than reactive. How genotyping can be used to find out the disease risks that individuals face due to genetic mutations? Multi-factorial traits and diseases – how genetic only partially affects them. Combining genetic information with personal data and health records to develop a holistic idea about one’s health. Gut bacteria – their importance, functions, effects, diversity, and even transplants. A diverse diet is essential to maintain one’s health for a long period of time. How Sergey’s company aims to push science Sergey and Atlas Biomed Connect on LinkedIn (https://www.linkedin.com/in/sergeymusienko/) Atlas Biomed (https://atlasbiomed.com/) ABOUT THE HOST My name is Sam Harris. I am a British entrepreneur, investor and explorer. From hitchhiking across Kazakstan to programming AI doctors I am always pushing myself in the spirit of curiosity and Growth. My background is in Biology and Psychology with a passion for improving the world and human behaviour. I have built and sold companies from an early age and love coming up with unique ways to make life more enjoyable and meaningful. Sam: Instagram (https://www.instagram.com/samjamsnaps/) Quora (https://www.quora.com/profile/Sam-Harris-58) Twitter (https://twitter.com/samharristweets) LinkedIn (https://www.linkedin.com/in/sharris48/) Sam's blog - SamWebsterHarris.com (https://samwebsterharris.com/) Support the Show - Patreon (https://www.patreon.com/growthmindset) Subscribe! If you enjoyed the podcast please subscribe and rate it. And of course, share with your friends! Special Guest: Sergey Musienko.

Your genome contains the specific code for how you respond to training, how quickly you recover, how predisposed you are to injury, and so much more. Genotyping services like 23andMe and Ancestry.com give you easy access to your genome. Learn how TriDot's Physiogenomix technology unlocks this code to leverage your DNA so you can train more efficiently and stay injury free.

Modern genotyping is discussed in this second part.

In this episode, Justin & Jordan discuss the vegan and vegetarian diets as put forth within the 2018 film, The Game Changers. Their discussion offers input on the gut microbiome, expands upon ideas presented in the film and outlines considerations regarding the proper implementation of the vegan or vegetarian diet  for those exploring this option. Episode Breakdown03:15 Vegan vs. Vegetarian 06:35 Kellogg's Money vs. USDA08:00 Diet Extremes-Carnivore Diet & Immunology & Subjective Results09:50 VARIETY & Gut Health13:10 Meat & Veggies-Take Home Idea15:30 Protein & Athletic Performance16:45 Before & After Meat? 19:00 Pre Game Popeyes? WHY?!19:42 Protein for energy? Carbs?21:09 Gladiator Arguments. Paleo diet?25:24 Genotyping for Your Diet27:00 Muscle: The Largest Organ(s) & Functions28:20 Carbs vs. Protein-Biochemical Breakdown28:58 Protein for Metabolic Pathways29:30 Caloric Intake & Macronutrient Breakdown+Micronutrients30:55 Daily Change in Nutrient Absorption vs. Gut Microbiome34:45 Meat & Inflammation35:30 Cholesterol TeaserReading List for The Game Changers review!!SponsorsConsistency Breeds Growth Use Promo Code: "CBG" Genopalate (United States Only)Use Promo Code: "CBG" Xendurance The Starving PodcastInstagram:  @the_starving_podcastJustin's Instagram:  @jrome_cbgJordan's Instagram:  @sleepinginonschooldaysGmail: thestarvingpodcast@gmail.comMusic: The New Idea Store FB: The New Idea Store Gmail: thenewideastore@gmail.com

Genotyping is at the foundation of modern microbiology. We discuss all of the techniques used in the preNGS era.

September 2019 See acast.com/privacy for privacy and opt-out information.

Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at the cost of the increased error rate. Trevor Pesout describes how he and his colleagues leverage long reads for simultaneous variant calling/genotyping and phasing. This is possible thanks to a clever use of a hidden Markov model, and two different algorithms based on this model are now implemented in the MarginPhase and WhatsHap tools. Links: Preprint: Haplotype-aware genotyping from noisy long reads (Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten)

In this episode we explore a hybrid approach for genotyping one of the most variable parts of the vertebrate genome: the major histocompatibility complex (MHC). Join Dr Silvia Fuselli (University of Ferrara) and Dr Rodrigo Baptista (University of Georgia) as they explain their work combining the best aspects of both next and third generation sequencing platforms—an approach that is bringing us ever closer to solving the genome puzzle. See acast.com/privacy for privacy and opt-out information.

Samantha Esselmann is a content & curation scientist at the genotyping company, 23andMe, where she works on the Ancestry team. Samantha joined 23andMe late in 2017. As a content scientist on the team, Samantha works closely with 23andMe's population geneticists and content writers to craft an engaging (and educational!) product experience. Samantha became passionate about science communication during her Neuroscience PhD at the University of California, San Francisco, where she also captained the UCSF Science Policy Group. In 2016, she served as the BRCA Foundation's Multimedia Science Communications Coordinator, where she produced a podcast series highlighting a diversity of experiences related to hereditary forms of cancer." Today we talk genetic composition, ancestry, and how sometimes, when you want to find someone, instead of going through Facebook or google searches, you can simply take a look into the oldest text on Earth, your DNA. That’s how I found my long lost second and third cousins through 23andme, and visited them in Santa Barbara, California. Errata: "People who have two copies of hereditary hemochromatosis variants have between 2%-36% risk for developing the disease based on a number of factors. It is one of 23andMe's Genetic Health Risk reports."

George Church, professor at Harvard & MIT, co-author of 480 papers, 130 patent publications & one book "Regenesis", originally published in 2012. His contributions have enabled nearly all advancements in “next generation” DNA sequencing methods, he’s cofounded over 20 companies and he was listed as one of TIME’s 100 most influential people of 2017. Also considered the father of synthetic biology. George M. Church - http://arep.med.harvard.edu/gmc/ Nebula Genomics - https://www.nebulagenomics.io/ Veritas Genetics - https://www.veritasgenetics.com/ Show Notes • Nebula Genomics origins and Veritas Genetics traction • Genotyping vs. Medical grade whole genome sequencing – prices, value, and utility • Data ownership of personal genomes • Personal Genome Project is an open source/open access collaboration to share genomic and phenotypic information with researchers • 3 Axes: How close to useful medical genome (technically); who controls it (self or corporate); how useful on a day-to-day basis (understandability and interactivity). • Genome sequencing technology adoption and Seat-belts • What scientific and social problems are you most concerned or obsessed with today? • Aging Reversal • Human life extension limitations and perceptions • How Genome sequencing is like the internet back in the late 1980s. • Genome editing risks and biohacking ethics • Equitable distribution of gene editing technology among all the people require lower cost • What’s more important- Information Systems R&D or microbiology wet-lab experiments? How dependent are they on each other? • How did you first hear about blockchain technology? • Personal Genetics Education Project - PGed.org • Cambrian explosion of blockchains • Exploring possibilities of genomic research • What is the basis of consciousness? • George’s favorite scientists Quick Quote: Decoding the human genome sequence is the most significant undertaking that we have mounted so far in an organized way in all of science. I believe that reading our blueprints, cataloguing our own instruction book, will be judged by history as more significant than even splitting the atom or going to the moon. -Francis S. Collins [Director of the National Institute of Health (NIH)] News Corner 23andMe announces $300M deal for your DNA with giant drug company GSK - https://www.digitaltrends.com/cool-tech/23andme-gsk-drugs/

Try Dashlane here: http://bit.ly/minutedash. Plus, here’s a 10% off promo code for Dashlane Premium: youtube2018 Thanks also to our Patreon patrons https://www.patreon.com/MinuteEarth and our YouTube sponsors. Once it’s out of your body, your genetic information is valuable to a variety of people, but you can keep it safe(ish) with a few simple steps. ___________________________________________ To learn more, start your googling with these keywords: Personal Genetic Analysis: Direct-to-consumer DNA testing, usually through mail-in saliva samples. Single Nucleotide Polymorphism: A variation at a single spot on the genome that is present in some part of the population. Genotyping chip: A microarray that allows genetic testing companies to test a DNA sample for hundreds of thousands of single nucleotide polymorphisms. Health Care Fraud: A crime that usually involves misrepresenting medical information in order to make money. Targeted Advertising: The practice of placing ads based on consumer demographics or behavior. Genetic Information Nondiscrimination Act: A 2008 American law that prohibits health insurers and employers from using genetic information when making coverage or hiring decisions. ___________________________________________ Subscribe to MinuteEarth on YouTube: http://goo.gl/EpIDGd Support us on Patreon: https://goo.gl/ZVgLQZ And visit our website: https://www.minuteearth.com/ Say hello on Facebook: http://goo.gl/FpAvo6 And Twitter: http://goo.gl/Y1aWVC And download our videos on itunes: https://goo.gl/sfwS6n ___________________________________________ Credits (and Twitter handles): Script Writer: David Goldenberg (@dgoldenberg) Script Editor: Emily Elert (@eelert) Video Illustrator: Jesse Agar Video Director: Emily Elert (@eelert) Video Narrator: Kate Yoshida (@KateYoshida) With Contributions From: Henry Reich, Alex Reich, Ever Salazar, Peter Reich Music by: Nathaniel Schroeder: http://www.soundcloud.com/drschroeder ___________________________________________ References: Melissa Gymrek, Amy L. McGuire, David Golan, Eran Halperin, Yaniv Erlich (2013). Identifying Personal Genomes by Surname Inference. Science. 339:6117 (321-324). Retrieved from: http://science.sciencemag.org/content... Joh, E. (2011). DNA Theft: Recognizing the Crime of Nonconsensual Genetic Collection and Testing. Boston University Law Review. 91:2 (666-700) Retrieved from: https://www.bu.edu/law/journals-archi... Tanner, A. (2017). Our Bodies, Our Data: How Companies Make Billions Selling Our Medical Records. Available at: https://www.amazon.com/gp/search?inde... Koerner, B. (2015). Your Relative’s DNA Could Turn You Into A Suspect. Wired. Retrieved from: https://www.wired.com/2015/10/familia... Pollack, A. (2015). Building a Face, and a Case, on DNA. New Yourk Times. Retrieved from: https://www.nytimes.com/2015/02/24/sc... Cappos, Justin. (2017). Professor of Computer Science and Engineering, NYU. Personal Communication.

Hiding from Hep C? Dive in with experts Dr. Gina Simoncini, MD, MPH Associate Professor of Clinical Medicine at Temple University Hospital, & Dr. David Koren, PharmD, BCPS, AAHIVP,  board-certified pharmacotherapy specialist and infectious diseases clinical pharmacist at Temple University Hospital. They walk us through a simplified approach on whom to screen, how to start antiviral therapy, what to follow up on, and how to navigate insurance waters along the way. Special thanks to Sarah Roberts and Jordana Kozupsky who wrote and produced this episode and the show notes! Full show notes available at http://thecurbsiders.com/podcast Join our mailing list and receive a PDF copy of our show notes every Monday. Rate us on iTunes, recommend a guest or topic and give feedback at thecurbsiders@gmail.com. Time Stamps 00:00 Intro 01:00 Guest bios 03:00 Getting to know our guests 05:35 Picks of the week 10:05 Clinical case 10:54 Diagnosing HCV 12:00 ASCEND study 13:14 Restrictions on HCV treatment 15:17 Ordering and interpreting pre-treatment tests 19:30 Prescribing medication 22:00 Genotyping and drug resistance 24:10 Patient counseling 25:49 Understanding drug classes 27:33 Drug interactions 30:06 Multidisciplinary approach to treatment 33:01 Follow-up 36:47 Reinfection/cure rates 39:35 Patient counseling revisited 41:25 Side effects of treatment 42:53 Screening 44:02 Take home points Tags: hepatitis, virus, hcv, direct-acting, antiviral, therapy, management, primary, care, liver, ultrasound, fibrosis, cirrhosis, side, effects, monitoring, hcc, hiv, infectious, disease, assistant, education, doctor, family, foam, foamed, health, hospitalist, hospital, internal, internist, nurse, meded, medicine, medical, primary, physician, resident, student

Sponsored By 23 And Me (Click here to get your own test kit) DISCUSS THIS EPISODE HERE Intro Contra Theme Song   Airplane Body Slams Guy getting body slammed on a United flight  United CEO’s response CEO’s second response Overbooking video by Wendover Productions Making it Podcast with Bob Clagett   23 And Me Click here to use our sponsor link to get a test kit http://www.23andme.com/nodumbquestions Sandlin Family Crest History of the Atlantic slave trade Genotyping   James Bond Sean Connery strangling woman with bikini Daniel Craig Skyfall Trailer Goldeneye N64 Play Through James Bond intro with rifling looking down the barrel   Wrap Up Stuff GI Joe Public Service Announcement Follow links: Our podcast YouTube channel Our website is nodumbquestions.fm No Dumb Questions Twitter Matt's Twitter  Destin's Twitter Subscribe links: Subscribe on iTunes Subscribe on Android Feedback options: No Dumb Questions Subreddit (on reddit.com) Share thoughts on our Patreon   Our YouTube channels are also fun:     Matt's YouTube Channel (The Ten Minute Bible Hour)     Destin's YouTube Channel (Smarter Every Day)  

Dr Janjira Thaipadungpanit from our MORU unit in Bangkok, Thailand, tells us about her research on molecular diagnosis and bacterial genotyping A molecular microbiologist, Dr Janjira's research focusses on using bacterial typing based on genome to confirm which disease is present in a patient. She aims to develop a single whole genome sequence type test using mutliple-PCR assays that can determine from a single sample of blood what bacteria or viruses are present in a patient's blood – thereby speeding up diagnosis and potentially saving lives in resource-limited settings. Head of Molecular Microbiology at MORU, Dr Janjira Thaipadungpanit's research interests include the molecular epidemiology of leptospirosis and melioidosis using multilocus sequence typing or genome data and molecular diagnosis to identify the causes of acute febrile illness and sepsis in patients.

Dr Janjira Thaipadungpanit from our MORU unit in Bangkok, Thailand, tells us about her research on molecular diagnosis and bacterial genotyping A molecular microbiologist, Dr Janjira's research focusses on using bacterial typing based on genome to confirm which disease is present in a patient. She aims to develop a single whole genome sequence type test using mutliple-PCR assays that can determine from a single sample of blood what bacteria or viruses are present in a patient's blood – thereby speeding up diagnosis and potentially saving lives in resource-limited settings. Head of Molecular Microbiology at MORU, Dr Janjira Thaipadungpanit's research interests include the molecular epidemiology of leptospirosis and melioidosis using multilocus sequence typing or genome data and molecular diagnosis to identify the causes of acute febrile illness and sepsis in patients.

Listen to the full conversation w/ Dr. Glenn pierce in this piece of bonus content from Episode 1 of BloodStream.

Dr. Connie Westhoff from the New York Blood Center outlines D variant types (weak and partial D in particular) and describes a way to manage pregnant ladies and transfusion recipients with this serologic type.

Giulia Siravegna of the University of Torino and the IRCCS-Candiolo Cancer Institute discusses the recent study on the potential of circulating tumor DNA (ctDNA) to evaluate response to chemotherapy in colorectal cancer patients; how ctDNA will be used in conjunction with other tests in the standard of care for colorectal cancer; exciting applications emerging for liquid biopsies; and results from the recent liquid biopsy study published in Nature. Find more at http://www.NextGenerationDx.com/Cell-Free-DNA Watch the interview at https://youtu.be/JHD9YR4NYX0

There were many advances in lung cancer targeted treatments in 2014. The one that most excites Dr. Geoffrey Oxnard from Dana-Farber Cancer Institute is the use of liquid biopsies.

There were many advances in lung cancer targeted treatments in 2014. The one that most excites Dr. Geoffrey Oxnard from Dana-Farber Cancer Institute is the use of liquid biopsies.

There were many advances in lung cancer targeted treatments in 2014. The one that most excites Dr. Geoffrey Oxnard from Dana-Farber Cancer Institute is the use of liquid biopsies.

Turnaround times are often long in PCR-based tests because multiple reactions are usually performed in parallel using programmable thermal cyclers. These methods typically use a single protocol, placing constraints on assay design.

Dr Mario Sideri talks to ecancer at the 2013 ESGO meeting about new methods of screening for cervical cancer.

Background: Patients diagnosed for a serous ovarian borderline tumor (s-BOT) typically present with an excellent clinical outcome. However there have been controversies concerning the prognostic impact of so-called implants, an extra ovarian spread occurring alongside the s-BOT in certain cases. It remains obscure whether these implants actually resemble metastasis owning the same genetic pattern as the ovarian primary or whether they develop independently. Methods: The current study, in the aim of further clarifying the genetic origin of implants, assessed BRAF/KRAS hot spot mutations and the p53/p16(INK4a) immunophenotype of s-BOTs and corresponding implants (n = 49) of 15 patients by pyro-sequencing and immunostaining, respectively. Results: A significant proportion of both s-BOTs and implants showed KRAS or BRAF mutation and though p16(INK4a) was found to be abundantly expressed, p53 immunoreactivity was rather low. When genotypes of BRAF/KRAS mutated s-BOTs and corresponding implants were compared no patient presented with a fully matching mutation profile of s-BOTs and all corresponding implants. Conclusions: The current study reveals genetic heterogeneity of s-BOTs and implants, as none of the markers examined showed constant reciprocity. Hence, our findings may assist to explain the different clinical presentation of s-BOTs and implants and might encourage to applying more individualized follow up protocols.

Background: The throughput of next-generation sequencing machines has increased dramatically over the last few years; yet the cost and time for library preparation have not changed proportionally, thus representing the main bottleneck for sequencing large numbers of samples. Here we present an economical, high-throughput library preparation method for the Illumina platform, comprising a 96-well based method for DNA isolation for yeast cells, a low-cost DNA shearing alternative, and adapter ligation using heat inactivation of enzymes instead of bead cleanups. Results: Up to 384 whole-genome libraries can be prepared from yeast cells in one week using this method, for less than 15 euros per sample. We demonstrate the robustness of this protocol by sequencing over 1000 yeast genomes at similar to 30x coverage. The sequence information from 768 yeast segregants derived from two divergent S. cerevisiae strains was used to generate a meiotic recombination map at unprecedented resolution. Comparisons to other datasets indicate a high conservation of recombination at a chromosome-wide scale, but differences at the local scale. Additionally, we detected a high degree of aneuploidy (3.6%) by examining the sequencing coverage in these segregants. Differences in allele frequency allowed us to attribute instances of aneuploidy to gains of chromosomes during meiosis or mitosis, both of which showed a strong tendency to missegregate specific chromosomes. Conclusions: Here we present a high throughput workflow to sequence genomes of large number of yeast strains at a low price. We have used this workflow to obtain recombination and aneuploidy data from hundreds of segregants, which can serve as a foundation for future studies of linkage, recombination, and chromosomal aberrations in yeast and higher eukaryotes.

Prevent Cancer with Alkaline Diet! Cindy Bryant Topic Eat Green  Genotyping Website http://HealthyPerspectives@gmail.com Healthy Perspective Wellness Center 928-472-7120 Meet January http://www.januaryjones.com Join http://www.successimo.com/join Contact http://januaryjonesinfo@gmail.com  

This presentation will 1) Present a concept on the financial viability starting a molecular diagnostics lab testing practice in terms most convincing to CFOs. 2) Determine what molecular tests should be considered based on internal and external factors and how to gain overall organizational support for doing them in-house. 3) Develop and track the information necessary to convince budget makers and key stake holders to expand molecular diagnostics testing over time. Speaker: Terry Petersen, MST, CLS, BMS, MT(ASCP), Laboratory Director, Kalispell Regional Medical Center, Montana Duration: 135 minutes Credit hours: 2.5

The PR interval on the electrocardiogram reflects atrial and atrioventricular nodal conduction time. The PR interval is heritable, provides important information about arrhythmia risk, and has been suggested to differ among human races. Genome-wide association (GWA) studies have identified common genetic determinants of the PR interval in individuals of European and Asian ancestry, but there is a general paucity of GWA studies in individuals of African ancestry. We performed GWA studies in African American individuals from four cohorts (n = 6,247) to identify genetic variants associated with PR interval duration. Genotyping was performed using the Affymetrix 6.0 microarray. Imputation was performed for 2.8 million single nucleotide polymorphisms (SNPs) using combined YRI and CEU HapMap phase II panels. We observed a strong signal (rs3922844) within the gene encoding the cardiac sodium channel (SCN5A) with genome-wide significant association (p < 2.5 > 10(-8)) in two of the four cohorts and in the meta-analysis. The signal explained 2% of PR interval variability in African Americans (beta = 5.1 msec per minor allele, 95% CI = 4.1-6.1, p = 3 x 10(-23)). This SNP was also associated with PR interval (beta = 2.4 msec per minor allele, 95% CI = 1.8-3.0, p = 3 x 10(-16)) in individuals of European ancestry (n = 14,042), but with a smaller effect size (p for heterogeneity < 0.001) and variability explained (0.5%). Further meta-analysis of the four cohorts identified genome-wide significant associations with SNPs in SCN10A (rs6798015), MEIS1 (rs10865355), and TBX5 (rs7312625) that were highly correlated with SNPs identified in European and Asian GWA studies. African ancestry was associated with increased PR duration (13.3 msec, p = 0.009) in one but not the other three cohorts. Our findings demonstrate the relevance of common variants to African Americans at four loci previously associated with PR interval in European and Asian samples and identify an association signal at one of these loci that is more strongly associated with PR interval in African Americans than in Europeans.

Apart from its regulatory function in lipid and glucose metabolism, peroxisome proliferator-activated receptor (PPAR)γ has impact on the regulation of inflammation and bone metabolism. The aim of the study was to investigate the association of five polymorphisms (rs10865710, rs2067819, rs3892175, rs1801282, rs3856806) within the PPARG gene with chronic periodontitis. The study population comprised 402 periodontitis patients and 793 healthy individuals. Genotyping of the PPARG gene polymorphisms was performed by PCR and melting curve analysis. Comparison of frequency distribution of genotypes between individuals with periodontal disease and healthy controls for the polymorphism rs3856806 showed a P-value of 0.04 but failed to reach significance after correction for multiple testing (P  0.90). A 3-site analysis (rs2067819-rs1801282-rs3856860) revealed five haplotypes with a frequency of ≥1% among cases and controls. Following adjustment for age, gender and smoking, none of the haplotypes was significantly different between periodontitis and healthy controls after Bonferroni correction. This study could not show a significant association between PPARG gene variants and chronic periodontitis.

The first genome wide association study (GWAS) for childhood asthma identified a novel major susceptibility locus on chromosome 17q21 harboring the ORMDL3 gene, but the role of previous asthma candidate genes was not specifically analyzed in this GWAS. We systematically identified 89 SNPs in 14 candidate genes previously associated with asthma in >3 independent study populations. We re-genotyped 39 SNPs in these genes not covered by GWAS performed in 703 asthmatics and 658 reference children. Genotyping data were compared to imputation data derived from Illumina HumanHap300 chip genotyping. Results were combined to analyze 566 SNPs covering all 14 candidate gene loci. Genotyped polymorphisms in ADAM33, GSTP1 and VDR showed effects with p-values

HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.

The outcome of Genome-Wide Association Studies (GWAS) has challenged the field of blood pressure (BP) genetics as previous candidate genes have not been among the top loci in these scans. We used Affymetrix 500K genotyping data of KORA S3 cohort (n = 1,644; Southern-Germany) to address (i) SNP coverage in 160 BP candidate genes; (ii) the evidence for associations with BP traits in genome-wide and replication data, and haplotype analysis. In total, 160 gene regions (genic region+/-10 kb) covered 2,411 SNPs across 11.4 Mb. Marker densities in genes varied from 0 (n = 11) to 0.6 SNPs/kb. On average 52.5% of the HAPMAP SNPs per gene were captured. No evidence for association with BP was obtained for 1,449 tested SNPs. Considerable associations (P50% of HAPMAP SNPs were tagged. In general, genes with higher marker density (>0.2 SNPs/kb) revealed a better chance to reach close to significance associations. Although, none of the detected P-values remained significant after Bonferroni correction (P

Background: We investigated the influence of genotyping errors on the type I error rate and empirical power of two haplotype based association methods applied to candidate regions. We compared the performance of the Mantel Statistic Using Haplotype Sharing and the haplotype frequency based score test with that of the Armitage trend test. Our study is based on 1000 replication of simulated case-control data settings with 500 cases and 500 controls, respectively. One of the examined markers was set to be the disease locus with a simulated odds ratio of 3. Differential and non-differential genotyping errors were introduced following a misclassification model with varying mean error rates per locus in the range of 0.2% to 15.6%. Results: We found that the type I error rate of all three test statistics hold the nominal significance level in the presence of nondifferential genotyping errors and low error rates. For high and differential error rates, the type I error rate of all three test statistics was inflated, even when genetic markers not in Hardy-Weinberg Equilibrium were removed. The empirical power of all three association test statistics remained high at around 89% to 94% when genotyping error rates were low, but decreased to 48% to 80% for high and nondifferential genotyping error rates. Conclusion: Currently realistic genotyping error rates for candidate gene analysis (mean error rate per locus of 0.2%) pose no significant problem for the type I error rate as well as the power of all three investigated test statistics.

The IL23R gene has been identified as a susceptibility gene for inflammatory bowel disease (IBD) in the North American population. The aim of our study was to test this association in a large German IBD cohort and to elucidate potential interactions with other IBD genes as well as phenotypic consequences of IL23R variants. Genomic DNA from 2670 Caucasian individuals including 833 patients with Crohn's disease (CD), 456 patients with ulcerative colitis (UC), and 1381 healthy unrelated controls was analyzed for 10 IL23R SNPs. Genotyping included the NOD2 variants p.Arg702Trp, p.Gly908Arg, and p.Leu1007fsX1008 and polymorphisms in SLC22A4/OCTN1 (1672 C-->T) and SLC22A5/OCTN2 (-207 G-->C). All IL23R gene variants analyzed displayed highly significant associations with CD. The strongest association was found for the SNP rs1004819 [P = 1.92x10(-11); OR 1.56; 95 % CI (1.37-1.78)]. 93.2% of the rs1004819 TT homozygous carriers as compared to 78% of CC wildtype carriers had ileal involvement [P = 0.004; OR 4.24; CI (1.46-12.34)]. The coding SNP rs11209026 (p.Arg381Gln) was protective for CD [P = 8.04x10(-8); OR 0.43; CI (0.31-0.59)]. Similar, but weaker associations were found in UC. There was no evidence for epistasis between the IL23R gene and the CD susceptibility genes CARD15 and SLC22A4/5. IL23R is an IBD susceptibility gene, but has no epistatic interaction with CARD15 and SLC22A4/5. rs1004819 is the major IL23R variant associated with CD in the German population, while the p.Arg381Gln IL23R variant is a protective marker for CD and UC.

Interspecific genome-plastome incompatibility is a widely observed phenomenon but its primary causes are still unknown. It reflects genome-plastome interactions that play a direct role in speciation processes, such interspecific combinations of nuclear genomes and plastomes that fail to develop fully autotrophic plants which then are usually eliminated by natural selection. We have investigated two plant models displaying genome-plastome incompatibility, Oenothera and Passiflora, using strategies of molecular biology in order to contribute to an analysis of primary causes of interspecific genome-plastome incompatibility. 1. Expressed sequence tags in Oenothera: In this study we present the first analyzed EST data set for Oenothera. 3,532 cDNA sequences derived from 9-week-old Oenothera plantlets were the analysed and assembled into 1,621 nonredundant clusters, including 1,133 singletons and 488 multi-member unigenes which contain a total of 875,940 nonredundand nucleotides. EST sequences were analysed by Sputnik algorithm. They were also used in the development of gene-specific PCR-based codominant markers (SNPs, CAPS, micro-satellites). The cDNA library could be directly used for macroarray applications including gene expression studies and for physical mapping. 2. Genotyping analyses in Oenothera using AFLP technology: The comparison of AFLPs from Oenothera with AFLPs from Arabidopsis was used to obtain an approximation of the genome size. The genotyping data provide evidence that genome of Oenothera is only six times larger than that of Arabidopsis corresponding to a size of about 750 Mb. The AFLP markers were also successfully applied to construct first genetic maps using F2 mapping population of interspecific hybrids between Oenothera elata ssp. hookeri, line johansen, AA-III, x Oenothera grandiflora ssp. tuscaloosa, BB-III. The linkage maps contain 88 AFLP markers covering a total map length of 154.4 cM for dominant markers in johansen, AA-III and 104 AFLP markers and a total size of 155.3 cM for dominant markers in grandiflora, BB-III. In addition, it was possible to assign genome-plastome incompatibility locus to the margin of coupling group 2B with 13 cM distance to the next AFLP marker. SUMMARY 91 The EST project followed by genotyping analysis increases knowledge and requirements in discovering primary causes of genome-plastome incompatibility. Oenothera with genome-plastome incompatibility, chromosomal translocations and many chromosomal arrangements provides an elegant tool in the study of genomeplastome interactions, speciation processes and species evolution. 3. Investigation of genome-plastome incompatibility in Passiflora: We present the first evidence of hybrid bleaching in this genus. The hybrid between Passiflora menispermifolia x Passiflora oerstedii showed bleaching regions during plant development. Reciprocal crosses have also shown hybrid bleaching but as well significant differences in leaf shape. Molecular analyses of cpDNA showed that Passiflora plastids are inherited bi-parentally and that the P. menispermifolia plastome is incompatible in F1 hybrids with P. oerstedii. This is the first evidence of genome-plastome incompatibility in Passiflora, which differ from Oenothera incompatibilities. The analysis of plastid ultrastructure showed that green tissues in the F1 generation have fully developed chloroplasts with thylakoids and grana; the incompatible material in F1 hybrids lacks differentiated plastids and contains plastids with only rudimentary membranes. An unexpected plastid ultrastructure was found in P. menispermifolia. The leaf from plant growing at greenhouse conditions contains plastids in different development stages including etioplasts, which normally develop from proplastids in darkness. Electron micrographs also indicated retardation of grana formation in P. menispermifolia which shows that vesicles could deliver parts of thylakoid components and that they may directly participate in the formation grana stacks. Northern and Western analyses demonstrated that genome-plastome incompatibility affects both transcription and translation, but with differences for nuclear and plastome encoded genes.

Background: A single nucleotide polymorphism (SNP) in the coding region of the prion protein gene (PRNP) at codon 129 has been repeatedly shown to be an associated factor to sporadic Creutzfeldt-Jakob disease (sCJD), but additional major predisposing DNA variants for sCJD are still unknown. Several previous studies focused on the characterisation of polymorphisms in PRNP and the prion-like doppel gene (PRND), generating contradictory results on relatively small sample sets. Thus, extensive studies are required for validation of the polymorphisms in PRNP and PRND.Methods: We evaluated a set of nine SNPs of PRNP and one SNP of PRND in 593 German sCJD patients and 748 German healthy controls. Genotyping was performed using MALDI-TOF mass spectrometry.Results: In addition to PRNP 129, we detected a significant association between sCJD and allele frequencies of six further PRNP SNPs. No significant association of PRND T174M with sCJD was shown. We observed strong linkage disequilibrium within eight adjacent PRNP SNPs, including PRNP 129. However, the association of sCJD with PRNP 1368 and PRNP 34296 appeared to be independent on the genotype of PRNP 129. We additionally identified the most common haplotypes of PRNP to be over-represented or under-represented in our cohort of patients with sCJD.Conclusion: Our study evaluated previous findings of the association of SNPs in the PRNP and PRND genes in the largest cohorts for association study in sCJD to date, and extends previous findings by defining for the first time the haplotypes associated with sCJD in a large population of the German CJD surveillance study.

Two inbred rat lines have been developed that show either high (HAB) or low (LAB) anxiety-related behavior. The behavioral phenotype correlates with arginine vasopressin (AVP) expression at the level of the hypothalamic paraventricular nucleus (PVN), but not supraoptic nucleus, with HAB animals overexpressing the neuropeptide in both magnocellular and parvocellular subdivisions of the PVN. This study aimed to investigate the molecular cause of the AVP overexpression in the PVN of the HAB animals. Sequencing of the AVP locus resulted in the detection of a number of single nucleotide polymorphisms (SNPs) in the promoter differing between the HAB and LAB animals. Two of the SNPs were embedded in cis-regulatory elements. Genotyping further revealed that the HAB-specific allele of the AVP gene promoter occurs in 1.5% of outbred Wistar rats. An assay was developed to address the question of differential allele-specific transcription rates between the LAB and HAB alleles using cross-mated HAB/LAB F1 animals. Results from the experiment revealed the HAB AVP promoter to be more transcriptionally active in vivo. EMSA assays confirmed that one specific SNP [A(-1276)G] conferred reduced binding of the transcriptional repressor CArG binding factor A (CBF-A) in the HAB allele. Reporter gene assays supported the view that the A(-1276)G transition in the CArG element impairs CBF-A repression in the HAB allele, which in turn relates to a weakened repression of the intact HAB AVP promoter by CBF-A. Furthermore, CBF-A is highly co-expressed in AVP-containing neurons of the PVN supporting an important role for regulation of AVP gene expression in vivo. Taken together, these results demonstrate a role for an AVP gene polymorphism and CBF-A in elevated AVP expression in the PVN of HAB rats likely to contribute to their behavioral and neuroendocrine phenotype. Phenotypic variation among organisms is central to evolutionary adaptations underlying natural and artificial selection, and also determines individual susceptibility to common diseases including cardiovascular, metabolic and age related and psychiatric diseases. Most phenotypic diversity in natural populations is characterised by differences in degree rather than in kind. In accordance with this view, HAB rats lacked changes in the coding part of the vasopressin gene, but instead were homozygous for the polymorphic promoter region. Therefore, the HAB specific AVP promoter represents a natural model for AVP overexpression and highlights, in turn, cognate molecular pathways which potentially fuel the resulting pathologies. Specifically, our finding that the SNP in position 1276 of the AVP gene promoter underlies AVP overexpression in the PVN of HAB rats, makes this SNP a potential target for further studies aimed at improving therapeutic tools. Finally, further studies are necessary to understand to which degree and in concert with which vulnerability loci vasopressin overexpression underlies the complex neuroendocrine and behavioural stigmata in the HAB line. Certainly, such studies will yield important insights into gene-gene interactions between susceptibility genes and shed light on additional pathways suitable for therapeutic interventions. In conclusion, this present work exemplifies that selective inbreeding for behavioural traits and combined phenotypic and molecular analysis of candidate genes is an important step and tool to address these issues.