Ryota Shimada, Emily N Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M Halasz, Wei Zhou, Jeremy S Edwards
{"title":"SARS-CoV-2 variant identification using a genome tiling array and genotyping probes.","authors":"Ryota Shimada, Emily N Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M Halasz, Wei Zhou, Jeremy S Edwards","doi":"10.2217/pme-2022-0013","DOIUrl":"https://doi.org/10.2217/pme-2022-0013","url":null,"abstract":"<p><p>With over 5.5 million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. The authors previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"20 1","pages":"13-25"},"PeriodicalIF":2.3,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10350312/pdf/nihms-1907630.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9780379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cheng Chen, Melissa H Roberts, Dennis W Raisch, Todd A Thompson, Amy Bachyrycz, Matthew E Borrego
{"title":"Preferences for pharmacogenomic testing in polypharmacy patients: a discrete choice experiment.","authors":"Cheng Chen, Melissa H Roberts, Dennis W Raisch, Todd A Thompson, Amy Bachyrycz, Matthew E Borrego","doi":"10.2217/pme-2022-0056","DOIUrl":"10.2217/pme-2022-0056","url":null,"abstract":"<p><p><b>Aim:</b> To elicit preferences for pharmacogenomic (PGx) testing in polypharmacy patients. <b>Materials & methods:</b> A face-to-face discrete choice experiment survey was designed and administered to adult polypharmacy patients recruited at a local retail pharmacy in Albuquerque (NM, USA). <b>Results:</b> A total of 128 eligible polypharmacy patients completed the discrete choice experiment survey and significantly preferred a PGx test with lower cost, better confidentiality and higher certainty of identifying best medication/dose and side effects and one that can be used to advocate for their treatment needs (all p < 0.01). <b>Conclusion:</b> This is the first study eliciting preferences for PGx testing among polypharmacy patients. The study found most polypharmacy patients were willing to take a PGx test and their preferences were mostly influenced by test cost.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 6","pages":"535-548"},"PeriodicalIF":2.3,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10859042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10828352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Hassan, Omneya Hassanain, S. Kamal, L. Shalaby, M. Nagy
{"title":"Knowledge, attitudes and practices of Egyptian healthcare professionals toward therapeutic drug monitoring service as a principal component of personalized medicine.","authors":"S. Hassan, Omneya Hassanain, S. Kamal, L. Shalaby, M. Nagy","doi":"10.2217/pme-2022-0031","DOIUrl":"https://doi.org/10.2217/pme-2022-0031","url":null,"abstract":"Aim: To assess pharmacists' and physicians' knowledge, attitudes and practices toward therapeutic drug monitoring (TDM) service at the Children's Cancer Hospital Egypt 57357. Materials & methods: This was a single-site cross-sectional study where all practicing pharmacists and physicians were eligible to participate. Results: A statistically significant difference in the knowledge scores between pharmacists and physicians (p = 0.022) was found. In general, attitudes toward TDM among pharmacists and physicians were positive. Regarding practices, pharmacists were more likely than physicians to agree or strongly agree that they have studied some scientific references on TDM (p = 0.034), but more physicians recommend the TDM service (p = 0.046). Conclusion: A multidisciplinary educational program in Egypt for TDM for both medicine and pharmacy staff will improve interprofessional collaboration in the clinical setting, leading to better personalized medication management.","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42598508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Conference Report: NHGRI Research Training and Career Development Annual Meeting.","authors":"S. Haga","doi":"10.2217/pme-2022-0095","DOIUrl":"https://doi.org/10.2217/pme-2022-0095","url":null,"abstract":"Since 2016, the National Human Genome Research Institute of the US NIH has convened a meeting for their trainees. Training programs supported by the Institute are located throughout the US and provide funding to trainees from the undergraduate to the postdoctoral and junior faculty levels. The annual training meeting provides trainees with a novel opportunity to network, learn about a wide range of genomic research and gain skills and information to support their educational and career path in genomic research. The pandemic forced a transition to virtual meetings in 2020 and 2021, but the 2022 meeting was convened as a hybrid format, with 383 attendees (59% in-person) in Durham, NC, US.","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42714121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Personalized medicinePub Date : 2022-09-01Epub Date: 2022-08-03DOI: 10.2217/pme-2022-0026
Adi Caspi, Ariana A Entezari, Madison Crutcher, Adam E Snook, Scott A Waldman
{"title":"Guanylyl cyclase C as a diagnostic and therapeutic target in colorectal cancer.","authors":"Adi Caspi, Ariana A Entezari, Madison Crutcher, Adam E Snook, Scott A Waldman","doi":"10.2217/pme-2022-0026","DOIUrl":"10.2217/pme-2022-0026","url":null,"abstract":"<p><p>Colorectal cancer remains a major cause of mortality in the USA, despite advances in prevention and screening. Existing therapies focus primarily on generic treatment such as surgical intervention and chemotherapy, depending on disease severity. As personalized medicine and targeted molecular oncology continue to develop as promising treatment avenues, there has emerged a need for effective targets and biomarkers of colorectal cancer. The transmembrane receptor guanylyl cyclase C (GUCY2C) regulates intestinal homeostasis and has emerged as a tumor suppressor. Further, it is universally expressed in advanced metastatic colorectal tumors, as well as other cancer types that arise through intestinal metaplasia. In this context, GUCY2C satisfies many characteristics of a compelling target and biomarker for gastrointestinal malignancies.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"457-472"},"PeriodicalIF":1.7,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40577583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Personalized medicinePub Date : 2022-09-01Epub Date: 2022-08-01DOI: 10.2217/pme-2021-0179
Carly E Waldman, Jean H Min, Heba Wassif, Andrew M Freeman, Anne K Rzeszut, Jack Reilly, Paul Theriot, Ahmed M Soliman, Ritu Thamman, Ami Bhatt, Sanjeev P Bhavnani
{"title":"COVID-19 telehealth preparedness: a cross-sectional assessment of cardiology practices in the USA.","authors":"Carly E Waldman, Jean H Min, Heba Wassif, Andrew M Freeman, Anne K Rzeszut, Jack Reilly, Paul Theriot, Ahmed M Soliman, Ritu Thamman, Ami Bhatt, Sanjeev P Bhavnani","doi":"10.2217/pme-2021-0179","DOIUrl":"https://doi.org/10.2217/pme-2021-0179","url":null,"abstract":"<p><p><b>Aim:</b> The COVID-19 pandemic forced medical practices to augment healthcare delivery to remote and virtual services. We describe the results of a nationwide survey of cardiovascular professionals regarding telehealth perspectives. <b>Materials & methods:</b> A 31-question survey was sent early in the pandemic to assess the impact of COVID-19 on telehealth adoption & reimbursement. <b>Results:</b> A total of 342 clinicians across 42 states participated. 77% were using telehealth, with the majority initiating usage 2 months after the COVID-19 shutdown. A variety of video-based systems were used. Telehealth integration requirements differed, with electronic medical record integration being mandated in more urban than rural practices (70 vs 59%; p < 0.005). Many implementation barriers surfaced, with over 75% of respondents emphasizing reimbursement uncertainty and concerns for telehealth generalizability given the complexity of cardiovascular diseases. <b>Conclusion:</b> Substantial variation exists in telehealth practices. Further studies and legislation are needed to improve access, reimbursement and the quality of telehealth-based cardiovascular care.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"411-422"},"PeriodicalIF":2.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40672906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Personalized medicinePub Date : 2022-09-01Epub Date: 2022-07-26DOI: 10.2217/pme-2021-0047
Mehtap Cevik, Esat Namal, Nur Dinc Sener, Ulkuhan Iner Koksal, Penbe Cagatay, Gokce Deliorman, Cavlan Ciftci, Atila Karaalp, Belgin Susleyici
{"title":"Investigation of <i>DPYD</i>, <i>MTHFR</i> and <i>TYMS</i> polymorphisms on 5-fluorouracil related toxicities in colorectal cancer.","authors":"Mehtap Cevik, Esat Namal, Nur Dinc Sener, Ulkuhan Iner Koksal, Penbe Cagatay, Gokce Deliorman, Cavlan Ciftci, Atila Karaalp, Belgin Susleyici","doi":"10.2217/pme-2021-0047","DOIUrl":"https://doi.org/10.2217/pme-2021-0047","url":null,"abstract":"<p><p><b>Aim:</b> To investigate the association of <i>DPYD</i>, <i>MTHFR</i> and <i>TYMS</i> polymorphisms on 5-fluorouracil (5-FU) related toxicities and patient survival. <b>Materials & methods:</b> A total of 103 colorectal cancer patients prescribed 5-FU were included in the study. Genotyping was conducted for several <i>DPYD</i>, <i>MTHFR</i> and <i>TYMS</i> polymorphisms using a microarray analyzer. <b>Results:</b> <i>DPYD</i> 496A>G polymorphism was found to be significantly associated with 5-FU related grade 0-2, but not severe toxicities (p = 0.02). Furthermore, patients with <i>DPYD</i> 85TC and CC genotypes had longer progression and overall survival times compared to TT genotypes in our study group (log rank = 6.60; p = 0.01 and log rank = 4.40; p = 0.04, respectively). <b>Conclusion:</b> According to our results, <i>DPYD</i> 496AG and GG genotypes might be protective against severe adverse events compared to the AA genotype. Another <i>DPYD</i> polymorphism, 85T>C, may be useful in colorectal cancer prognosis. Further studies for both polymorphisms should be conducted in larger populations to achieve accurate results.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"435-444"},"PeriodicalIF":2.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40554983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Personalized medicinePub Date : 2022-09-01Epub Date: 2022-07-08DOI: 10.2217/pme-2022-0020
Caterina De Luca, Francesco Pepe, Pasquale Pisapia, Antonino Iaccarino, Luisella Righi, Angela Listì, Gianluca Russo, Severo Campione, Fabio Pagni, Mariantonia Nacchio, Floriana Conticelli, Maria Russo, Teresa Fabozzi, Elena Vigliar, Claudio Bellevicine, Danilo Rocco, Stefano Laudati, Giuseppe Iannaci, Bruno Daniele, Cesare Gridelli, Diego Luigi Cortinovis, Silvia Novello, Miguel Angel Molina-Vila, Rafael Rosell, Giancarlo Troncone, Umberto Malapelle
{"title":"RNA-based next-generation sequencing in non-small-cell lung cancer in a routine setting: an experience from an Italian referral center.","authors":"Caterina De Luca, Francesco Pepe, Pasquale Pisapia, Antonino Iaccarino, Luisella Righi, Angela Listì, Gianluca Russo, Severo Campione, Fabio Pagni, Mariantonia Nacchio, Floriana Conticelli, Maria Russo, Teresa Fabozzi, Elena Vigliar, Claudio Bellevicine, Danilo Rocco, Stefano Laudati, Giuseppe Iannaci, Bruno Daniele, Cesare Gridelli, Diego Luigi Cortinovis, Silvia Novello, Miguel Angel Molina-Vila, Rafael Rosell, Giancarlo Troncone, Umberto Malapelle","doi":"10.2217/pme-2022-0020","DOIUrl":"https://doi.org/10.2217/pme-2022-0020","url":null,"abstract":"<p><p><b>Aim:</b> <i>ALK</i>, <i>ROS1</i>, <i>NTRK</i> and <i>RET</i> gene fusions and <i>MET</i> exon 14 skipping alterations represent novel predictive biomarkers for advanced non-small-cell lung cancer (NSCLC). Therefore, testing patients for these genetic variants is crucial for choosing the best selective treatment. Over the last couple of decades, next-generation sequencing (NGS) platforms have emerged as an extremely useful tool for detecting these variants. <b>Materials & methods:</b> In the present study, we report our NGS molecular records produced during a year of diagnostic activity. <b>Results:</b> Overall, our in-house developed NGS workflow successfully analyzed n = 116/131 (88.5%) NSCLC samples. Of these, eight (6.8%) and five (4.3%) out of 116 patients harbored <i>ALK</i> and <i>RET</i> gene rearrangements, respectively: one case harbored <i>ROS1</i> gene fusion (0.7%). <b>Conclusion:</b> Our results highlight that an RNA-based NGS analysis can reliably detect gene fusion alterations, thereby playing a pivotal role in the management of NSCLC patients.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"395-401"},"PeriodicalIF":2.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40594802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The pharmacogenetics of mycophenolate mofetil in Tunisian renal transplant patients.","authors":"Amani Abderahmene, Amel Ellouz, Dorra Amor, Marwa Ajmi, Yassine Khalij, Haithem Hamdouni, Wissal Sahtout, Awatef Azzabi, Asma Omezzine, Abdellatif Achour, Ali Bouslama","doi":"10.2217/pme-2021-0092","DOIUrl":"https://doi.org/10.2217/pme-2021-0092","url":null,"abstract":"<p><p><b>Aim:</b> The effects of variants in <i>IMPDH, UGT1A9, UGT1A8, UGT2B7</i> and <i>SLCO1B1</i> genes on the efficacy and safety of mycophenolate mofetil (MMF) in the Tunisian population were investigated. <b>Materials & methods:</b> A total of 245 kidney transplant patients being treated with MMF were recruited and cotreated with cyclosporine or tacrolimus. Genotyping was performed using the polymerase chain reaction-restriction fragment length polymorphism method. MMF, cyclosporine and tacrolimus trough levels were measured by immunoassay. The AUC (AUC<sub>0-12h</sub>MPA) was estimated by a Bayesian method. <b>Results:</b> In the tacrolimus-treated group, anemia and diarrhea were associated with the <i>UGT1A9-98C</i> and <i>UGT1A9-275T</i> alleles, respectively (p < 0.05). In the cyclosporine-treated group, leukopenia was associated with the SLCO1B1-521T allele (p < 0.05). Both groups had an increased risk of rejection (p < 0.05) associated with the variant alleles of <i>IMPDH2-3757T>C</i>, <i>UGT1A9-2152C>T</i> and <i>UGT1A9-275C>A</i> and the common allele of <i>SLCO1B1-388A>G</i>. However, no significant association was found between the studied genotypes and AUC<sub>0-12h</sub>MPA or cotreatment levels. <b>Conclusion:</b> The results constitute preliminary evidence for the inclusion of the pharmacogenetics of MMF in kidney pretransplantation evaluations.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"383-393"},"PeriodicalIF":2.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40411049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Personalized medicinePub Date : 2022-09-01Epub Date: 2022-07-13DOI: 10.2217/pme-2021-0150
Marie-Anne Pépin, Anne-Sophie Otis, Zoë Tremblay, Marianne Boulé, Denis Lebel, Philippe Major, Anne Lortie, Elana Pinchefsky, Elsa Rossignol, Bruce Carleton, Jean-François Bussières, Marie-Élaine Métras
{"title":"Pharmacogenetic testing in pediatric neurology: a pragmatic study evaluating clinician and patient perceptions.","authors":"Marie-Anne Pépin, Anne-Sophie Otis, Zoë Tremblay, Marianne Boulé, Denis Lebel, Philippe Major, Anne Lortie, Elana Pinchefsky, Elsa Rossignol, Bruce Carleton, Jean-François Bussières, Marie-Élaine Métras","doi":"10.2217/pme-2021-0150","DOIUrl":"https://doi.org/10.2217/pme-2021-0150","url":null,"abstract":"<p><p><b>Aim:</b> To evaluate clinicians' and patients' perceptions of pharmacogenetic testing in a clinical setting. <b>Materials & methods:</b> This is a pragmatic mixed-method prospective observational study. Hospital pharmacists and neurologists participated in focus groups regarding pharmacogenetic testing; patients who received pharmacogenetic testing and their community pharmacists completed surveys to assess their perception of these tests. <b>Results:</b> Most study participants had a positive view of pharmacogenetic testing. Three major themes were identified from the focus groups: receptiveness to pharmacogenetic testing, pharmacogenetic test characteristics and integrating pharmacogenetic tests into practice. <b>Conclusion:</b> The views reported are encouraging for the eventual implementation of pharmacogenetics in practice. Local integration of these tests is an essential step to improve patient care through personalized medicine.</p>","PeriodicalId":19753,"journal":{"name":"Personalized medicine","volume":"19 5","pages":"423-434"},"PeriodicalIF":2.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40501674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}