Tag: PGS

No Significant Differences at 5 Year Follow-Up Between Palbociclib-Based Treatment Regimens

Results from the PARSIFAL-LONG study investigating endocrine-sensitive hormone receptor-positive/HER2-negative (HR+/HER2-) advanced breast cancer demonstrated the efficacy of 2 combined option therapies, palbociclib (Ibrance; Pfizer) plus letrozole (Femara; Novartis) and palbociclib plus fulvestrant (Faslodex; Hikma), as first-line treatments for metastatic breast cancer. The study found no significant differences in progression-free survival…

Continue Reading No Significant Differences at 5 Year Follow-Up Between Palbociclib-Based Treatment Regimens

Genomic Workstation Market Dynamics 2023-2030: Also about Its Market Trends, Projections, and Opportunities

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Opportunities”}],”lineInfo”:{“truncatedLoc”:”76″,”truncatedSloc”:”76″},”mode”:”file”},”image”:false,”isCodeownersFile”:null,”isPlain”:false,”isValidLegacyIssueTemplate”:false,”issueTemplateHelpUrl”:”docs.github.com/articles/about-issue-and-pull-request-templates”,”issueTemplate”:null,”discussionTemplate”:null,”language”:”Markdown”,”languageID”:222,”large”:false,”loggedIn”:false,”newDiscussionPath”:”/melchekhinf/Market-Research-Report-List-1/discussions/new”,”newIssuePath”:”/melchekhinf/Market-Research-Report-List-1/issues/new”,”planSupportInfo”:{“repoIsFork”:null,”repoOwnedByCurrentUser”:null,”requestFullPath”:”/melchekhinf/Market-Research-Report-List-1/blob/main/genomic-workstation-market.md”,”showFreeOrgGatedFeatureMessage”:null,”showPlanSupportBanner”:null,”upgradeDataAttributes”:null,”upgradePath”:null},”publishBannersInfo”:{“dismissActionNoticePath”:”/settings/dismiss-notice/publish_action_from_dockerfile”,”dismissStackNoticePath”:”/settings/dismiss-notice/publish_stack_from_file”,”releasePath”:”/melchekhinf/Market-Research-Report-List-1/releases/new?marketplace=true”,”showPublishActionBanner”:false,”showPublishStackBanner”:false},”rawBlobUrl”:”github.com/melchekhinf/Market-Research-Report-List-1/raw/main/genomic-workstation-market.md”,”renderImageOrRaw”:false,”richText”:” Market Overview and Report Coverage \n…

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The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article  PubMed  CAS  Google Scholar  Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…

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Population-specific distribution of TPMT deficiency variants

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

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CRISPR-created strawberries that stay firmer and fresher longer could revolutionize fruit industry

The cultivated strawberry (Fragaria × ananassa, Duch.) is one of the Rosaceae family renowned for its flavor and health benefits, making it an important agricultural commodity. However, its soft texture leads to a brief shelf life and consequent economic losses. Current breeding aims to enhance firmness without compromising quality, but…

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Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

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CRISPR/Cas9 editing enhances fruit firmness and extends shelf life

Susceptibility to Botrytis in wild type and FaPG1 edited line #13. Credit: Horticulture Research The cultivated strawberry (Fragaria × ananassa, Duch.) is one of the Rosaceae family renowned for its flavor and health benefits, making it an important agricultural commodity. However, its soft texture leads to a brief shelf life…

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Quality control on imputed genotypes for GWAS / application of PGS

Quality control on imputed genotypes for GWAS / application of PGS 0 Hi everyone, I want to run a GWAS on imputed genotypes from UKB. Unfortunately, I only found tutorials that describe the quality control of genotypes in preparation for a GWAS. Are there tutorials for imputed datasets? I suppose…

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Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer

mRNA expressions of DDR-related genes are upregulated in CRPC compared to those in Pca To identify a cluster of upregulated genes in CRPC, we previously conducted directional RNA-seq analysis using clinical samples obtained from localized Pca and CRPC patients21. We used RNA samples obtained from prostate cancer patients by radical…

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Calculating height prediction from PGS

Calculating height prediction from PGS 1 You double really get a “predicted” height per-sec, rather, you get a score that has correlates with the height. With the provided weights, you can directly use plink –score to generate the polygenic score, but most likely they won’t look like height (e.g. mean…

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Need help to setup a PGS pipeline

Job:Need help to setup a PGS pipeline 0 I seek a bioinformatician with experience setting up pipelines in an academic environment. I want to be able to take different file formats from WGS and then do QC, imputation, and then run PGS using different industry-standard libraries and tools. I am…

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TGS Clears Path to Starting Sarawak Phase 3

TGS, together with its partners PGS and SLB, has secured pre-funding for the multi-client 3D coverage expansion in the Sarawak Basin, offshore Malaysia. The company said that the survey is the third phase of a multi-year contract awarded by Petronas in August 2020 to acquire and process up to 40,500…

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TGS Announces Commencement of Sarawak Phase 3 in Malaysia

OSLO, Norway (30 August 2023) – TGS, the leading global energy data and intelligence provider, and JV consortium partners PGS and SLB announce that pre-funding has been secured to expand the multi-client 3D coverage in the Sarawak Basin, offshore Malaysia. The survey is the third phase of a multi-year contract…

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Seismic giants advance Malaysia mega-shoot

Oslo-listed seismic giants PGS and TGS and joint venture partner SLB (formerly Schlumberger) are forging ahead with the third phase of their multi-client 3D survey in the Sarawak basin, offshore Malaysia, after securing the required pre-funding. PGS’ survey vessel Ramform Sovereign is expected to imminently mobilise for phase three, which…

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Experts Call for Better FDA Policing of Direct-to-Consumer Polygenic Risk Scores

NEW YORK—Experts have called for US Food and Drug Administration regulation of direct-to-consumer (DTC) tests that use a polygenic risk score (PRS) to estimate an individual’s disease risk. PRS are genome-wide measures of individuals’ genetic propensities for diseases that, combined with other lifestyle factors, can give a better idea of…

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Autism Study Unveils New Genetic Players and Role of Language Delay

Summary: Researchers shed new light on how genetics may influence the development of autism spectrum disorder (ASD). The study, the largest ever to focus on families with multiple children diagnosed with autism, has revealed seven potential risk genes. Additionally, it has provided genetic evidence for reconsidering language delay as a…

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Profiling of pharmacogenomic variants in CYP2D6 and DPYD in indigenous Arab breast cancer patients

doi: 10.2217/pgs-2023-0029. Online ahead of print. Abdullah Alsulaiman  1 , Hoyin Chu  2   3 , Mohammed Al-Jumaan  1 , Mohammed Alyahya  1 , Yousef Al Marzooq  1 , Fatmah Almulhim  1 , Chittibabu Vatte  1 , Areej Alnimer  1 , Afnan Almuhanna  1 , Amein Al-Ali  1 , Saud H AlDubayan  2   3   4   5 Affiliations…

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MTX Therapy Outcomes in Early Rheumatoid Arthritis

Introduction Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease, mainly characterised by symmetrical pain and swelling of small joints in the hands and the feet.1 When chronic inflammation is not properly controlled over a long period of time, it can eventually lead to irreversible damage to the joint structures….

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Genetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots

Samples This study was based on the Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) sample37, a population-based case-cohort design to study the genetic and environmental factors associated with severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005 (N = 1,472,762). In total,…

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Manual Polygenic Risk Score calculation

Manual Polygenic Risk Score calculation 1 Hi all, I am attempted to calculate PRS manually, and I’m very close to to obtaining a score. To recap what has been done, I have a patients individual in which I annotated their VCF with RSIDs. From there, I went to PGS catalog…

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Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications.

Liau Y et al. Pharmacogenomics. 2019 Sep; 20(14):1033-1047 doi.org/10.2217/pgs-2019-0080PMID: 31559921 Show Details AbstractAuthors Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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LOCS files not found during MiSeq run?

Hi everyone! We experienced a problem that our team had not encountered for almost 10 years of working with the MiSeq platform. We ran a 24-sample VeriSeq PGS library on MiSeq. On the next day when the data was expected to be generated, we noticed that the run had stopped…

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PRS from a dataset on which the GWAS is based on

PRS from a dataset on which the GWAS is based on 0 I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the weights were generated from a different cohort (d2), it appears that the original…

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PRS using PGS Catalog

PRS using PGS Catalog 1 When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as “base data” in the tutorial)? I had previously found this similar…

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PRSice-2 without Ref SNP ID

PRSice-2 without Ref SNP ID 1 Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file? I’m trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only…

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