10 results on '"Pratt, Victoria M."'
Search Results
2. Recommendations for Clinical Warfarin Genotyping Allele Selection: A Report of the Association for Molecular Pathology and the College of American Pathologists.
- Author
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Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, and Weck KE
- Subjects
- Dose-Response Relationship, Drug, Drug Resistance genetics, Gene Frequency, Genetic Testing methods, Humans, Polymorphism, Single Nucleotide, Precision Medicine methods, Research Report, Alleles, Anticoagulants administration & dosage, Cytochrome P-450 CYP2C9 genetics, Genotype, Genotyping Techniques methods, Vitamin K Epoxide Reductases genetics, Warfarin administration & dosage
- Abstract
The goal of the Association for Molecular Pathology (AMP) Clinical Practice Committee's AMP Pharmacogenomics (PGx) Working Group is to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The AMP PGx Working Group considered functional impact of the variants, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal is to promote standardization of PGx gene/allele testing across clinical laboratories. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Of note, a separate article with recommendations for CYP2C9 allele selection was previously developed by the PGx Working Group that can be applied broadly to CYP2C9-related medications. The warfarin allele recommendations in this report incorporate the previous CYP2C9 allele recommendations and additional genes and alleles that are specific to warfarin testing., (Copyright © 2020 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
3. Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles: A GeT-RM Collaborative Project.
- Author
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Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, and Kalman LV
- Subjects
- Genetic Variation, Haplotypes genetics, High-Throughput Nucleotide Sequencing, Humans, Intersectoral Collaboration, Multiplex Polymerase Chain Reaction, Real-Time Polymerase Chain Reaction, Reference Standards, Alleles, Cytochrome P-450 CYP2D6 genetics, Genotyping Techniques standards
- Abstract
Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination Program studies and 42 additional samples that had not been characterized previously. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory-developed tests. These publicly available samples will support the quality-assurance and quality-control programs of clinical laboratories performing CYP2D6 testing., (Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
4. Recommendations for Clinical CYP2C19 Genotyping Allele Selection: A Report of the Association for Molecular Pathology.
- Author
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Pratt VM, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Scott SA, and Weck KE
- Subjects
- Guidelines as Topic, Humans, Alleles, Cytochrome P-450 CYP2C19 genetics, Genotyping Techniques methods, Health Planning Guidelines, Pathology, Molecular, Research Report
- Abstract
This document was developed by the Pharmacogenomics (PGx) Working Group of the Association for Molecular Pathology Clinical Practice Committee, whose aim is to recommend variants for inclusion in clinical pharmacogenomic testing panels. The goals of the Association for Molecular Pathology PGx Working Group are to define the key attributes of PGx alleles recommended for clinical testing and to define a minimum set of variants that should be included in clinical PGx genotyping assays. These recommendations include a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing PGx assays. The Working Group considered variant allele frequencies in different populations and ethnicities, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. These CYP2C19 genotyping recommendations are the first of a series of recommendations for PGx testing. These recommendations are not to be interpreted as restrictive, but they are meant to provide a helpful guide., (Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
- Full Text
- View/download PDF
5. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.
- Author
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Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, and Sahinalp SC
- Subjects
- Chromosome Mapping, Cytochrome P-450 CYP2D6 classification, Cytochrome P-450 CYP2D6 metabolism, DNA Copy Number Variations, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Isoenzymes classification, Isoenzymes genetics, Isoenzymes metabolism, Phenotype, Sequence Analysis, DNA, Alleles, Cytochrome P-450 CYP2D6 genetics, Genome, Human, Genotype, Polymorphism, Genetic, Software
- Abstract
High-throughput sequencing provides the means to determine the allelic decomposition for any gene of interest-the number of copies and the exact sequence content of each copy of a gene. Although many clinically and functionally important genes are highly polymorphic and have undergone structural alterations, no high-throughput sequencing data analysis tool has yet been designed to effectively solve the full allelic decomposition problem. Here we introduce a combinatorial optimization framework that successfully resolves this challenging problem, including for genes with structural alterations. We provide an associated computational tool Aldy that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data. For a large diverse sequencing data set, Aldy identifies multiple rare and novel alleles for several important pharmacogenes, significantly improving upon the accuracy and utility of current genotyping assays. As more data sets become available, we expect Aldy to become an essential component of genotyping toolkits.
- Published
- 2018
- Full Text
- View/download PDF
6. CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project
- Author
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Gaedigk, Andrea, Boone, Erin C., Scherer, Steven E., Lee, Seung-been, Numanagić, Ibrahim, Sahinalp, Cenk, Smith, Joshua D., McGee, Sean, Radhakrishnan, Aparna, Qin, Xiang, Wang, Wendy Y., Farrow, Emily G., Gonzaludo, Nina, Halpern, Aaron L., Nickerson, Deborah A., Miller, Neil A., Pratt, Victoria M., and Kalman, Lisa V.
- Subjects
Cytochrome P-450 CYP2C19 ,Cytochrome P-450 CYP2C8 ,Genotype ,Haplotypes ,High-Throughput Nucleotide Sequencing ,Humans ,Regular Article ,Genetic Testing ,Alleles ,Cytochrome P-450 CYP2C9 - Abstract
Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that are often defined by star (∗) allele nomenclature. Due to their design, these targeted genotyping assays are unable to detect novel variants that may change the function of the gene product and thereby affect phenotype prediction and patient care. In the current study, 137 DNA samples that were previously characterized by the Genetic Testing Reference Material (GeT-RM) program using a variety of targeted genotyping methods were recharacterized using targeted and whole genome sequencing analysis. Sequence data were analyzed using three genotype calling tools to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19. The genotype calls from next-generation sequencing (NGS) correlated well to those previously reported, except when novel alleles were present in a sample. Six novel alleles and 38 novel suballeles were identified in the three genes due to identification of variants not covered by targeted genotyping assays. In addition, several ambiguous genotype calls from a previous study were resolved using the NGS and/or long-read NGS data. Diplotype calls were mostly consistent between the calling algorithms, although several discrepancies were noted. This study highlights the utility of NGS for pharmacogenetic testing and demonstrates that there are many novel alleles that are yet to be discovered, even in highly characterized genes such as CYP2C9 and CYP2C19.
- Published
- 2022
7. Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing: A Genetic Testing Reference Materials Coordination Program Collaborative Project
- Author
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Prior, Thomas W., Bayrak-Toydemir, Pinar, Lynnes, Ty C., Mao, Rong, Metcalf, James D., Muralidharan, Kasinathan, Iwata-Otsubo, Aiko, Pham, Ha T., Pratt, Victoria M., Qureshi, Shumaila, Requesens, Deborah, Shen, Junqing, Vetrini, Francesco, and Kalman, Lisa
- Subjects
DNA Copy Number Variations ,Genotyping Techniques ,Genetic Carrier Screening ,Gene Dosage ,Infant, Newborn ,Genetic Counseling ,Real-Time Polymerase Chain Reaction ,Survival of Motor Neuron 1 Protein ,Article ,Cell Line ,Muscular Atrophy, Spinal ,Survival of Motor Neuron 2 Protein ,Neonatal Screening ,Phenotype ,Humans ,Alleles - Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disorder predominately caused by bi-allelic loss of the SMN1 gene. Increased copies of SMN2, a low functioning nearly identical paralog, are associated with a less severe phenotype. SMA was recently recommended for inclusion in newborn screening. Clinical laboratories must accurately measure SMN1 and SMN2 copy number to identify SMA patients and carriers, and to identify individuals likely to benefit from therapeutic interventions. Having publicly available and appropriately characterized reference materials with various combinations of SMN1 and SMN2 copy number variants is critical to assure accurate SMA clinical testing. To address this need, the CDC-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and the Coriell Institute for Medical Research, has characterized 15 SMA reference materials derived from publicly available cell lines. DNA samples were distributed to four volunteer testing laboratories for genotyping using three different methods. The characterized samples had zero to four copies of SMN1 and zero to five copies SMN2. The samples also contained clinically important allele combinations (eg, zero copies SMN1, three copies SMN2), and several had markers indicative of an SMA carrier. These and other reference materials characterized by the Genetic Testing Reference Materials Coordination Program are available from the Coriell Institute and are proposed to support the quality of clinical laboratory testing.
- Published
- 2020
8. Recommendations for Clinical Warfarin Genotyping Allele Selection: A Report of the Association for Molecular Pathology and the College of American Pathologists
- Author
-
Pratt, Victoria M., Cavallari, Larisa H., Del Tredici, Andria L., Hachad, Houda, Ji, Yuan, Kalman, Lisa V., Ly, Reynold C., Moyer, Ann M., Scott, Stuart A., Whirl-Carrillo, Michelle, and Weck, Karen E.
- Subjects
Research Report ,Dose-Response Relationship, Drug ,Genotype ,Genotyping Techniques ,Drug Resistance ,Anticoagulants ,Polymorphism, Single Nucleotide ,Special Article ,Gene Frequency ,Vitamin K Epoxide Reductases ,Humans ,Genetic Testing ,Warfarin ,Precision Medicine ,Alleles ,Cytochrome P-450 CYP2C9 - Abstract
The goal of the Association for Molecular Pathology (AMP) Clinical Practice Committee's AMP Pharmacogenomics (PGx) Working Group is to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The AMP PGx Working Group considered functional impact of the variants, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal is to promote standardization of PGx gene/allele testing across clinical laboratories. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Of note, a separate article with recommendations for CYP2C9 allele selection was previously developed by the PGx Working Group that can be applied broadly to CYP2C9-related medications. The warfarin allele recommendations in this report incorporate the previous CYP2C9 allele recommendations and additional genes and alleles that are specific to warfarin testing.
- Published
- 2020
9. PharmVar and the Landscape of Pharmacogenetic Resources.
- Author
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Gaedigk, Andrea, Whirl‐Carrillo, Michelle, Pratt, Victoria M., Miller, Neil A., and Klein, Teri E.
- Subjects
GENOMICS ,MOLECULAR pathology ,PHARMACOGENOMICS ,MEDICAL sciences ,NETWORK hubs ,ALLELES - Abstract
Testing, reporting, and translation of pharmacogenetics (PGx) into clinical recommendations require vast knowledge resources. The first non-CYP gene, I NUDT15 i , was introduced into the PharmVar database in 2018.[2] PharmVar offers a growing number of features and tools facilitating easy and intuitive access to relevant gene information.[3] For example, star allele definitions utilized by the PharmGKB are based on those defined by PharmVar, PharmVar gene expert panels include PharmGKB representatives, and a PharmVar representative is participating in CPIC guidelines ensuring consistent use of allele definitions and terminology. Recently implemented PharmVar features and tools (e.g., core allele definitions and the graphic allele comparison tool) are exemplified. [Extracted from the article]
- Published
- 2020
- Full Text
- View/download PDF
10. Report of Confirmation of the rs7853758 and rs885004 Haplotype in SLC28A3.
- Author
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Stansberry, Wesley M., Swart, Marelize, Medeiros, Elizabeth B., Skaar, Todd C., and Pratt, Victoria M.
- Subjects
- *
HAPLOTYPES , *SINGLE nucleotide polymorphisms , *ALLELES , *NUCLEOSIDE transport proteins , *CARRIER proteins - Abstract
Aims: To validate a laboratory-developed test for the nucleoside transporter, SLC28A3, which has been associated with an increased risk of anthracycline-induced cardiomyopathy. Methods: We used Taqman® allele discrimination to test for two variants of the SLC28A3 gene: rs7853758 (c.1381C>T) and rs885004 (c.862-360C>T). Results: During the validation process, we noted that several DNA samples obtained from the Coriell Cell Repository (Camden, NJ) were positive for both the c.1381 C > T and c.862-360C>T variants and another variant allele for either c.1381 C > T or c.862-360C>T (e.g., c.1381C>T homozygous/c.862-360C>T heterozygous, c.1381C>T homozygous/c.862-360C>T homozygous). We used de-identified DNA samples from trios of family members (mother, father, and child) to establish that the c.1381 C > T and c.862-360C>T variant alleles could be inherited in cis on the same chromosome. Conclusions: Samples containing three variant alleles suggest that the c.1381 C > T and c.862-360C>T are in cis on the chromosome in some individuals and may have implications when calculating anthracycline-induced cardiomyopathy risk. In this study, we confirm a novel haplotype of SLC28A3 using familial studies. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
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