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Mitchell TR, Ryan M. An enhanced appreciation of cultural competency: Get off your island! J Am Pharm Assoc (2003) 2017; 57:294-295. [DOI: 10.1016/j.japh.2017.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kalman LV, Datta V, Williams M, Zook JM, Salit ML, Han JY. Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships. Ann Lab Med 2017; 36:513-20. [PMID: 27578503 PMCID: PMC5011103 DOI: 10.3343/alm.2016.36.6.513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/08/2016] [Accepted: 07/18/2016] [Indexed: 01/29/2023] Open
Abstract
Characterized reference materials (RMs) are needed for clinical laboratory test development and validation, quality control procedures, and proficiency testing to assure their quality. In this article, we review the development and characterization of RMs for clinical molecular genetic tests. We describe various types of RMs and how to access and utilize them, especially focusing on the Genetic Testing Reference Materials Coordination Program (Get-RM) and the Genome in a Bottle (GIAB) Consortium. This review also reinforces the need for collaborative efforts in the clinical genetic testing community to develop additional RMs.
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Affiliation(s)
- Lisa V Kalman
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivekananda Datta
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Mickey Williams
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Marc L Salit
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jin Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea.
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Lih CJ, Si H, Das B, Harrington RD, Harper KN, Sims DJ, McGregor PM, Camalier CE, Kayserian AY, Williams PM, He HJ, Almeida JL, Lund SP, Choquette S, Cole KD. Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods. J Mol Diagn 2016; 18:753-761. [PMID: 27455875 PMCID: PMC5397679 DOI: 10.1016/j.jmoldx.2016.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/12/2016] [Accepted: 05/27/2016] [Indexed: 01/29/2023] Open
Abstract
The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications.
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Affiliation(s)
- Chih-Jian Lih
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Han Si
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Biswajit Das
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Robin D Harrington
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kneshay N Harper
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - David J Sims
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Paul M McGregor
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Corinne E Camalier
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Andrew Y Kayserian
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - P Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua-Jun He
- Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Jamie L Almeida
- Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Steve P Lund
- Division of Statistical Engineering, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Steve Choquette
- Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Kenneth D Cole
- Division of Biosystems and Biomaterials, National Institute of Standards and Technology, Gaithersburg, Maryland.
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Glicksman S, Borgen C, Blackstein M, Gordon A, Hanon I, Kusin D, Leibowitz B, Halle J. A thematic review of scientific and family interests in Canavan Disease: where are the developmentalists? JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2013; 57:815-825. [PMID: 22676184 DOI: 10.1111/j.1365-2788.2012.01576.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Canavan Disease is a degenerative neurological condition resulting in a spongy deterioration of the brain. Much research has been conducted by the medical community regarding this condition, but little research can be found in the psychological literature. METHOD A review of the scientific literature related to Canavan Disease using the Psychinfo and PubMed databases was conducted covering a 5-year span from 2006 through 2011. Concurrently, a review of parent initiated topics found on the most popular Canavan Disease Internet discussion board was conducted for comparison purposes. RESULTS When comparing the topics discussed and information sought among parents with the themes noted in the extant scientific literature, researchers found an exceedingly small overlap between the two communities of interest. In the scientific literature, published research on Canavan Disease focused on three areas: the biochemistry of Canavan Disease, diagnosis and genetic counselling, and clinical therapeutic approaches in Canavan Disease. Of the 42 unique topics raised on a popular Internet discussion board, however, only three (7%) fell into the category of diagnosis and genetic counselling, none (0%) fell into the category of the biochemistry of Canavan Disease, and four fell into the category of clinical therapeutic approaches in Canavan Disease (10%). Of the four posts addressing clinical therapeutic approaches to Canavan Disease, only one post truly overlapped with the topics addressed by the scientific community. Worded differently, while these three categories comprise 100% of the extant scientific literature regarding Canavan Disease, they comprise only 17% of the parent-raised topics. The remaining 83% of parent-raised topics addressed concerns not currently being focusing upon by the scientific community, namely, non-medical practical issues, information regarding specific characteristics of Canavan Disease, non-medical developmental and quality of life issues, and day-to-day developmental and medical concerns. CONCLUSION By comparing the extant literature on Canavan Disease with the topics of interest raised by parents and caregivers, it seems clear that there is a significant 'underlap' of topics raised by these two communities of interest, one that may reflect a lack of sensitivity on the part of the scientific community to meet the needs of this population of knowledge seekers. It is the suggestion of these authors that developmental psychology may be the appropriate scientific field within which to address this need and fill this gap in the current literature.
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Shirley MD, Baugher JD, Stevens EL, Tang Z, Gerry N, Beiswanger CM, Berlin DS, Pevsner J. Chromosomal variation in lymphoblastoid cell lines. Hum Mutat 2012; 33:1075-86. [PMID: 22374857 PMCID: PMC3370055 DOI: 10.1002/humu.22062] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 02/06/2012] [Indexed: 12/31/2022]
Abstract
Tens of thousands of lymphoblastoid cell lines (LCLs) have been established by the research community, providing nearly unlimited source material from samples of interest. LCLs are used to address questions in population genomics, mechanisms of disease, and pharmacogenomics. Thus, it is of fundamental importance to define the extent of chromosomal variation in LCLs. We measured variation in genotype and copy number in multiple LCLs derived from peripheral blood mononuclear cells (PBMCs) of single individuals as well as two comparison groups: (1) three types of differentiated cell lines (DCLs) and (2) triplicate HapMap samples. We then validated and extended our findings using data from a large study consisting of samples from blood or LCLs. We observed high concordances between genotypes and copy number estimates within all sample groups. While the genotypes of LCLs tended to faithfully reflect the genotypes of PBMCs, 13.7% (4 of 29) of immortalized cell lines harbored mosaic regions greater than 20 megabases, which were not present in PBMCs, DCLs, or HapMap replicate samples. We created a list of putative LCL-specific changes (affecting regions such as immunoglobulin loci) that is available as a community resource.
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Affiliation(s)
- Matthew D. Shirley
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Joseph D. Baugher
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Eric L. Stevens
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Zhenya Tang
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden NJ 08103
| | - Norman Gerry
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden NJ 08103
| | | | - Dorit S. Berlin
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden NJ 08103
| | - Jonathan Pevsner
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD 21205
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205
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Williams PM, Lively TG, Jessup JM, Conley BA. Bridging the gap: moving predictive and prognostic assays from research to clinical use. Clin Cancer Res 2012; 18:1531-9. [PMID: 22422405 PMCID: PMC3307151 DOI: 10.1158/1078-0432.ccr-11-2203] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of clinically useful molecular diagnostics requires validation of clinical assay performance and achievement of clinical qualification in clinical trials. As discussed elsewhere in this Focus section on molecular diagnostics, validation of assay performance must be rigorous, especially when the assay will be used to guide treatment decisions. Here we review some of the problems associated with assay development, especially for academic investigators. These include lack of expertise and resources for analytical validation, lack of experience in designing projects for a specific clinical use, lack of specimens from appropriate patient groups, and lack of access to Clinical Laboratory Improvement Amendments-certified laboratories. In addition, financial support for assay validation has lagged behind financial support for marker discovery or drug development, even though the molecular diagnostic may be considered necessary for the successful use of the companion therapeutic. The National Cancer Institute supports a large number of clinical trials and a significant effort in drug development. In order to address some of these barriers for predictive and prognostic assays that will be used in clinical trials to select patients for a particular treatment, stratify patients into molecularly defined subgroups, or choose between treatments for molecularly defined tumors, the National Cancer Institute has begun a pilot program designed to lessen barriers to the development of validated prognostic and predictive assays.
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Affiliation(s)
- P. Michael Williams
- Molecular Characterization-Clinical Assay development Laboratory, Fairview Center, Suite 505, 1003 West 7 Street Frederick, MD 21702; phone 301-228-4654;
| | - Tracy G. Lively
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20892-7420
| | - J. Milburn Jessup
- Diagnostics Evaluation Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20892-7420
| | - Barbara A. Conley
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20892-7420
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Holden MJ, Madej RM, Minor P, Kalman LV. Molecular diagnostics: harmonization through reference materials, documentary standards and proficiency testing. Expert Rev Mol Diagn 2012; 11:741-55. [PMID: 21902536 DOI: 10.1586/erm.11.50] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There is a great need for harmonization in nucleic acid testing for infectious disease and clinical genetics. The proliferation of assay methods, the number of targets for molecular diagnostics and the absence of standard reference materials contribute to variability in test results among laboratories. This article provides a comprehensive overview of reference materials, related documentary standards and proficiency testing programs. The article explores the relationships among these resources and provides necessary information for people practicing in this area that is not taught in formal courses and frequently is obtained on an ad hoc basis. The aim of this article is to provide helpful tools for molecular diagnostic laboratories.
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Affiliation(s)
- Marcia J Holden
- National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899-8312, USA.
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Scott SA, Edelmann L, Liu L, Luo M, Desnick RJ, Kornreich R. Experience with carrier screening and prenatal diagnosis for 16 Ashkenazi Jewish genetic diseases. Hum Mutat 2010; 31:1240-50. [PMID: 20672374 DOI: 10.1002/humu.21327] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The success of prenatal carrier screening as a disease prevention strategy in the Ashkenazi Jewish (AJ) population has driven the expansion of screening panels as disease-causing founder mutations have been identified. However, the carrier frequencies of many of these mutations have not been reported in large AJ cohorts. We determined the carrier frequencies of over 100 mutations for 16 recessive disorders in the New York metropolitan area AJ population. Among the 100% AJ-descended individuals, screening for 16 disorders resulted in ∼1 in 3.3 being a carrier for one disease and ∼1 in 24 for two diseases. The carrier frequencies ranged from 0.066 (1 in 15.2; Gaucher disease) to 0.006 (1 in 168; nemaline myopathy), which averaged ∼15% higher than those for all screenees. Importantly, over 95% of screenees chose to be screened for all possible AJ diseases, including disorders with lower carrier frequencies and/or detectability. Carrier screening also identified rare individuals homozygous for disease-causing mutations who had previously unrecognized clinical manifestations. Additionally, prenatal testing results and experience for all 16 disorders (n = 574) are reported. Together, these data indicate the general acceptance, carrier frequencies, and prenatal testing results for an expanded panel of 16 diseases in the AJ population.
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Affiliation(s)
- Stuart A Scott
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA
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Barker SD, Bale S, Booker J, Buller A, Das S, Friedman K, Godwin AK, Grody WW, Highsmith E, Kant JA, Lyon E, Mao R, Monaghan KG, Payne DA, Pratt VM, Schrijver I, Shrimpton AE, Spector E, Telatar M, Toji L, Weck K, Zehnbauer B, Kalman LV. Development and characterization of reference materials for MTHFR, SERPINA1, RET, BRCA1, and BRCA2 genetic testing. J Mol Diagn 2009; 11:553-61. [PMID: 19767587 DOI: 10.2353/jmoldx.2009.090078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Well-characterized reference materials (RMs) are integral in maintaining clinical laboratory quality assurance for genetic testing. These RMs can be used for quality control, monitoring of test performance, test validation, and proficiency testing of DNA-based genetic tests. To address the need for such materials, the Centers for Disease Control and Prevention established the Genetic Testing Reference Material Coordination Program (GeT-RM), which works with the genetics community to improve public availability of characterized RMs for genetic testing. To date, the GeT-RM program has coordinated the characterization of publicly available genomic DNA RMs for a number of disorders, including cystic fibrosis, Huntington disease, fragile X, and several genetic conditions with relatively high prevalence in the Ashkenazi Jewish population. Genotypic information about a number of other cell lines has been collected and is also available. The present study includes the development and commutability/genotype characterization of 10 DNA samples for clinically relevant mutations or sequence variants in the following genes: MTHFR; SERPINA1; RET; BRCA1; and BRCA2. DNA samples were analyzed by 19 clinical genetic laboratories using a variety of assays and technology platforms. Concordance was 100% for all samples, with no differences observed between laboratories using different methods. All DNA samples are available from Coriell Cell Repositories and characterization information can be found on the GeT-RM website.
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Affiliation(s)
- Shannon D Barker
- Division of Laboratory Systems, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, G23, Atlanta, GA 30329-4018, USA.
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