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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Insights into National Laboratory Newborn Screening and Future Prospects. Medicina (B Aires) 2022; 58:medicina58020272. [PMID: 35208595 PMCID: PMC8879506 DOI: 10.3390/medicina58020272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
Newborn screening (NBS) is a group of tests that check all newborns for certain rare conditions, covering several genetic or metabolic disorders. The laboratory NBS is performed through blood testing. However, the conditions that newborn babies are screened for vary from one country to another. Since NBS began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders, and there is a national trend to further expand the NBS program. The use of mass spectrometry (MS) for the diagnosis of inborn errors of metabolism (IEM) obviously helps in the expansion of the screening panels. This technology allows the detection of different metabolic disorders at one run, replacing the use of traditional techniques. Analysis of the targeted pathogenic gene variant is a routine application in the molecular techniques for the NBS program as a confirmatory testing to the positive laboratory screening results. Recently, a lot of molecular investigations, such as next generation sequencing (NGS), have been introduced in the routine NBS program. Nowadays, NGS techniques are widely used in the diagnosis of IMD where its results are rapid, confirmed and reliable, but, due to its uncertainties and the nature of IEM, it necessitates a holistic approach for diagnosis. However, various characteristics found in NGS make it a potentially powerful tool for NBS. A range of disorders can be analyzed with a single assay directly, and samples can reduce costs and can largely be automated. For the implementation of a robust technology such as NGS in a mass NBS program, the main focus should not be just technologically biased; it should also be tested for its long- and short-term impact on the family and the child. The crucial question here is whether large-scale genomic sequencing can provide useful medical information beyond what current NBS is already providing and at what economical and emotional cost? Currently, the topic of newborn genome sequencing as a public health initiative remains argumentative. Thus, this article seeks the answer to the question: NGS for newborn screening- are we there yet?
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Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-Khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Cruzado JCM, Mezey JG, Shakaki AA, Malek JA, Greenblatt MB, Fakhro KA, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail SI, Althani A, Crystal RG. The QChip1 knowledgebase and microarray for precision medicine in Qatar. NPJ Genom Med 2022; 7:3. [PMID: 35046417 PMCID: PMC8770564 DOI: 10.1038/s41525-021-00270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Ramzi Temanni
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Monika Markovic
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Eiman Al-Khayat
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Fatima Qafoud
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Weill Cornell Medicine, Doha, Qatar
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
| | | | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Khalid A Fakhro
- Weill Cornell Medicine, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Ajayeb Al-Nabet
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Nahla Afifi
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Andrew Brooks
- RUCDR Infinite Biologics, Piscataway, NJ, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | | | - Asmaa Althani
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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Dondorp WJ, de Wert GMWR. The 'thousand-dollar genome': an ethical exploration. Eur J Hum Genet 2013; 21 Suppl 1:S6-26. [PMID: 23677179 DOI: 10.1038/ejhg.2013.73] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Sequencing an individual's complete genome is expected to be possible for a relatively low sum 'one thousand dollars' within a few years. Sequencing refers to determining the order of base pairs that make up the genome. The result is a library of three billion letter combinations. Cheap whole-genome sequencing is of greatest importance to medical scientific research. Comparing individual complete genomes will lead to a better understanding of the contribution genetic variation makes to health and disease. As knowledge increases, the 'thousand-dollar genome' will also become increasingly important to healthcare. The applications that come within reach raise a number of ethical questions. This monitoring report addresses the issue.
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Affiliation(s)
- Wybo J Dondorp
- Department of Health, Ethics and Society, Research Institutes CAPHRI and GROW, Maastricht University, Maastricht, The Netherlands.
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7
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Klassen TL, Drabek J, Tomson T, Sveinsson O, von Döbeln U, Noebels JL, Goldman AM. Visual automated fluorescence electrophoresis provides simultaneous quality, quantity, and molecular weight spectra for genomic DNA from archived neonatal blood spots. J Mol Diagn 2013; 15:283-90. [PMID: 23518217 DOI: 10.1016/j.jmoldx.2013.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/15/2013] [Accepted: 01/23/2013] [Indexed: 01/26/2023] Open
Abstract
The Guthrie 903 card archived dried blood spots (DBSs) are a unique but terminal resource amenable for individual and population-wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole genome amplified, producing sufficient gDNA for genomic applications, albeit with variable success; optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Agarose gel electrophoresis and spectrophotometry are established postextraction quality control (QC) methods but lack the power to disclose detailed structural, qualitative, or quantitative aspects that underlie gDNA failure in downstream applications. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology that affords precise quality, quantity, and molecular weight of double-stranded DNA from a single microliter of sample. We extracted DNA from 3-mm DBSs archived in the Swedish Neonatal Repository for >30 years and performed the first quantitative and qualitative analyses of DBS-derived DNA on VAFE, before and after whole genome amplified, in parallel with traditional QC methods. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array. We observed improved standardization of nucleic acid quantity, quality and integrity, and high performance in the downstream genomic technologies. Addition of VAFE measures in QC increases confidence in the validity of genetic data and allows cost-effective downstream analysis of gDNA for investigational and diagnostic applications.
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Affiliation(s)
- Tara L Klassen
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA.
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Ozben T. Expanded newborn screening and confirmatory follow-up testing for inborn errors of metabolism detected by tandem mass spectrometry. Clin Chem Lab Med 2013; 51:157-176. [DOI: 10.1515/cclm-2012-0472] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
Newborn screening (NBS) of inborn errors of metabolism (IEM) is a coordinated comprehensive system consisting of education, screening, follow-up of abnormal test results, confirmatory testing, diagnosis, treatment, and evaluation of periodic outcome and efficiency. The ultimate goal of NBS and follow-up programs is to reduce morbidity and mortality from the disorders. Over the past decade, tandem mass spectrometry (MS/MS) has become a key technology in the field of NBS. It has replaced classic screening techniques of one-analysis, one-metabolite, one-disease with one analysis, many-metabolites, and many-diseases. The development of electrospray ionization (ESI), automation of sample handling and data manipulation have allowed the introduction of expanded NBS for the identification of numerous conditions on a single sample and new conditions to be added to the list of disorders being screened for using MS/MS. In the case of a screened positive result, a follow-up analytical test should be performed for confirmation of the primary result. The most common confirmatory follow-up tests are amino acids and acylcarnitine analysis in plasma and organic acid analysis in urine. NBS should be integrated with follow-up and clinical management. Recent improvements in therapy have caused some disorders to be considered as potential candidates for NBS. This review covers some of the basic theory of expanded MS/MS and follow-up confirmatory tests applied for NBS of IEM.
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Affiliation(s)
- Tomris Ozben
- Faculty of Medicine, Department of Clinical Biochemistry, Akdeniz University, 07070 , Antalya , Turkey
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9
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Resau JH, Ho NT, Dykema K, Faber MS, Busik JV, Nickolov RZ, Furge KA, Paneth N, Jewell S, Khoo SK. Evaluation of sex-specific gene expression in archived dried blood spots (DBS). Int J Mol Sci 2012; 13:9599-9608. [PMID: 22949818 PMCID: PMC3431816 DOI: 10.3390/ijms13089599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 11/16/2022] Open
Abstract
Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.
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Affiliation(s)
- James H. Resau
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Nhan T. Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
| | - Karl Dykema
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Matthew S. Faber
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Julia V. Busik
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Radoslav Z. Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA; E-Mail:
| | - Kyle A. Furge
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
- Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Scott Jewell
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-616-234-5536; Fax: +1-616-234-5537
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Jebrail MJ, Yang H, Mudrik JM, Lafrenière NM, McRoberts C, Al-Dirbashi OY, Fisher L, Chakraborty P, Wheeler AR. A digital microfluidic method for dried blood spot analysis. LAB ON A CHIP 2011; 11:3218-3224. [PMID: 21869989 DOI: 10.1039/c1lc20524b] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Blood samples stored as dried blood spots (DBSs) are emerging as a useful sampling and storage vehicle for a wide range of applications. Unfortunately, the surging popularity of DBS samples has not yet been accompanied by an improvement in automated techniques for extraction and analysis. As a first step towards overcoming this challenge, we have developed a prototype microfluidic system for quantification of amino acids in dried blood spots, in which analytes are extracted, mixed with internal standards, derivatized, and reconstituted for analysis by (off-line and in-line) tandem mass spectrometry. The new method is fast, robust, precise, and most importantly, compatible with automation. We propose that the new method can potentially contribute to a new generation of analytical techniques for quantifying analytes in DBS samples for a wide range of applications.
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Affiliation(s)
- Mais J Jebrail
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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11
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Khoo SK, Dykema K, Vadlapatla NM, LaHaie D, Valle S, Satterthwaite D, Ramirez SA, Carruthers JA, Haak PT, Resau JH. Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays. Pathol Int 2010; 61:1-6. [DOI: 10.1111/j.1440-1827.2010.02611.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hasegawa LE, Fergus KA, Ojeda N, Au SM. Parental attitudes toward ethical and social issues surrounding the expansion of newborn screening using new technologies. Public Health Genomics 2010; 14:298-306. [PMID: 20689248 PMCID: PMC3214890 DOI: 10.1159/000314644] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
AIMS This study assessed parent knowledge of newborn screening (NBS) and parent attitudes toward NBS for untreatable conditions, NBS for late-onset disorders and informed consent in NBS. METHODS Seventeen qualitative focus groups were held in Alaska, California, Hawaii, and Washington with mothers of children 10 years old or younger. RESULTS Most participants did not recall receiving information about NBS, and all wanted this information prenatally. In addition, most felt that the current system of 'informed dissent' was adequate, provided they were told about NBS prior to delivery. All women supported NBS for conditions that occur in infancy without a proven treatment. However, they disagreed about NBS for disorders that manifest in late childhood or adulthood. CONCLUSIONS The results show a general consensus among the focus group participants about issues that cause dissent among public health and health care professionals. Parent attitudes differ from those of many professional communities with regard to timing of NBS education, informed consent, NBS for disorders that lack an effective treatment, and predictive testing of children for late-onset disorders. The results highlight the need to further research parent opinions about expanded NBS using new technologies and to include parents in the development of NBS policies.
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Affiliation(s)
- L E Hasegawa
- Hawaii Genetics Program, Children with Special Needs Branch, Hawaii Department of Health, Honolulu, Hawaii 96816, USA.
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13
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Janik DK, Lindau-Shepard B, Comeau AM, Pass KA. A multiplex immunoassay using the Guthrie specimen to detect T-cell deficiencies including severe combined immunodeficiency disease. Clin Chem 2010; 56:1460-5. [PMID: 20660143 DOI: 10.1373/clinchem.2010.144329] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) fulfills many of the requirements for addition to a newborn screening panel. Two newborn screening SCID pilot studies are now underway using the T-cell receptor excision circle (TREC) assay, a molecular technique. Here we describe an immunoassay with CD3 as a marker for T cells and CD45 as a marker for total leukocytes that can be used with the Guthrie specimen. METHODS The multiplexing capabilities of the Luminex platform were used. Antibody pairs were used to capture and detect CD3 and CD45 from a single 3-mm punch of the Guthrie specimen. The assay for each biomarker was developed separately in identical buffers and then combined to create a multiplex assay. RESULTS Using calibrators made from known amounts of leukocytes, a detection limit of 0.25 x 10(6) cells/mL for CD3 and 0.125 x 10(6) cells/mL for CD45 was obtained. Affinity tests showed no cross-reactivity between the antibodies to CD3 and CD45. The multiplex assay was validated against 8 coded specimens of known clinical status and linked to results from the TREC assay that had identified them. All were correctly identified by the CD345 assay. CONCLUSIONS The performance parameters of the CD345 assay met the performance characteristics generally accepted for immunoassays. Our assay classifications of positive specimens concur with previous TREC results. This CD345 assay warrants evaluation as a viable alternative or complement to the TREC assay as a primary screening tool for detecting T-cell immunodeficiencies, including SCID, in Guthrie specimens.
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Affiliation(s)
- David K Janik
- Biggs Laboratory, Wadsworth Center, Department of Health, NYS, Albany, NY 12201-0509, USA
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Prior TW. Spinal muscular atrophy: newborn and carrier screening. Obstet Gynecol Clin North Am 2010; 37:23-36, Table of Contents. [PMID: 20494255 DOI: 10.1016/j.ogc.2010.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spinal muscular atrophy (SMA) is a common autosomal-recessive neuromuscular disorder caused by mutations in the survival motor neuron (SMN1) gene, affecting approximately 1 in 10,000 live births. The disease is characterized by progressive symmetric muscle weakness resulting from the degeneration and loss of anterior horn cells in the spinal cord and brainstem nuclei. The management of SMA involves supportive and preventive strategies. New treatments based on increasing the expression of full-length SMN protein levels from the SMN2 gene are being investigated and may be dependent on early detection of the disorder, before the irreversible loss of motor neurons. This article focuses on the prevention of SMA through population carrier screening and newborn screening as a means of ensuring early intervention for SMA.
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Affiliation(s)
- Thomas W Prior
- Department of Pathology, The Ohio State University, 125 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA.
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Hiraki S, Green NS. Newborn screening for treatable genetic conditions: past, present and future. Obstet Gynecol Clin North Am 2010; 37:11-21. [PMID: 20494254 DOI: 10.1016/j.ogc.2010.01.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Newborn screening is a complex public health program that has been very successful at significantly reducing infant morbidity and mortality from specific genetic conditions. As this program continues to expand, the role of the obstetrician as patient educator has become increasingly important. The need and desire for prenatal education about newborn screening has been demonstrated, and obstetricians are in the prime position to satisfy this vital role.
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Affiliation(s)
- Susan Hiraki
- Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
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Prior TW, Snyder PJ, Rink BD, Pearl DK, Pyatt RE, Mihal DC, Conlan T, Schmalz B, Montgomery L, Ziegler K, Noonan C, Hashimoto S, Garner S. Newborn and carrier screening for spinal muscular atrophy. Am J Med Genet A 2010; 152A:1608-16. [DOI: 10.1002/ajmg.a.33474] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Impact of false-positive newborn metabolic screening results on early health care utilization. Genet Med 2009; 11:716-21. [PMID: 19661808 DOI: 10.1097/gim.0b013e3181b3a61e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To analyze the association between false-positive newborn screening results and health care utilization. METHODS We surveyed parents regarding their children's health care utilization. Parents of children who received false-positive newborn screening results were primarily enrolled by a screening laboratory in Pennsylvania. Parents of children with normal results were recruited through the Massachusetts birth registry. We used bivariate tests and multivariate regression to assess the association between newborn screening results and primary care utilization, emergency room use, and hospitalization by the age of 6 months. RESULTS Our sample included 200 children with false-positive results and 137 with normal results. Variation in recruitment strategies led to sample children with false-positive results being more likely to be non-white, have unmarried parents, and be of lower socioeconomic status. After adjusting for significant covariates, such as age, race, and socioeconomic status, there were no significant associations between newborn screening results and child health care utilization. CONCLUSIONS Despite the reported negative psychosocial effects of false-positive results, our study found no impact on early health care utilization. These results may assist in economic analyses of newborn screening as they suggest that medical costs associated with false-positive results are limited to the cost of diagnostic testing and follow-up.
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Abstract
Congenital hypothyroidism and congenital adrenal hyperplasia are included in many newborn screening (NBS) panels worldwide and in all state-sponsored programs in the United States. Both conditions meet the fundamental prerequisites for NBS: high incidence in the population; biomarkers in the dried blood specimen that are easily detected; and, effective therapies to lessen, if not prevent, the sequelae of late or no treatment. In this review, the history of NBS is discussed for these 2 conditions. The technologies and protocols used in their detection, and related subjects such as genetics, and treatment and outcomes, are also discussed.
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Affiliation(s)
- Kenneth A Pass
- Wadsworth Center, NYS Department of Health, Albany, NY 12201-2002, USA.
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20
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Sørensen KM, Andersen PS, Larsen LA, Schwartz M, Schouten JP, Nygren AOH. Multiplex ligation-dependent probe amplification technique for copy number analysis on small amounts of DNA material. Anal Chem 2009; 80:9363-8. [PMID: 19551952 DOI: 10.1021/ac801688c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The multiplex ligation-dependent probe amplification (MLPA) technique is a sensitive technique for relative quantification of up to 50 different nucleic acid sequences in a single reaction, and the technique is routinely used for copy number analysis in various syndromes and diseases. The aim of the study was to exploit the potential of MLPA when the DNA material is limited. The DNA concentration required in standard MLPA analysis is not attainable from dried blood spot samples (DBSS) often used in neonatal screening programs. A novel design of MLPA probes has been developed to permit for MLPA analysis on small amounts of DNA. Six patients with congenital adrenal hyperplasia (CAH) were used in this study. DNA was extracted from both whole blood and DBSS and subjected to MLPA analysis using normal and modified probes. Results were analyzed using GeneMarker and manual Excel analysis. A total number of 792 ligation events were analyzed. In DNA extracted from dried blood spot samples, 99.1% of the results were accurate compared to 99.9% of the results obtained in DNA from whole blood samples. This study clearly demonstrates that MLPA reactions with modified probes are successful and reliable with DNA concentrations down to 0.3 ng/microL (1.6 ng total). This broadens the diagnostic perspectives of samples of DBSS allowing for copy number variation analysis in general and particularly testing for CAH.
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Affiliation(s)
- Karina Meden Sørensen
- National Center for Antimicrobials and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
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Hardin J, Finnell RH, Wong D, Hogan ME, Horovitz J, Shu J, Shaw GM. Whole genome microarray analysis, from neonatal blood cards. BMC Genet 2009; 10:38. [PMID: 19624846 PMCID: PMC2722673 DOI: 10.1186/1471-2156-10-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 07/22/2009] [Indexed: 11/24/2022] Open
Abstract
Background Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. Results A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Conclusion Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.
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Affiliation(s)
- Jill Hardin
- University of California Berkeley, School of Public Health, Berkeley, CA 94720, USA.
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Miller FA, Robert JS, Hayeems RZ. Questioning the consensus: managing carrier status results generated by newborn screening. Am J Public Health 2009; 99:210-5. [PMID: 19059852 PMCID: PMC2622768 DOI: 10.2105/ajph.2008.136614] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2008] [Indexed: 11/04/2022]
Abstract
An apparent consensus governs the management of carrier status information generated incidentally through newborn screening: results cannot be withheld from parents. This normative stance encodes the focus on autonomy and distaste for paternalism that characterize the principles of clinical bioethics. However, newborn screening is a classic public health intervention in which paternalism may trump autonomy and through which parents are-in effect-required to receive carrier information. In truth, the disposition of carrier results generates competing moral infringements: to withhold information or require its possession. Resolving this dilemma demands consideration of a distinctive body of public health ethics to highlight the moral imperatives associated with the exercise of collective authority in the pursuit of public health benefits.
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Affiliation(s)
- Fiona Alice Miller
- Department of Health Policy, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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Haak PT, Busik JV, Kort EJ, Tikhonenko M, Paneth N, Resau JH. Archived unfrozen neonatal blood spots are amenable to quantitative gene expression analysis. Neonatology 2009; 95:210-6. [PMID: 18799893 PMCID: PMC2693916 DOI: 10.1159/000155652] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 04/22/2008] [Indexed: 01/11/2023]
Abstract
BACKGROUND State laws in the USA mandate that blood be drawn from all newborn infants to screen for health-threatening conditions. These screening assays consume only a small portion of the blood samples, which are collected on filter paper ('Guthrie') cards. Many states archive unused blood spots, often in unrefrigerated storage. OBJECTIVES While individual RNA transcripts have been identified from archived neonatal blood spots, no study to date has performed quantitative analysis of archived blood spot RNA. METHODS We demonstrate that RNA can be isolated and amplified from newborn blood spots stored unfrozen for as long as 9 years, and can be analyzed by microarray and qPCR. RESULTS Microarray assays of archived neonatal blood spots consistently detected 3,000-4,000 expressed genes with correlations of 0.90 between replicates. Blood spot mRNA is amenable to qPCR and we detected biologically relevant expression levels of housekeeping and immune-mediating genes. CONCLUSIONS These experiments demonstrate the feasibility of using blood spots as a source of RNA which can be analyzed using quantitative microarray and qPCR assays. The application of these methods to the analysis of widely collected biological specimens may be a valuable resource for the study of perinatal determinants of disease development.
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Affiliation(s)
- Peterson T Haak
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, Mich. 49503, USA
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25
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Abstract
Abstract
The hemoglobinopathies encompass a heterogeneous group of disorders associated with mutations in both the alpha-globin and beta-globin genes. Non-sickling disorders are found primarily in individuals of Mediterranean, Asian and Southeast Asian ancestry. With rapid growth in the Asian and Hispanic segments of the US population, the geographic distribution of hemoglobinopathies is expected to become significantly different from what it is today. The epidemiologic changes in the prevalence of non-sickling hemoglobin disorders have important implications for future public health programs, including newborn screening.
The purpose of newborn screening for hemoglobinopathies is to identify clinically significant disorders and provide early education and specialized care prior to the onset of clinical symptoms. Although newborn screening for sickle cell disease is mandated in all states, screening for non-sickling hemoglobinopathies is directed in only one state and limited to reporting of a presumptive diagnosis in most other states. Early delivery of comprehensive care, as well as new and potentially curative therapies, has significantly improved the prognosis for affected patients. This review will consider the increasing prevalence of once uncommon hemoglobinopathies in the US, highlighting the rationale for expanding newborn screening beyond sickle cell disorders.
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Hayeems RZ, Bytautas JP, Miller FA. A systematic review of the effects of disclosing carrier results generated through newborn screening. J Genet Couns 2008; 17:538-49. [PMID: 18956236 DOI: 10.1007/s10897-008-9180-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Accepted: 06/24/2008] [Indexed: 11/25/2022]
Abstract
Evidence on the effects of disclosing carrier results identified through newborn screening (NBS) is needed to develop effective strategies for managing these results, and to inform debate about contradictory policies governing genetic testing in minors in the context of NBS relative to clinical care. This is likely to be even more important as technological opportunities for carrier identification through NBS increase. We report the results of a systematic review of evidence related to the generation of carrier results through NBS to summarize what is known about: (1) the outcomes associated with these results; (2) the best strategies for providing information and follow-up care to parents; and (3) the impact they have on reproductive decision-making. Our study expands the existing body of knowledge and identifies gaps in the evidence base. As key players in the management of carrier results clinically, genetic counselors are well positioned to engage in formative research and policy development in this area.
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Affiliation(s)
- R Z Hayeems
- Department of Health Policy Management and Evaluation, University of Toronto, 155 College Street, 4th Floor, Toronto, ON, M5T 3M6, Canada.
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27
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Abstract
BACKGROUND We stand on the verge of integrating individual genetic and genomic information into health care provision and maintenance to improve health, increase efficiency, and decrease costs. We are beginning to integrate information on inherited susceptibility, gene expression, and predicted pharmacogenomic response to refine our medical management. OBJECTIVE This article reviews the current utility of genetics and genomics in a wide array of clinical circumstances, considers the future applications, and defines some of the obstacles and potential solutions to clinical integration of genomic medicine. METHODS Using the search terms genetics, genomics, pharmacogenomics, newborn screening, long QT syndrome, BRCA1/BRCA2, maturity onset diabetes of youth, diabetes, hemochromatosis, coronary artery disease, copy number changes, genetic discrimination, and genetic education, the PubMed database was searched from January 2000 to March 2007 to identify pertinent articles. Search results were restricted to English-language and human studies. RESULTS Several areas of medicine have begun to incorporate genetics into clinical practice, including newborn screening and breast cancer risk stratification and treatment. Molecular genetic tests are, and will increasingly become, available for inherited arrhythmias, diabetes, cancer, coronary artery disease, and pharmacogenomics. However, there are many barriers to implementation, including the cost of testing, the genetic literacy of patients and health care providers, and concerns about genetic discrimination. CONCLUSION Genetics and genomics will be increasingly utilized in every field of medicine; however, health care providers and patients must have realistic expectations about its predictive power and current limitations.
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Affiliation(s)
- Wendy K Chung
- Division of Molecular Genetics, Columbia University, New York, New York 10032, USA.
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Pyatt RE, Mihal DC, Prior TW. Assessment of liquid microbead arrays for the screening of newborns for spinal muscular atrophy. Clin Chem 2007; 53:1879-85. [PMID: 17890438 DOI: 10.1373/clinchem.2007.092312] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Spinal muscular atrophy is a common neurodegenerative disorder that has recently been considered for inclusion in the next generation of newborn screening regimens. We sought to validate liquid microbead arrays for the identification of affected individuals by direct DNA analysis. METHODS Assays were created to detect the homozygous deletions in exon 7 of the SMN1 gene found in approximately 95% of affected individuals by use of 2 different microbead chemistries on the Luminex 200: MultiCode-PLx and Tag-It. A series of 367 blood spots including 164 from affected individuals, 46 from known carriers, and 157 from unaffected individuals were then analyzed with each assay. RESULTS The MultiCode-PLx assay required 4.2 h to perform and provided correct identification of all 164 samples from affected individuals. Correct exclusion was also made for all 46 carrier and 157 unaffected individual samples. The Tag-It assay required 6.8 h, detected all samples from affected individuals, and excluded all but 1 (99.5%) of the samples from carriers and unaffected individuals. Neither method was sensitive to increasing copy numbers of the SMN2 gene. CONCLUSIONS Both methods showed high sensitivity and specificity for the detection of patients with spinal muscular atrophy. For both methods, ample DNA was extracted from all blood spots for analysis, and SMN2 copy numbers did not interfere. Liquid bead arrays represent a robust method for DNA analysis in newborn screening laboratories.
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Affiliation(s)
- Robert E Pyatt
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
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29
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Therrell BL, Adams J. Newborn screening in North America. J Inherit Metab Dis 2007; 30:447-65. [PMID: 17643194 DOI: 10.1007/s10545-007-0690-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 05/25/2007] [Accepted: 05/31/2007] [Indexed: 10/23/2022]
Abstract
Newborn screening in North America dates to the early work of Bob Guthrie in the USA. Screening programmes in both the USA and Canada began in the early 1960s, with documented programmes in both countries as early as 1962. Throughout the 1960s and 1970s, many of the screening tests that later became part of routine screening around the world were developed in US and Canadian laboratories, including tests for phenylketonuria, other inborn errors of metabolism, congenital hypothyroidism, congenital adrenal hyperplasia, and haemoglobinopathies. An automated punching machine developed in the USA facilitated screening expansion by significantly reducing sample preparation time and effort. US and Canadian programmes were leaders in applying computerized data management to newborn screening in the 1980s. In the 1990s, DNA and tandem mass spectrometry testing protocols were developed in the USA and applied to newborn screening. US programmes have continually expanded over time, while most Canadian programmes have not. With impetus from private laboratories and professional and consumer groups, many US programmes now screen for more than 50 conditions and there is increased expansion activity in Canada. NBS research in the USA is focused on improving system efficiency and translating other genetic testing to NBS, particularly where new technologies and treatment therapies exist. Although national newborn screening policies do not exist in either Canada or the USA, there are intense efforts to provide uniform access to screening nationwide in both countries. New partnerships between health professionals, consumers and politicians are benefiting the overall screening systems in both countries.
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Affiliation(s)
- Bradford L Therrell
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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Nørgaard-Pedersen B, Hougaard DM. Storage policies and use of the Danish Newborn Screening Biobank. J Inherit Metab Dis 2007; 30:530-6. [PMID: 17632694 DOI: 10.1007/s10545-007-0631-x] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 03/15/2007] [Accepted: 05/31/2007] [Indexed: 01/13/2023]
Abstract
After routine newborn screening, residual dried blood spot samples (DBSS) are stored at -20 degrees C in the Danish Newborn Screening Biobank (NBS-Biobank), which contains DBSS from virtually all newborns in Denmark since 1982--about 1.8 million samples. The purpose of the storage is: (1) diagnosis and treatment of congenital disorders including documentation, repeat testing, quality assurance, statistics and improvement of screening methods; (2) diagnostic use later in infancy after informed consent; (3) legal use after court order; (4) the possibility of research projects after approval by the Scientific Ethical Committee System in Denmark, The Danish Data Protection Agency and the NBS-Biobank Steering Committee. The operation and use of the NBS-Biobank has until recently been regulated by an executive order of 1993 from the Danish Ministry of Health. The Ethical Council, the Central Scientific Ethical Committee and the National Board of Health were also involved in the regulations. These regulations have now been replaced by detailed general operational guidelines for biobanks in Denmark according to Acts on Processing of Personal Data, Patient's Rights, Health 546/2005 and the Biomedical Research Ethics Committee System. No specific Act on biobanks per se has been made in Denmark, but the new regulations and guidelines make the operations of the Danish NBS-Biobank even more clear-cut and safe. The Danish NBS-Biobank has been used in several research projects for aetiological studies of a number of disorders, recently employing new sensitive multiplex technologies and genetic analyses utilizing whole-genome amplified DNA.
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Affiliation(s)
- B Nørgaard-Pedersen
- Department of Clinical Biochemistry, Statens Serum Institut, Copenhagen, Denmark.
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Matern D, Tortorelli S, Oglesbee D, Gavrilov D, Rinaldo P. Reduction of the false-positive rate in newborn screening by implementation of MS/MS-based second-tier tests: the Mayo Clinic experience (2004-2007). J Inherit Metab Dis 2007; 30:585-92. [PMID: 17643193 DOI: 10.1007/s10545-007-0691-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2007] [Revised: 06/08/2007] [Accepted: 06/12/2007] [Indexed: 11/26/2022]
Abstract
The continued expansion of newborn screening programmes to include additional conditions increases the responsibility of newborn screening laboratories to provide testing with the highest sensitivity and specificity to allow for identification of affected patients while minimizing the false-positive rate. Some assays and analytes are particularly problematic. Over recent years, our laboratory tried to improve this situation by developing second-tier tests to reduce false-positive results in the screening for congenital adrenal hyperplasia (CAH), tyrosinaemia type I, methylmalonic acidaemias, homocystinuria, and maple syrup urine disease (MSUD). Beginning in 2004, this approach was applied to Mayo's newborn screening programme and resulted in a false-positive rate of 0.09%, a positive predictive value of 41%, and a positive detection rate of 1 affected case in 1672 babies screened.
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Affiliation(s)
- D Matern
- Biochemical Genetics Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
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Abstract
Boddaert and colleagues show the positive effects of selective iron chelation in young patients with Friedreich ataxia, a devastating inborn error of mitochondrial iron metabolism.
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Arranz JA, Riudor E, Marco-Marín C, Rubio V. Estimation of the total number of disease-causing mutations in ornithine transcarbamylase (OTC) deficiency. Value of the OTC structure in predicting a mutation pathogenic potential. J Inherit Metab Dis 2007; 30:217-26. [PMID: 17334707 DOI: 10.1007/s10545-007-0429-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 01/04/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
Ornithine transcarbamylase deficiency (OTCD), the X-linked, most frequent urea cycle error, results from mutations in the OTC gene, encoding a 354-residue polypeptide. To date 341 OTCD clinical mutations, including 222 missense single nucleotide changes (mSNCs), have been compiled (Hum Mutat 2006;27:626). OTCD mutation detection might be simplified if the entire repertoire of OTCD-causing mutations were known. We estimate the size of this repertoire from 23 new OTCD patients exhibiting 22 different mutations, of which 9, including 4 mSNCs, are novel. The complete repertoire of OTCD-causing mutations is estimated as 560 mutations (95% confidence interval, 422-833 mutations), including 290 mSNCs (95% confidence interval, 230-394 mSNCs). Thus, OTCD diagnosis based on the screening for known mutations might attain 90% sensitivity in <5 years. Since disease-causing mSNCs represent <20% of the 2064 possible OTC mSNCs, simple approaches are essential for discrimination between causative and trivial mSNCs. Observation of the OTC structure appears a simple approach for such discrimination, comparing favourably in our sample with three formalized structure-based and/or sequence-based in silico assessment methods, and supporting the causation of complete deficiency by the mutations p.Pro305Arg and p.Ser96Phe, and of partial deficiency by p.Asp41Gly, p.Glu122Gly, p.Leu179Phe, p.Pro220Thr and p.Glu273del. Five non-mSNC novel mutations (p.Gly71X, a 7-nucleotide and a 10-nucleotide duplication and deletion in exon 5, G>A transitions at bases +1 and +5 of introns 4 and 9, respectively) are obviously pathogenic. The previously reported mSNCs p.Arg26Gln, p.Arg40His, p.Glu52Lys, pLys88Asn, p.Arg129His, p.Asn161Ser, p.Thr178Met, p.His202Tyr, p.Ala208Thr and p.His302Arg, found in our cohort, are also discussed.
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Affiliation(s)
- J A Arranz
- Unitat de Metabolopaties, Hospital Materno-Infantil Vall d'Hebron, Barcelona, Spain
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Green NS, Murray TH. GREEN AND MURRAY RESPOND. Am J Public Health 2007. [DOI: 10.2105/ajph.2006.107367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Nancy S. Green
- Nancy S. Green is with the March of Dimes, White Plains, NY. Thomas H. Murray is with the Hastings Center, Garrison, NY
| | - Thomas H. Murray
- Nancy S. Green is with the March of Dimes, White Plains, NY. Thomas H. Murray is with the Hastings Center, Garrison, NY
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Hiraki S, Ormond KE, Kim K, Ross LF. Attitudes of genetic counselors towards expanding newborn screening and offering predictive genetic testing to children. Am J Med Genet A 2006; 140:2312-9. [PMID: 17036312 DOI: 10.1002/ajmg.a.31485] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
There is movement to expand newborn screening (NBS) to include conditions that challenge the traditional public health screening criteria. Little is known about the attitudes of genetic counselors towards expanding NBS and offering predictive genetic tests to children. For our study genetic counselors completed an internet survey posted on the National Society of Genetic Counselors Listserv regarding five conditions: cystic fibrosis (CF), Duchenne muscular dystrophy (DMD), glucose-6-phosphate dehydrogenase deficiency (G6PD), fragile X (FraX), and type 1 diabetes (T1D). The survey addressed attitudes towards: (1) testing high-risk infants; (2) mandatory NBS; (3) population screening beyond the newborn period; and (4) testing one's own child. Two hundred sixty-seven usable surveys were received. Over two-thirds of respondents supported testing high-risk infants for all conditions except T1D (22%). CF was the only condition for which there was majority support for both mandatory NBS (56%) and later population screening (60%). For all other conditions, later population screening was preferred over NBS (P <or= 0.01). Genetic counselors were most likely to test their own child for CF (46%) and least likely to test their own child for T1D (6%). For each condition, genetic counselors were more likely to support NBS if they chose to screen their own newborn (P < 0.001). Attitudes towards NBS were not influenced by year of graduation or professional experience. We can conclude that genetic counselors are supportive of targeted testing of high-risk infants. They prefer voluntary population screening with consent to mandatory NBS for conditions that challenge Wilson and Jungner criteria. Their support for NBS correlates with their interest in testing their own children and not with professional experience.
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Affiliation(s)
- Susan Hiraki
- Alzheimer's Disease Center, Boston University, School of Medicine, Boston, Massachusetts, USA
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Coppola G, Geschwind DH. Technology Insight: querying the genome with microarrays--progress and hope for neurological disease. ACTA ACUST UNITED AC 2006; 2:147-58. [PMID: 16932541 DOI: 10.1038/ncpneuro0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 01/09/2006] [Indexed: 01/23/2023]
Abstract
The ability to perform large-scale analysis of the genome at the level of gene sequence, gene copy number and messenger RNA transcript expression characterizes the post-genomic era. In the past decade, the microarray-based approach has emerged as one of the major tools in this area of genome biology, contributing to advances in the understanding of Mendelian and complex neurological disorders. Despite technical issues regarding design, data analysis and validation that have to be addressed in the planning and interpretation of a microarray study, microarray-based approaches for studying transcript expression, single-nucleotide-polymorphism genotyping and gene resequencing are becoming more widely adopted. Genomic microarrays are providing an unprecedented opportunity to dissect the genetic risk for complex neurological disorders. Numerous clinical and preclinical applications are likely to dominate the ambitious microarray agenda within the next decade.
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Affiliation(s)
- Giovanni Coppola
- Neurogenetics Program, Center for Autism Research, University of California Los Angeles, CA 90095, USA
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Ward K. Microarray technology in obstetrics and gynecology: a guide for clinicians. Am J Obstet Gynecol 2006; 195:364-72. [PMID: 16615920 PMCID: PMC7093878 DOI: 10.1016/j.ajog.2005.12.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/29/2005] [Accepted: 12/05/2005] [Indexed: 11/28/2022]
Abstract
Microarrays can be constructed with dozens to millions of probes on their surface to allow high-throughput analyses of many biologic processes to be performed simultaneously on the same sample. Microarrays are now widely used for gene expression analysis, deoxyribonucleic acid resequencing, single-nucleotide polymorphism genotyping, and comparative genomic hybridization. Microarray technology is accelerating research in many fields and now microarrays are moving into clinical application. This review discusses the emerging role of microarrays in molecular diagnostics, pathogen detection, oncology, and pharmacogenomics.
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Affiliation(s)
- Kenneth Ward
- Department of Obstetrics and Gynecology and Women's Health and the Pacific Research Center for Early Human Development, University of Hawaii, John A. Burns School of Medicine, Honolulu, HI 96826, USA.
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Marsden D, Larson C, Levy HL. Newborn screening for metabolic disorders. J Pediatr 2006; 148:577-584. [PMID: 16737864 DOI: 10.1016/j.jpeds.2005.12.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 11/03/2005] [Accepted: 12/12/2005] [Indexed: 11/25/2022]
Affiliation(s)
- Deborah Marsden
- Division of Genetics, Children's Hospital Boston, MA 02115, USA.
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Abstract
Newborn screening (NBS)--in which each newborn infant is screened for up to 50 specific metabolic disorders for early detection and intervention--is the first program of populationwide genetic testing. As a public health intervention, NBS has greatly improved the lives of thousands of affected children. New technologies and new economic and social forces pose significant ethical and clinical challenges to NBS. Two primary challenges concern (1) accommodating clinical and ethical standards to rapid technological developments in NBS and (2) preparing public health systems to respond to the medical advances and social forces driving expansion of NBS programs. We describe and analyze these challenges through consideration of 3 disorders: phenylketonuria, medium-chain acyl-CoA dehydrogenase deficiency, and cystic fibrosis.
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Affiliation(s)
- Nancy S Green
- March of Dimes Birth Defects Foundation, White Plains, NY, USA.
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Abstract
There is rapid expansion of newborn screening throughout the United States. A recent report from the American College of Medical Genetics has recommended a mechanism by which decisions are made about adding tests to the screening panel, and a core panel of 29 conditions has been recommended. Implementing such a program is a major undertaking in every state and involves not only the laboratory but also a number of diagnostic and follow-up services. It is essential to have laboratory programs in place to minimize false positive screening tests and at the same time communicate in the most effective manner possible about the nature of false positives.
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Affiliation(s)
- R Rodney Howell
- Miller School of Medicine, University of Miami, Miami, FL 33101, USA.
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Abstract
Identifying genetic factors that could reliably predict health risks for individuals has the potential to bring great health benefits, both for the individuals concerned and for health-care providers. Genetic profiling at birth would allow a person's genome to be analysed at an early stage, and the data electronically stored for future use. However, although this might seem like an attractive proposition, it carries with it serious ethical and social concerns that would need to be addressed if the genetic profiling of newborns were ever to be considered on a population-wide basis.
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Affiliation(s)
- Brenda Almond
- Social Values Research Centre, University of Hull, Hull HU6 7RX, UK.
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Ross LF. Heterozygote carrier testing in high schools abroad: what are the lessons for the U.S.? THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2006; 34:753-64. [PMID: 17199818 DOI: 10.1111/j.1748-720x.2006.00096.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The main value of carrier detection in the general population is to determine reproductive risks. In this manuscript I examine the practice of providing carrier screening programs in the school setting. While the data show that high school screening programs can achieve high uptake, I argue that this may reflect a lack of full understanding about risks, benefits, and alternatives, and the right not to know. It may also reflect the inherent coercion in group testing, particularly for adolescents who are prone to peer pressure. The problem of carrier screening in the schools is compounded when the condition has a predilection for certain groups based on race, ethnicity or religion. I examine programs around the world that seek to test high school students for Tay Sachs and Cystic Fibrosis carrier status. I argue that carrier programs should be designed so as to minimize stigma and to allow individuals to refuse. The mandatory school environment cannot achieve this. Rather, I conclude that screening programs should be designed to attract young adults and not adolescents to participate in a more voluntary venue.
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Moore CA, Khoury MJ, Bradley LA. From genetics to genomics: using gene-based medicine to prevent disease and promote health in children. Semin Perinatol 2005; 29:135-43. [PMID: 16114576 DOI: 10.1053/j.semperi.2005.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The remarkable achievements of the Human Genome Project promise great opportunities for disease prediction, treatment, and prevention. In this paper, we discuss the continuum of genetic variation as medical practice begins to shift focus from the study of single genes (genetics) to the study of the entire genome (genomics). Pediatricians should anticipate an influx of genetic information and will need to become as facile in interpreting this type of predictive information as they are with other types of medical data, while recognizing the unique ethical, legal, and social implications of genetic testing in children. We discuss an approach to assist pediatricians in decision-making that emphasizes the need for knowledge about the analytic performance of genetic tests, their validity in predicting health outcomes, and the utility of the genetic information in improving health and preventing disease.
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Affiliation(s)
- Cynthia A Moore
- Office of Genomics and Disease Prevention, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
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Abstract
Since the beginning of newborn screening for metabolic and other disorders in 1964, advances in the understanding of the disorders identified and development of new methods of testing newborn screening blood spots have contributed to improved health in children. Pediatricians and others involved in the health care of infants must be able to participate in the assessment and confirmatory testing of infants who have an abnormal test result and in the care of infants identified with a disorder. Expansion in the technology and number of disorders identified has complicated this process. As more and a greater variety of disorders are tested for and identified, a crucial collaborative role has emerged for the newborn screening programs and their public health professionals, the tertiary care specialists in the disorders and the primary care clinicians who comprise the medical home of the infants identified. This collaboration needs to provide prompt results of the newborn screening tests, expeditious and expert confirmatory testing and an effective care plan for the affected infant to realize the benefits of treatment for children with otherwise devastating disorders.
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Affiliation(s)
- Margretta R Seashore
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
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