1
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Lee K, Tripathi A. Insight into Increased Recovery and Simplification of Genomic DNA Extraction Methods from Dried Blood Spots. Biopreserv Biobank 2024; 22:130-138. [PMID: 37410524 DOI: 10.1089/bio.2022.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
There is no consensus on how to perform the manual extraction of nucleic acids from dried blood spots (DBSs). Current methods typically involve agitation of the DBSs in a solution for varying amounts of time with or without heat, and then purification of the eluted nucleic acids with a purification protocol. We explored several characteristics of genomic DNA (gDNA) DBS extraction such as extraction efficiency, the role of red blood cells (RBCs) in extraction and critical kinetic factors to understand if these protocols can be simplified while maintaining sufficient gDNA recovery. We found that agitation in a RBC lysis buffer before performing a DBS gDNA extraction protocol increases yield 1.5 to 5-fold, depending upon the anticoagulant used. The use of an alkaline lysing agent along with either heat or agitation was sufficient to elute quantitative polymerase chain reaction (qPCR) amplifiable gDNA in 5 minutes. This work adds insight into the extraction of gDNA from DBSs with the intention of informing a simple, standardized manual protocol for extraction.
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Affiliation(s)
- Kiara Lee
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
- Brown University School of Public Health, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
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2
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Tang C, Li L, Chen T, Li Y, Zhu B, Zhang Y, Yin Y, Liu X, Huang C, Miao J, Zhu B, Wang X, Zou H, Han L, Feng J, Huang Y. Newborn Screening for Inborn Errors of Metabolism by Next-Generation Sequencing Combined with Tandem Mass Spectrometry. Int J Neonatal Screen 2024; 10:28. [PMID: 38651393 PMCID: PMC11036227 DOI: 10.3390/ijns10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
The aim of this study was to observe the outcomes of newborn screening (NBS) in a certain population by using next-generation sequencing (NGS) as a first-tier screening test combined with tandem mass spectrometry (MS/MS). We performed a multicenter study of 29,601 newborns from eight screening centers with NBS via NGS combined with MS/MS. A custom-designed panel targeting the coding region of the 142 genes of 128 inborn errors of metabolism (IEMs) was applied as a first-tier screening test, and expanded NBS using MS/MS was executed simultaneously. In total, 52 genes associated with the 38 IEMs screened by MS/MS were analyzed. The NBS performance of these two methods was analyzed and compared respectively. A total of 23 IEMs were diagnosed via NGS combined with MS/MS. The incidence of IEMs was approximately 1 in 1287. Within separate statistical analyses, the positive predictive value (PPV) for MS/MS was 5.29%, and the sensitivity was 91.3%. However, for genetic screening alone, the PPV for NGS was 70.83%, with 73.91% sensitivity. The three most common IEMs were methylmalonic academia (MMA), primary carnitine deficiency (PCD) and phenylketonuria (PKU). The five genes with the most common carrier frequencies were PAH (1:42), PRODH (1:51), MMACHC (1:52), SLC25A13 (1:55) and SLC22A5 (1:63). Our study showed that NBS combined with NGS and MS/MS improves the performance of screening methods, optimizes the process, and provides accurate diagnoses.
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Affiliation(s)
- Chengfang Tang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
| | - Lixin Li
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Ting Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Yulin Li
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Bo Zhu
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Yinhong Zhang
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Yifan Yin
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Xiulian Liu
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Cidan Huang
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Jingkun Miao
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Baosheng Zhu
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Xiaohua Wang
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Hui Zou
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Jizhen Feng
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Yonglan Huang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
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3
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McBride DJ, Fielding C, Newington T, Vatsiou A, Fischl H, Bajracharya M, Thomson VS, Fraser LJ, Fujita PA, Becq J, Kingsbury Z, Ross MT, Moat SJ, Morgan S. Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen. Int J Neonatal Screen 2023; 9:52. [PMID: 37754778 PMCID: PMC10532340 DOI: 10.3390/ijns9030052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
The collection of dried blood spots (DBS) facilitates newborn screening for a variety of rare, but very serious conditions in healthcare systems around the world. Sub-punches of varying sizes (1.5-6 mm) can be taken from DBS specimens to use as inputs for a range of biochemical assays. Advances in DNA sequencing workflows allow whole-genome sequencing (WGS) libraries to be generated directly from inputs such as peripheral blood, saliva, and DBS. We compared WGS metrics obtained from libraries generated directly from DBS to those generated from DNA extracted from peripheral blood, the standard input for this type of assay. We explored the flexibility of DBS as an input for WGS by altering the punch number and size as inputs to the assay. We showed that WGS libraries can be successfully generated from a variety of DBS inputs, including a single 3 mm or 6 mm diameter punch, with equivalent data quality observed across a number of key metrics of importance in the detection of gene variants. We observed no difference in the performance of DBS and peripheral-blood-extracted DNA in the detection of likely pathogenic gene variants in samples taken from individuals with cystic fibrosis or phenylketonuria. WGS can be performed directly from DBS and is a powerful method for the rapid discovery of clinically relevant, disease-causing gene variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Stuart J. Moat
- Wales Newborn Screening Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
- School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
| | - Sian Morgan
- All Wales Genetics Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
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4
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Ding Y, Owen M, Le J, Batalov S, Chau K, Kwon YH, Van Der Kraan L, Bezares-Orin Z, Zhu Z, Veeraraghavan N, Nahas S, Bainbridge M, Gleeson J, Baer RJ, Bandoli G, Chambers C, Kingsmore SF. Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots. NPJ Genom Med 2023; 8:5. [PMID: 36788231 PMCID: PMC9929090 DOI: 10.1038/s41525-023-00349-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Universal newborn screening (NBS) is a highly successful public health intervention. Archived dried bloodspots (DBS) collected for NBS represent a rich resource for population genomic studies. To fully harness this resource in such studies, DBS must yield high-quality genomic DNA (gDNA) for whole genome sequencing (WGS). In this pilot study, we hypothesized that gDNA of sufficient quality and quantity for WGS could be extracted from archived DBS up to 20 years old without PCR (Polymerase Chain Reaction) amplification. We describe simple methods for gDNA extraction and WGS library preparation from several types of DBS. We tested these methods in DBS from 25 individuals who had previously undergone diagnostic, clinical WGS and 29 randomly selected DBS cards collected for NBS from the California State Biobank. While gDNA from DBS had significantly less yield than from EDTA blood from the same individuals, it was of sufficient quality and quantity for WGS without PCR. All samples DBS yielded WGS that met quality control metrics for high-confidence variant calling. Twenty-eight variants of various types that had been reported clinically in 19 samples were recapitulated in WGS from DBS. There were no significant effects of age or paper type on WGS quality. Archived DBS appear to be a suitable sample type for WGS in population genomic studies.
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Affiliation(s)
- Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Mallory Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA.
| | - Jennie Le
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kevin Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong Hyun Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucita Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zaira Bezares-Orin
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shareef Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Matthew Bainbridge
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Joe Gleeson
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Rebecca J. Baer
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA ,grid.266102.10000 0001 2297 6811California Preterm Birth Initiative, University of California San Francisco, San Francisco, CA USA
| | - Gretchen Bandoli
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Christina Chambers
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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5
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Munch TN, Hedley PL, Hagen CM, Bækvad-Hansen M, Geller F, Bybjerg-Grauholm J, Nordentoft M, Børglum AD, Werge TM, Melbye M, Hougaard DM, Larsen LA, Christensen ST, Christiansen M. The genetic background of hydrocephalus in a population-based cohort: implication of ciliary involvement. Brain Commun 2023; 5:fcad004. [PMID: 36694575 PMCID: PMC9866251 DOI: 10.1093/braincomms/fcad004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/04/2022] [Accepted: 01/08/2023] [Indexed: 01/11/2023] Open
Abstract
Hydrocephalus is one of the most common congenital disorders of the central nervous system and often displays psychiatric co-morbidities, in particular autism spectrum disorder. The disease mechanisms behind hydrocephalus are complex and not well understood, but some association with dysfunctional cilia in the brain ventricles and subarachnoid space has been indicated. A better understanding of the genetic aetiology of hydrocephalus, including the role of ciliopathies, may bring insights into a potentially shared genetic aetiology. In this population-based case-cohort study, we, for the first time, investigated variants of postulated hydrocephalus candidate genes. Using these data, we aimed to investigate potential involvement of the ciliome in hydrocephalus and describe genotype-phenotype associations with an autism spectrum disorder. One-hundred and twenty-one hydrocephalus candidate genes were screened in a whole-exome-sequenced sub-cohort of the Lundbeck Foundation Initiative for Integrative Psychiatric Research study, comprising 72 hydrocephalus patients and 4181 background population controls. Candidate genes containing high-impact variants of interest were systematically evaluated for their involvement in ciliary function and an autism spectrum disorder. The median age at diagnosis for the hydrocephalus patients was 0 years (range 0-27 years), the median age at analysis was 22 years (11-35 years), and 70.5% were males. The median age for controls was 18 years (range 11-26 years) and 53.3% were males. Fifty-two putative hydrocephalus-associated variants in 34 genes were identified in 42 patients (58.3%). In hydrocephalus cases, we found increased, but not significant, enrichment of high-impact protein altering variants (odds ratio 1.51, 95% confidence interval 0.92-2.51, P = 0.096), which was driven by a significant enrichment of rare protein truncating variants (odds ratio 2.71, 95% confidence interval 1.17-5.58, P = 0.011). Fourteen of the genes with high-impact variants are part of the ciliome, whereas another six genes affect cilia-dependent processes during neurogenesis. Furthermore, 15 of the 34 genes with high-impact variants and three of eight genes with protein truncating variants were associated with an autism spectrum disorder. Because symptoms of other diseases may be neglected or masked by the hydrocephalus-associated symptoms, we suggest that patients with congenital hydrocephalus undergo clinical genetic assessment with respect to ciliopathies and an autism spectrum disorder. Our results point to the significance of hydrocephalus as a ciliary disease in some cases. Future studies in brain ciliopathies may not only reveal new insights into hydrocephalus but also, brain disease in the broadest sense, given the essential role of cilia in neurodevelopment.
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Affiliation(s)
- Tina N Munch
- Correspondence to: Tina Nørgaard Munch, MD Associate Professor, Department of Neurosurgery 6031 Copenhagen University Hospital, Inge Lehmanns Vej 6 DK-2100 Copenhagen Ø, Denmark E-mail:
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Brazen Bio, Los Angeles, 90502 CA, USA
| | - Christian M Hagen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Merete Nordentoft
- Department of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Mental Health Centre, Capital Region of Denmark, 2900 Hellerup, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Center for Genomics and Personalized Medicine, Aarhus University, DK-8000 Aarhus, Denmark,Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Mental Health Centre, Capital Region of Denmark, 2900 Hellerup, Denmark
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark,Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0473, Norway,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Søren T Christensen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Department of Biomedical Science, University of Copenhagen, DK-2100 Copenhagen, Denmark
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6
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Rajagopal VM, Duan J, Vilar-Ribó L, Grove J, Zayats T, Ramos-Quiroga JA, Satterstrom FK, Artigas MS, Bybjerg-Grauholm J, Bækvad-Hansen M, Als TD, Rosengren A, Daly MJ, Neale BM, Nordentoft M, Werge T, Mors O, Hougaard DM, Mortensen PB, Ribasés M, Børglum AD, Demontis D. Differences in the genetic architecture of common and rare variants in childhood, persistent and late-diagnosed attention-deficit hyperactivity disorder. Nat Genet 2022; 54:1117-1124. [PMID: 35927488 PMCID: PMC10028590 DOI: 10.1038/s41588-022-01143-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/22/2022] [Indexed: 02/02/2023]
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with onset in childhood (childhood ADHD); two-thirds of affected individuals continue to have ADHD in adulthood (persistent ADHD), and sometimes ADHD is diagnosed in adulthood (late-diagnosed ADHD). We evaluated genetic differences among childhood (n = 14,878), persistent (n = 1,473) and late-diagnosed (n = 6,961) ADHD cases alongside 38,303 controls, and rare variant differences in 7,650 ADHD cases and 8,649 controls. We identified four genome-wide significant loci for childhood ADHD and one for late-diagnosed ADHD. We found increased polygenic scores for ADHD in persistent ADHD compared with the other two groups. Childhood ADHD had higher genetic overlap with hyperactivity and autism compared with late-diagnosed ADHD and the highest burden of rare protein-truncating variants in evolutionarily constrained genes. Late-diagnosed ADHD had a larger genetic overlap with depression than childhood ADHD and no increased burden in rare protein-truncating variants. Overall, these results suggest a genetic influence on age at first ADHD diagnosis, persistence of ADHD and the different comorbidity patterns among the groups.
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Affiliation(s)
- Veera M Rajagopal
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jinjie Duan
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Jakob Grove
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- BiRC, Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Tetyana Zayats
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway
| | - J Antoni Ramos-Quiroga
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas D Als
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Anders D Børglum
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Center for Genomics and Personalized Medicine, Aarhus, Denmark.
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7
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Allaway D, Alexander JE, Carvell-Miller LJ, Reynolds RM, Winder CL, Weber RJM, Lloyd GR, Southam AD, Dunn WB. Suitability of Dried Blood Spots for Accelerating Veterinary Biobank Collections and Identifying Metabolomics Biomarkers With Minimal Resources. Front Vet Sci 2022; 9:887163. [PMID: 35812865 PMCID: PMC9258959 DOI: 10.3389/fvets.2022.887163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biomarker discovery using biobank samples collected from veterinary clinics would deliver insights into the diverse population of pets and accelerate diagnostic development. The acquisition, preparation, processing, and storage of biofluid samples in sufficient volumes and at a quality suitable for later analysis with most suitable discovery methods remain challenging. Metabolomics analysis is a valuable approach to detect health/disease phenotypes. Pre-processing changes during preparation of plasma/serum samples may induce variability that may be overcome using dried blood spots (DBSs). We report a proof of principle study by metabolite fingerprinting applying UHPLC-MS of plasma and DBSs acquired from healthy adult dogs and cats (age range 1–9 years), representing each of 4 dog breeds (Labrador retriever, Beagle, Petit Basset Griffon Vendeen, and Norfolk terrier) and the British domestic shorthair cat (n = 10 per group). Blood samples (20 and 40 μL) for DBSs were loaded onto filter paper, air-dried at room temperature (3 h), and sealed and stored (4°C for ~72 h) prior to storage at −80°C. Plasma from the same blood draw (250 μL) was prepared and stored at −80°C within 1 h of sampling. Metabolite fingerprinting of the DBSs and plasma produced similar numbers of metabolite features that had similar abilities to discriminate between biological classes and correctly assign blinded samples. These provide evidence that DBSs, sampled in a manner amenable to application in in-clinic/in-field processing, are a suitable sample for biomarker discovery using UHPLC-MS metabolomics. Further, given appropriate owner consent, the volumes tested (20–40 μL) make the acquisition of remnant blood from blood samples drawn for other reasons available for biobanking and other research activities. Together, this makes possible large-scale biobanking of veterinary samples, gaining sufficient material sooner and enabling quicker identification of biomarkers of interest.
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Affiliation(s)
- David Allaway
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
- *Correspondence: David Allaway
| | - Janet E. Alexander
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Laura J. Carvell-Miller
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Rhiannon M. Reynolds
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Catherine L. Winder
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ralf J. M. Weber
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Gavin R. Lloyd
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Southam
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Warwick B. Dunn
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
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8
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Boelt SG, Plana-Ripoll O, Albiñana C, Vilhjálmsson B, McGrath JJ, Cohen AS. A method to correct for the influence of bovine serum albumin-associated vitamin D metabolites in protein extracts from neonatal dried blood spots. BMC Res Notes 2022; 15:194. [PMID: 35659347 PMCID: PMC9166528 DOI: 10.1186/s13104-022-06077-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Objective We developed an assay to measure the concentration of 25 hydroxyvitamin D2 and D3 in protein extracts derived from stored neonatal dried blood spots. During this study, we postulated that these samples had been contaminated with exogenous vitamin D metabolites because of the addition of bovine serum albumin (BSA) as part of an extraction step undertaken 7 years earlier. The aim of the current study was to develop methods in order to adjust for this contamination. Results We identified between-plate variations in 25 hydroxyvitamin D2 and D3 concentrations which suggested the presence of three different BSA batches. Based on repeat extraction (without the addition of BSA) and testing of 395 samples, we developed models to correct for the exogenous 25 hydroxyvitamin D2 and D3. The regression models were Diff25OHD3 = − 8.2 + 1.8* Diff25OHD2 for low contamination, Diff25OHD3 = 23.8 + 1.7* Diff25OHD2 for middle contamination, and Diff25OHD3 = 14.3 + 3.0* Diff25OHD2 for high contamination. After these corrections, the three subsamples had comparable distributions within the expected range for both 25 hydroxyvitamin D2 and D3. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06077-1.
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Affiliation(s)
- Sanne Grundvad Boelt
- Center for Neonatal Screening, Department of Congenital Disorders-Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark.,Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Olof Palmes Allé 43-45 Aarhus N, 8200, Aarhus, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark
| | - Bjarni Vilhjálmsson
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, Building 1110 Aarhus C, DK-8000, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark. .,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, University of Queensland, St. Lucia, QLD-4072, Australia. .,Queensland Brain Institute, University of Queensland, St. Lucia, QLD-4072, Australia.
| | - Arieh S Cohen
- Center for Neonatal Screening, Department of Congenital Disorders-Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
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9
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Huang X, Wu D, Zhu L, Wang W, Yang R, Yang J, He Q, Zhu B, You Y, Xiao R, Zhao Z. Application of a next-generation sequencing (NGS) panel in newborn screening efficiently identifies inborn disorders of neonates. Orphanet J Rare Dis 2022; 17:66. [PMID: 35193651 PMCID: PMC8862216 DOI: 10.1186/s13023-022-02231-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Newborn screening (NBS) has been implemented for neonatal inborn disorders using various technology platforms, but false-positive and false-negative results are still common. In addition, target diseases of NBS are limited by suitable biomarkers. Here we sought to assess the feasibility of further improving the screening using next-generation sequencing technology. Methods We designed a newborn genetic sequencing (NBGS) panel based on multiplex PCR and next generation sequencing to analyze 134 genes of 74 inborn disorders, that were validated in 287 samples with previously known mutations. A retrospective cohort of 4986 newborns was analyzed and compared with the biochemical results to evaluate the performance of this panel. Results The accuracy of the panel was 99.65% with all samples, and 154 mutations from 287 samples were 100% detected. In 4986 newborns, a total of 113 newborns were detected with biallelic or hemizygous mutations, of which 36 newborns were positive for the same disorder by both NBGS and conventional NBS (C-NBS) and 77 individuals were NBGS positive/C-NBS negative. Importantly, 4 of the 77 newborns were diagnosed currently including 1 newborn with methylmalonic acidemia, 1 newborn with primary systemic carnitine deficiency and 2 newborns with Wilson’s disease. A total of 1326 newborns were found to be carriers with an overall carrier rate of 26.6%. Conclusion Analysis based on next generation sequencing could effectively identify neonates affected with more congenital disorders. Combined with C-NBS, this approach may improve the early and accurate identification of neonates with inborn disorders. Our study lays the foundation for prospective studies and for implementing NGS-based analysis in NBS. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02231-x.
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Affiliation(s)
- Xinwen Huang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Dingwen Wu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China.,Zhejiang Neonatal Screening Center, Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lin Zhu
- Hangzhou Biosan Clinical Laboratory Co. Ltd, 859 Shixiang West Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Wenjun Wang
- Hangzhou Biosan Clinical Laboratory Co. Ltd, 859 Shixiang West Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Rulai Yang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Jianbin Yang
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Qunyan He
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China
| | - Bingquan Zhu
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China.,Department of Child Healthcare, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China
| | - Ying You
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China
| | - Rui Xiao
- Zhejiang Biosan Biochemical Technologies Co. Ltd, 859 Shixiang West Rd, Hangzhou, 310007, Zhejiang Province, People's Republic of China.
| | - Zhengyan Zhao
- Department of Genetics and Metabolism, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, People's Republic of China. .,Department of PediatricsChildren's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Rd, Hangzhou, 310052, Zhejiang Province, People's Republic of China.
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10
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Farrell PM, Langfelder-Schwind E, Farrell MH. Challenging the dogma of the healthy heterozygote: Implications for newborn screening policies and practices. Mol Genet Metab 2021; 134:8-19. [PMID: 34483044 DOI: 10.1016/j.ymgme.2021.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Heterozygous (carrier) status for an autosomal recessive condition is traditionally considered to lack significance for an individual's health, but this assumption has been challenged by a growing body of evidence. Carriers of several autosomal recessive disorders and some X-linked diseases are potentially at risk for the pathology manifest in homozygotes. This minireview provides an overview of the literature regarding health risks to carriers of two common autosomal recessive conditions on the Recommended Uniform Screening Panel: sickle cell disease [sickle cell trait (SCT)] and cystic fibrosis (CF). We also consider and comment on bioethical and policy implications for newborn blood screening (NBS). Health risks for heterozygotes, while relatively low for individuals, are often influenced by intrinsic (e.g., other genomic variants or co-morbidities) and extrinsic (environmental) factors, which present opportunities for personalized genomic medicine and risk counseling. They create a special challenge, however, for developing screening/follow-up policies and for genetic counseling, particularly after identification and reporting of heterozygote status through NBS. Although more research is needed, this minireview of the SCT and CF literature to date leads us to propose that blanket terms such as "healthy heterozygotes" or "unaffected carriers" should be superseded in communications about NBS results, in favor of a more nuanced paradigm of setting expectations for health outcomes with "genotype-to-risk." In the molecular era of NBS, it remains clear that public health needs to become better prepared for the full range of applied genetics.
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Affiliation(s)
- Philip M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, Clinical Sciences Center (K4/948), Madison, WI 53792, USA.
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Mount Sinai Beth Israel, Department of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, 1st Ave at 16th Street, 8F18, New York, NY 10003, USA.
| | - Michael H Farrell
- Departments of Internal Medicine and Pediatrics, University of Minnesota Medical School, Division of General Internal Medicine (MMC 741), 420 Delaware St SE, Minneapolis, MN 55455, USA.
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11
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Lund AM, Wibrand F, Skogstrand K, Bækvad-Hansen M, Gregersen N, Andresen BS, Hougaard DM, Dunø M, Olsen RKJ. Use of Molecular Genetic Analyses in Danish Routine Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7030050. [PMID: 34449524 PMCID: PMC8395600 DOI: 10.3390/ijns7030050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 12/20/2022] Open
Abstract
Historically, the analyses used for newborn screening (NBS) were biochemical, but increasingly, molecular genetic analyses are being introduced in the workflow. We describe the application of molecular genetic analyses in the Danish NBS programme and show that second-tier molecular genetic testing is useful to reduce the false positive rate while simultaneously providing information about the precise molecular genetic variant and thus informing therapeutic strategy and easing providing information to parents. When molecular genetic analyses are applied as second-tier testing, valuable functional data from biochemical methods are available and in our view, such targeted NGS technology should be implemented when possible in the NBS workflow. First-tier NGS technology may be a promising future possibility for disorders without a reliable biomarker and as a general approach to increase the adaptability of NBS for a broader range of genetic diseases, which is important in the current landscape of quickly evolving new therapeutic possibilities. However, studies on feasibility, sensitivity, and specificity are needed as well as more insight into what views the general population has towards using genetic analyses in NBS. This may be sensitive to some and could have potentially negative consequences for the NBS programme.
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Affiliation(s)
- Allan Meldgaard Lund
- Center for Inherited Metabolic Disorders, Departments of Clinical Genetics and Pediatrics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Correspondence: ; Fax: +45-35454072
| | - Flemming Wibrand
- Metabolic Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Marie Bækvad-Hansen
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark;
| | - David M. Hougaard
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Morten Dunø
- Molecular Genetics Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Rikke Katrine Jentoft Olsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
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12
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Lunenburg CATC, Thirstrup JP, Bybjerg-Grauholm J, Bækvad-Hansen M, Hougaard DM, Nordentoft M, Werge T, Børglum AD, Mors O, Mortensen PB, Gasse C. Pharmacogenetic genotype and phenotype frequencies in a large Danish population-based case-cohort sample. Transl Psychiatry 2021; 11:294. [PMID: 34006849 PMCID: PMC8131614 DOI: 10.1038/s41398-021-01417-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 12/23/2022] Open
Abstract
Pharmacogenetics aims to improve clinical care by studying the relationship between genetic variation and variable drug response. Large population-based datasets could improve our current understanding of pharmacogenetics from selected study populations. We provide real-world pharmacogenetic frequencies of genotypes and (combined) phenotypes of a large Danish population-based case-cohort sample (iPSYCH2012; data of the Integrative Psychiatric Research consortium). The genotyped sample consists of 77,684 individuals, of which 51,464 individuals had diagnoses of severe mental disorders (SMD case-cohort) and 26,220 were individuals randomly selected from the Danish population (population cohort). Array-based genotype data imputed to 8.4 million genetic variants was searched for a selected pharmacogenetic panel of 42 clinically relevant variants and a CYP2D6 gene deletion and duplication. We identified 19 of 42 variants. Minor allele frequencies (MAFs) were consistent with previously reported MAFs, and did not differ between SMD cases and population cohorts. Almost all individuals carried at least one genetic variant (> 99.9%) and 87% carried three or more genetic variants. When genotypes were translated into phenotypes, also > 99.9% of individuals had at least one divergent phenotype (i.e. divergent from the common phenotypes considered normal, e.g. extensive metabolizer). The high number of identified individuals with at least one pharmacogenetic variant or divergent phenotype indicates the importance of pharmacogenetic panel-based genotyping. Combined CYP2C19-CYP2D6 phenotypes revealed that 72.7% of individuals had divergent phenotypes for one or both enzymes. As CYP2D6 and CYP2C19 have an important role in the metabolism of psychotropic drugs, this indicates the relevance of pharmacogenetic testing specifically in individuals using psychotropic drugs.
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Affiliation(s)
- Carin A. T. C. Lunenburg
- grid.154185.c0000 0004 0512 597XDepartment of Affective Disorders, Aarhus University Hospital Psychiatry, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Janne P. Thirstrup
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.7048.b0000 0001 1956 2722Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.6203.70000 0004 0417 4147Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- grid.6203.70000 0004 0417 4147Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - David M. Hougaard
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.6203.70000 0004 0417 4147Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Merete Nordentoft
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.4973.90000 0004 0646 7373Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XInstitute of Biological Psychiatry, Mental Health Services, Copenhagen University, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XLundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anders D. Børglum
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark ,grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.7048.b0000 0001 1956 2722Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital Psychiatry, Aarhus, Denmark
| | - Preben B. Mortensen
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus/Copenhagen, Denmark ,grid.7048.b0000 0001 1956 2722NCRR National Centre for Register-Based Research, School of Business and Social Sciences, Aarhus University, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Centre for Integrated Register-based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - Christiane Gasse
- Department of Affective Disorders, Aarhus University Hospital Psychiatry, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark. .,Psychosis Research Unit, Aarhus University Hospital Psychiatry, Aarhus, Denmark.
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13
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Carpentieri D, Colvard A, Petersen J, Marsh W, David-Dirgo V, Huentelman M, Pirrotte P, Sivakumaran TA. Mind the Quality Gap When Banking on Dry Blood Spots. Biopreserv Biobank 2021; 19:136-142. [PMID: 33567235 DOI: 10.1089/bio.2020.0131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dry blood spots (DBS) offer many advantages over other blood banking protocols due to the reduction of time and equipment needed for collection and the ease of processing, storage, and shipment. In addition, the sample size makes it a very attractive method when considering the banking of small pediatric samples. On that note, the Centers for Disease Control and Prevention (CDC) preanalytical standards for DBS are commonly used in the worldwide mass spectrometry-based inborn errors of metabolism screening programs. However, these guidelines may not apply for analytes and protocols not included in these programs. In fact, the availability of leftover samples and the ongoing interest in protocols outside this scenario are providing us with new DBS biobanking insights. Herein, we review the literature for indicators that should be considered in the design of prospective fit for purpose DBS biobanks, especially for those focused mostly on pediatric and OMIC platforms.
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Affiliation(s)
- David Carpentieri
- Department of Pathology and Laboratory Medicine, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Amber Colvard
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Jackie Petersen
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - William Marsh
- Department of Biorepository, Mayo Clinic, Phoenix, Arizona, USA
| | - Victoria David-Dirgo
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matt Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - T A Sivakumaran
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
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14
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Abstract
The potential for genomic screening of the newborn, specifically adding genomic screening to current newborn screening (NBS), raises very significant ethical issues. Regardless of whether NBS of this type would include entire genomes or only the coding region of the genome (exome screening) or even sequencing specific genes, the ethical issues raised would be enormous. These issues include the limitations of bioinformatic interpretation of identified variants in terms of pathogenicity and accurate prognosis, the potential for substantial uncertainty about appropriate diagnosis, therapy, and follow-up, the possibility of much anxiety among providers and parents, the potential for unnecessary treatment and "medicalizing" normal children, the possibility of adding large medical costs for otherwise unnecessary follow-up and testing, the potential for negatively impacting medical and life insurance, and the almost impossible task of obtaining truly-informed consent. Moreover, the potentially-negative consequences of adding genomic sequencing to NBS might jeopardize all of NBS which has been and continues to be so beneficial for thousands of children and their families throughout the world.
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Affiliation(s)
- Harvey L. Levy
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA;
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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15
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Fedida A, Ben Harouch S, Kalfon L, Abunassar Z, Omari H, Mandel H, Falik-Zaccai TC. Sedaghatian-type spondylometaphyseal dysplasia: Whole exome sequencing in neonatal dry blood spots enabled identification of a novel variant in GPX4. Eur J Med Genet 2020; 63:104020. [PMID: 32827718 DOI: 10.1016/j.ejmg.2020.104020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/25/2020] [Accepted: 07/20/2020] [Indexed: 11/23/2022]
Abstract
Accumulation of lipid peroxides causes membrane damage and cell death. Glutathione peroxidase 4 (GPX4) acts as a hydroperoxidase which prevents accumulation of toxic oxidized lipids and blocks ferroptosis, an iron-dependent, non-apoptotic mode of cell death. GPX4 deficiency causes Sedaghatian-type spondylo-metaphyseal dysplasia (SSMD), a lethal autosomal recessive disorder, featuring skeletal dysplasia, cardiac arrhythmia and brain anomalies with only three pathogenic GPX4 variants reported in two SSMD patients. Our objective was to identify the underlying genetic cause of neonatal death of two siblings presenting with hypotonia, cardiorespiratory failure and SSMD. Whole exome sequencing (WES) was performed in DNA samples from two siblings and their parents. Since "critical samples" were not available from the patients, DNA was extracted from dry blood spots (DBS) retrieved from the Israeli newborn-screening center. Sanger sequencing and segregation analysis followed the WES. Homozygous novel GPX4 variant, c.153_160del; p.His52fs*1 causing premature truncation of GPX4 was detected in both siblings; their parents were heterozygotes. Segregation analysis confirmed autosomal recessive inheritance. This report underscores the importance of DBS WES in identifying the genes and mutations causing devastating rare diseases. Obtaining critical samples from a dying patient is crucial for enabling genetic diagnosis.
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Chaudhari BP, Manickam K, McBride KL. A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020; 87:338-44. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
Abstract
We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.
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17
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Dafsari HS, Kawalia A, Sprute R, Karakaya M, Malenica A, Herkenrath P, Nürnberg P, Motameny S, Thiele H, Cirak S. Novel mutations in SLC6A5 with benign course in hyperekplexia. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004465. [PMID: 31604777 PMCID: PMC6913151 DOI: 10.1101/mcs.a004465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023] Open
Abstract
Infants suffering from life-threatening apnea, stridor, cyanosis, and increased muscle tone may often be misdiagnosed with infantile seizures and inappropriately treated because of lack and delay in genetic diagnosis. Here, we report a patient with increased muscle tone after birth and hypertonic attacks with life-threatening apnea but no epileptiform patterns in EEG recordings. We identified novel compound heterozygous variants in SLC6A5 (NM_004211.4:c.[1429T > C];[1430delC]) by trio whole-exome sequencing, containing a base deletion inherited by the asymptomatic mother leading to a frameshift (c.1430delC, p.Ser477PhefsTer9) and a de novo base exchange leading to an amino acid change (c.1429T > C, p.Ser477Pro). To date, there are four known disease-associated genes for primary hyperekplexia, all of which are involved in the functioning of glycinergic synapses. SLC6A5 encodes the sodium- and chloride-dependent glycine transporter 2 (GlyT2), which recaptures glycine, a major inhibitory transmitter in the brainstem and spinal cord. The diagnosis altered the patient's medical care to his benefit because SLC6A5 mutations with rather benign courses of hyperekplexia may be spared of needless pharmacotherapy. Symptoms eventually decreased in frequency until about once in 2 mo at 2 yr age. We present the first report of halting hyperekplexia episodes by maternal soothing in multiple instances. We highlight the importance of clarifying the genetic diagnosis by rapid next-generation sequencing techniques in this group of infantile apneic attacks with hyperekplexia due to the broad differential diagnoses.
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Affiliation(s)
- Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Amit Kawalia
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Rosanne Sprute
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Mert Karakaya
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Anna Malenica
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Peter Herkenrath
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Sebahattin Cirak
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany.,Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
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18
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Satterstrom FK, Walters RK, Singh T, Wigdor EM, Lescai F, Demontis D, Kosmicki JA, Grove J, Stevens C, Bybjerg-Grauholm J, Bækvad-Hansen M, Palmer DS, Maller JB, Nordentoft M, Mors O, Robinson EB, Hougaard DM, Werge TM, Bo Mortensen P, Neale BM, Børglum AD, Daly MJ. Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants. Nat Neurosci 2019; 22:1961-1965. [PMID: 31768057 PMCID: PMC6884695 DOI: 10.1038/s41593-019-0527-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
We analyze the exome sequences of approximately 8,000 children with autism spectrum disorder (ASD) and/or attention-deficit/hyperactivity disorder (ADHD) and 5,000 controls, and we find that ASD and ADHD have a similar burden of rare protein-truncating variants in evolutionarily constrained genes, both significantly higher than controls. This motivates a combined analysis across ASD and ADHD, which identifies microtubule-associated protein 1A (MAP1A) as a novel exome-wide significant gene conferring risk for childhood psychiatric disorders.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Raymond K Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emilie M Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Francesco Lescai
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Mental Health Services in the Capital Region of Denmark, Mental Health Centre Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
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19
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Fischer S, Obrist R, Ehlert U. How and when to use dried blood spots in psychoneuroendocrinological research. Psychoneuroendocrinology 2019; 108:190-196. [PMID: 31239081 DOI: 10.1016/j.psyneuen.2019.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/30/2019] [Accepted: 06/14/2019] [Indexed: 01/22/2023]
Abstract
OBJECTIVE The term "dried blood spot" (DBS) refers to a sampling technique in which capillary whole blood is spotted on filter paper. Given the possibility to determine a wide range of hormones and related biomarkers in DBS, the method should be of interest to researchers in psychoneuroendocrinology. So far, however, the how and when of using DBS in this context have not been outlined. METHODS A review of the literature was conducted in order to describe the materials and procedures necessary to determine relevant biological markers from DBS (how to use DBS). In addition, a comparison of the DBS method with other sampling techniques was undertaken and examples of its previous use in psychoneuroendocrinology were provided (when to use DBS). RESULTS Both dyadic and DBS self-sampling are feasible, and a number of protocols are available to determine endocrine and immune, genetic and epigenetic markers. Decisions to use DBS instead of venous blood or saliva sampling should mainly be guided by whether it is sensible and feasible to determine the parameter of interest in whole blood obtained from DBS. In addition, DBS are well suited for large study populations with specific vulnerabilities, and for remotely located studies with budgetary constraints. CONCLUSION Dried blood spots are a promising material as well as a simple sampling technique for psychoneuroendocrinological research. Future efforts should be directed at continuing to adapt existing serum and plasma analysis protocols for use with DBS, and at testing the feasibility of DBS self-sampling in field studies.
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Affiliation(s)
- Susanne Fischer
- University of Zurich, Institute of Psychology, Clinical Psychology and Psychotherapy, Switzerland.
| | - Ramona Obrist
- University of Zurich, Institute of Psychology, Clinical Psychology and Psychotherapy, Switzerland
| | - Ulrike Ehlert
- University of Zurich, Institute of Psychology, Clinical Psychology and Psychotherapy, Switzerland
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20
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Abstract
Neurologic symptoms in Wilson disease (WD) appear at an older age compared to hepatic symptoms and manifest in patients with misdiagnosed liver disease, in patients when the hepatic stage is clinically silent, in the case of non-compliance with anti-copper treatment, or with treatment failure. Neurologic symptoms in WD are caused by nervous tissue damage that is primarily a consequence of extrahepatic copper toxicity. Copper levels in brain tissues as well as cerebrospinal fluid (CSF) are diffusely increased by a factor of 10 and its toxicity involves various mechanisms such as mitochondrial toxicity, oxidative stress, cell membrane damage, crosslinking of DNA, and inhibition of enzymes. Excess copper is initially taken-up and buffered by astrocytes and oligodendrocytes but ultimately causes dysfunction of blood-brain-barrier and demyelination. Most severe neuropathologic abnormalities, including tissue rarefaction, reactive astrogliosis, myelin palor, and presence of iron-laden macrophages, are typically present in the putamen while other basal ganglia, thalami, and brainstem are usually less affected. The most common neurologic symptoms of WD are movement disorders including tremor, dystonia, parkinsonism, ataxia and chorea which are associated with dysphagia, dysarthria and drooling. Patients usually manifest with various combinations of these symptoms while purely monosymptomatic presentation is rare. Neurologic symptoms are largely reversible with anti-copper treatment, but a significant number of patients are left with residual impairment. The approach for symptomatic treatment in WD is based on guidelines for management of common movement disorders. The vast majority of WD patients with neurologic symptoms have abnormalities on brain magnetic resonance imaging (MRI). Pathologic MRI changes include T2 hyperintensities in the basal ganglia, thalami and white matter, T2 hypointensities in the basal ganglia, and atrophy. Most importantly, brain damage and neurologic symptoms can be prevented with an early initiation of anti-copper treatment. Introducing population WD screening, e.g., by exome sequencing genetic methods, would allow early treatment and decrease the neurologic burden of WD.
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Affiliation(s)
- Petr Dusek
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia.,Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - Tomasz Litwin
- 2nd Department of Neurology, Institute Psychiatry and Neurology, Warsaw, Poland
| | - Anna Członkowska
- 2nd Department of Neurology, Institute Psychiatry and Neurology, Warsaw, Poland
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21
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Mortensen Ó, Lydersen LN, Apol KD, Andorsdóttir G, Steig BÁ, Gregersen NO. Using dried blood spot samples from a trio for linked-read whole-exome sequencing. Eur J Hum Genet 2019; 27:980-988. [PMID: 30765883 PMCID: PMC6777531 DOI: 10.1038/s41431-019-0343-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/21/2018] [Accepted: 01/05/2019] [Indexed: 01/22/2023] Open
Abstract
Long-term collection of dried blood spot (DBS) samples through newborn screening may have retrospective and prospective advantages, especially in combination with advanced analytical techniques. This work concerns whether linked-reads may overcome some of the limitations of short-read sequencing of DBS samples, such as performing molecular phasing. We performed whole-exome sequencing of DNA extracted from DBS and corresponding whole blood (WB) reference samples, belonging to a trio with unaffected parents and a proband affected by primary carnitine deficiency (PCD). For the DBS samples we were able to phase >21% of the genes under 100 kb, >40% of the SNPs, and the longest phase block was >72 kb. Corresponding results for the WB reference samples was >85%, >75%, and >915 kb, respectively. Concerning the PCD causing variant (rs72552725:A > G) in the SLC22A5 gene we observe full genotype concordance between DBS and WB for all three samples. Furthermore, we were able to phase all variants within the SLC22A5 gene in the proband’s WB data, which shows that linked-read sequencing may replace the trio information for haplotype detection. However, due to smaller molecular lengths in the DBS data only small phase blocks were observed in the proband’s DBS sample. Therefore, further optimisation of the DBS workflow is needed in order to explore the full potential of DBS samples as a test bed for molecular phasing.
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Affiliation(s)
- Ólavur Mortensen
- FarGen, The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | | | | | | | - Bjarni Á Steig
- General Medical Department, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
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22
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Nordfalk F, Ekstrøm CT. Newborn dried blood spot samples in Denmark: the hidden figures of secondary use and research participation. Eur J Hum Genet 2019; 27:203-10. [PMID: 30287898 DOI: 10.1038/s41431-018-0276-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/11/2018] [Accepted: 08/19/2018] [Indexed: 01/30/2023] Open
Abstract
Each year millions of newborns are part of a newborn disease-screening program in which, after initial screening, the newborn dried blood spot (NDBS) samples can be stored and used as a population-based research resource. However, very little knowledge exists about how these samples are used for secondary purposes. Our objective is to estimate and describe the usage of a NDBS-based national population biobank for secondary research purposes. We therefore conducted a scoping study with a literature search for all published articles using samples from the Danish Newborn Screening Biobank. Our main inclusion criteria were that the articles had to have actively used and analyzed one or more of the Danish NDBS samples for a purpose beyond the primary screening. Our search led to a final 104 articles, which were coded for three main purposes: (1) how many samples were used in each article, (2) the field of their research, and (3) information on consent and ethics approval as research. From our analysis, we present two main findings: an estimated use of up to 37.5% of all samples in the newborn screening biobank have been part of published research, and a shift in the research areas from methodological and metabolic studies to studies concerning mental illness. This paper provides new insights into the use of a national biobank, and we hope that the results will contribute to the discussions on the use of biological samples for research purposes, and also inspire a greater transparency in the future use of NDBS samples.
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23
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Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genet Med 2018; 21:896-903. [PMID: 30209273 PMCID: PMC6416784 DOI: 10.1038/s41436-018-0272-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/03/2018] [Indexed: 11/27/2022] Open
Abstract
Purpose Improved second-tier tools are needed to reduce false-positive outcomes in newborn screening (NBS) for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP). Methods We designed an assay for multiplex sequencing of 72 metabolic genes (RUSPseq) from newborn dried blood spots. Analytical and clinical performance was evaluated in 60 screen-positive newborns for methylmalonic acidemia (MMA) reported by the California Department of Public Health NBS program. Additionally, we trained a Random Forest machine learning classifier on NBS data to improve prediction of true and false-positive MMA cases. Results Of 28 MMA patients sequenced, we found two pathogenic or likely pathogenic (P/LP) variants in a MMA-related gene in 24 patients, and one pathogenic variant and a variant of unknown significance (VUS) in 1 patient. No such variant combinations were detected in MMA false positives and healthy controls. Random Forest–based analysis of the entire NBS metabolic profile correctly identified the MMA patients and reduced MMA false-positive cases by 51%. MMA screen-positive newborns were more likely of Hispanic ethnicity. Conclusion Our two-pronged approach reduced false positives by half and provided a reportable molecular finding for 89% of MMA patients. Challenges remain in newborn metabolic screening and DNA variant interpretation in diverse multiethnic populations.
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Affiliation(s)
- Gang Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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24
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Abstract
Newborn screening programs aim to achieve presymptomatic diagnosis of treatable disorders allowing for early initiation of medical care to prevent or reduce significant morbidity and mortality. Many of the conditions included in the newborn screening panels are inborn errors of metabolism; however, screening for endocrine, hematologic, immunologic, and cardiovascular diseases, and hearing loss is also included in many panels. Newborn screening tests are not diagnostic and therefore diagnostic testing is needed to confirm or exclude the suspected diagnosis. Further advancement in technology is expected to allow continuous expansion of newborn screening.
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25
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Pedersen CB, Bybjerg-Grauholm J, Pedersen MG, Grove J, Agerbo E, Bækvad-Hansen M, Poulsen JB, Hansen CS, McGrath JJ, Als TD, Goldstein JI, Neale BM, Daly MJ, Hougaard DM, Mors O, Nordentoft M, Børglum AD, Werge T, Mortensen PB. The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders. Mol Psychiatry 2018; 23:6-14. [PMID: 28924187 PMCID: PMC5754466 DOI: 10.1038/mp.2017.196] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 12/16/2022]
Abstract
The Integrative Psychiatric Research (iPSYCH) consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005, including 1 472 762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3540), autism (N=16 146), attention-deficit/hyperactivity disorder (N=18 726) and affective disorder (N=26 380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30 000). Within the sample of 86 189 individuals, a total of 57 377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information, and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.
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Affiliation(s)
- C B Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Fuglesangs Allé 4, Aarhus 8210, Denmark. E-mail:
| | - J Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - M G Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - J Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark,BiRC-Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - E Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - M Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J B Poulsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - C S Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J J McGrath
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - T D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - J I Goldstein
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - B M Neale
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - M J Daly
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - D M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - O Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - M Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - A D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - T Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - P B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
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26
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Boemer F, Fasquelle C, d'Otreppe S, Josse C, Dideberg V, Segers K, Guissard V, Capraro V, Debray FG, Bours V. A next-generation newborn screening pilot study: NGS on dried blood spots detects causal mutations in patients with inherited metabolic diseases. Sci Rep 2017; 7:17641. [PMID: 29247206 DOI: 10.1038/s41598-017-18038-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023] Open
Abstract
The range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview of NGS capacities on DBS-extracted DNA but did not focus on the identification of specific disorders. We thus aimed to demonstrate that NGS was reliable for detecting pathogenic mutations on genomic material extracted from DBS. Assuming the future implementation of NGS technologies into newborn screening (NBS), we conducted a pilot study on fifteen patients with inherited metabolic disorders. Blood was collected from DBS. Whole-exome sequencing was performed, and sequences were analyzed with a specific focus on genes related to NBS. Results were compared to the known pathogenic mutations previously identified by Sanger sequencing. Causal mutations were readily characterized, and multiple polymorphisms have been identified. According to variant database prediction, an unexplained homozygote pathogenic mutation, unrelated to patient’s disorder, was also found in one sample. While amount and quality of DBS-extracted DNA are adequate to identify causal mutations by NGS, bioinformatics analysis revealed critical drawbacks: coverage fluctuations between regions, difficulties in identifying insertions/deletions, and inconsistent reliability of database-referenced variants. Nevertheless, results of this study lead us to consider future perspectives regarding “next-generation” NBS.
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27
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Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, Zhang J, He W, Dharmadhikari AV, Qu C, Ward P, Braxton A, Narayanan S, Ge X, Tokita MJ, Santiago-Sim T, Dai H, Chiang T, Smith H, Azamian MS, Robak L, Bostwick BL, Schaaf CP, Potocki L, Scaglia F, Bacino CA, Hanchard NA, Wangler MF, Scott D, Brown C, Hu J, Belmont JW, Burrage LC, Graham BH, Sutton VR, Craigen WJ, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Muzny DM, Miller MJ, Wang X, Leduc MS, Xiao R, Liu P, Shaw C, Walkiewicz M, Bi W, Xia F, Lee B, Eng C, Yang Y, Lalani SR. Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. JAMA Pediatr 2017; 171:e173438. [PMID: 28973083 PMCID: PMC6359927 DOI: 10.1001/jamapediatrics.2017.3438] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined. Objective To determine the diagnostic yield and use of clinical exome sequencing in critically ill infants. Design, Setting, and Participants Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants. Main Outcomes and Measures Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders. Results The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling. Conclusions and Relevance Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.
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Affiliation(s)
- Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine, Houston, Texas
| | - Anirudh Saronwala
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrew Ray Ghazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Jing Zhang
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin He
- Baylor Genetics Laboratory, Houston, Texas
| | | | | | - Patricia Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Swetha Narayanan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mari J. Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Theodore Chiang
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Hadley Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret L. Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas
| | - Daryl Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston Texas
| | - Chester Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Jianhong Hu
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Vernon Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - William J. Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Donna M. Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Marcus J. Miller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Magalie S. Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
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28
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Bassaganyas L, Freedman G, Vaka D, Wan E, Lao R, Chen F, Kvale M, Currier RJ, Puck JM, Kwok PY. Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification. Hum Mutat 2017; 39:167-171. [PMID: 29067733 DOI: 10.1002/humu.23356] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/06/2017] [Accepted: 10/10/2017] [Indexed: 12/16/2022]
Abstract
Newborn screening (NBS) for rare conditions is performed in all 50 states in the USA. We have partnered with the California Department of Public Health Genetic Disease Laboratory to determine whether sufficient DNA can be extracted from archived dried blood spots (DBS) for next-generation sequencing in the hopes that next-generation sequencing can play a role in NBS. We optimized the DNA extraction and sequencing library preparation protocols for residual infant DBS archived over 20 years ago and successfully obtained acceptable whole exome and whole genome sequencing data. This sequencing study using DBS DNA without whole genome amplification prior to sequencing library preparation provides evidence that properly stored residual newborn DBS are a satisfactory source of DNA for genetic studies.
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Affiliation(s)
- Laia Bassaganyas
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - George Freedman
- Department of Pediatrics, University of California, San Francisco, California
| | - Dedeepya Vaka
- Institute for Human Genetics, University of California, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California, San Francisco, California
| | - Richard Lao
- Institute for Human Genetics, University of California, San Francisco, California
| | - Flavia Chen
- Institute for Human Genetics, University of California, San Francisco, California
| | - Mark Kvale
- Institute for Human Genetics, University of California, San Francisco, California
| | - Robert J Currier
- Genetic Disease Screening Program, California Department of Public Health, Richmond, California
| | - Jennifer M Puck
- Department of Pediatrics, University of California, San Francisco, California.,Institute for Human Genetics, University of California, San Francisco, California
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, California.,Institute for Human Genetics, University of California, San Francisco, California.,Department of Dermatology, University of California, San Francisco, California
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29
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Cho Y, Lee CH, Jeong EG, Kim MH, Hong JH, Ko Y, Lee B, Yun G, Kim BJ, Jung J, Jung J, Lee JS. Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation. Sci Rep 2017; 7:9810. [PMID: 28851938 PMCID: PMC5574920 DOI: 10.1038/s41598-017-09247-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) technology has improved enough to discover mutations associated with genetic diseases. Our study evaluated the feasibility of targeted NGS as a primary screening tool to detect causal variants and subsequently predict genetic diseases. We performed parallel computations on 3.7-megabase-targeted regions to detect disease-causing mutations in 103 participants consisting of 81 patients and 22 controls. Data analysis of the participants took about 6 hours using local databases and 200 nodes of a supercomputer. All variants in the selected genes led on average to 3.6 putative diseases for each patient while variants restricted to disease-causing genes identified the correct disease. Notably, only 12% of predicted causal variants were recorded as causal mutations in public databases: 88% had no or insufficient records. In this study, most genetic diseases were caused by rare mutations and public records were inadequate. Most rare variants, however, were not associated with genetic diseases. These data implied that novel, rare variants should not be ignored but interpreted in conjunction with additional clinical data. This step is needed so appropriate advice can be given to primary doctors and parents, thus fulfilling the purpose of this method as a primary screen for rare genetic diseases.
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Affiliation(s)
- Yangrae Cho
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
- DFTBA, CALS, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chul-Ho Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eun-Goo Jeong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Min-Ho Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jong Hui Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin-si, Gyeonggi-do, 17035, Republic of Korea
| | - Bomnun Lee
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Gilly Yun
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Byong Joon Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongcheol Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongsun Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea.
| | - Jin-Sung Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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30
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Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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31
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Almannai M, Marom R, Sutton VR. Newborn screening: a review of history, recent advancements, and future perspectives in the era of next generation sequencing. Curr Opin Pediatr 2016; 28:694-9. [PMID: 27552071 DOI: 10.1097/MOP.0000000000000414] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize the development and recent advancements of newborn screening. RECENT FINDINGS Early initiation of medical care has modified the outcome for many disorders that were previously associated with high morbidity (such as cystic fibrosis, primary immune deficiencies, and inborn errors of metabolism) or with significant neurodevelopmental disabilities (such as phenylketonuria and congenital hypothyroidism). The new era of mass spectrometry and next generation sequencing enables the expansion of the newborn screen panel, and will help to address technical issues such as turnaround time, and decreasing false-positive and false-negative rates for the testing. SUMMARY The newborn screening program is a successful public health initiative that facilitates early diagnosis of treatable disorders to reduce long-term morbidity and mortality.
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