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Lin Y, Lin C, Zheng Z, Huang C, Peng W. Newborn screening for primary carnitine deficiency using a second-tier genetic test. J Pediatr Endocrinol Metab 2024; 37:163-169. [PMID: 38158618 DOI: 10.1515/jpem-2023-0513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVES Newborn screening (NBS) for primary carnitine deficiency (PCD) exhibits suboptimal performance. This study proposes a strategy to enhance the efficacy of second-tier genetic screening by adjusting the cutoff value for free carnitine (C0). METHODS Between January 2021 and December 2022, we screened 119,898 neonates for inborn metabolic disorders. Neonates with C0 levels below 12 μmol/L were randomly selected for second-tier genetic screening, employing a novel matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) assay. RESULTS In total, 2,515 neonates with C0 <12 μmol/L underwent further screening, including 206 neonates with C0 <8.5 μmol/L and 320 neonates with 8.5G, accounting for 25 % (7/28) of allelic frequencies. CONCLUSIONS A novel MALDI-TOF MS assay targeting 21 SLC22A5 variants in a Chinese population was successfully established. This assay exhibits a high detection and diagnostic rate, making it suitable for population-based genetic screening. Combined genetic screening is recommended to enhance the efficiency of PCD-NBS.
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Affiliation(s)
- Yiming Lin
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, Quanzhou, Fujian Province, P.R. China
| | - Chunmei Lin
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, Quanzhou, Fujian Province, P.R. China
| | - Zhenzhu Zheng
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, Quanzhou, Fujian Province, P.R. China
| | - Chenggang Huang
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang Province, P.R. China
| | - Weilin Peng
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, Quanzhou, Fujian Province, P.R. China
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Crefcoeur L, Ferdinandusse S, van der Crabben SN, Dekkers E, Fuchs SA, Huidekoper H, Janssen M, Langendonk J, Maase R, de Sain M, Rubio E, van Spronsen FJ, Vaz FM, Verschoof R, de Vries M, Wijburg F, Visser G, Langeveld M. Newborn screening for primary carnitine deficiency: who will benefit? - a retrospective cohort study. J Med Genet 2023; 60:1177-1185. [PMID: 37487700 DOI: 10.1136/jmg-2023-109206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/17/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Newborn screening (NBS) programmes identify a wide range of disease phenotypes, which raises the question whether early identification and treatment is beneficial for all. This study aims to answer this question for primary carnitine deficiency (PCD) taking into account that NBS for PCD identifies newborns with PCD and also until then undiagnosed mothers. METHODS We investigated clinical, genetic (variants in SLC22A5 gene) and functional (carnitine transport activity in fibroblasts) characteristics of all referred individuals through NBS (newborns and mothers) and clinically diagnosed patients with PCD (not through NBS). Disease phenotype in newborns was predicted using data from PCD mothers and cases published in literature with identical SLC22A5 variants. RESULTS PCD was confirmed in 19/131 referred newborns, 37/82 referred mothers and 5 clinically diagnosed patients. Severe symptoms were observed in all clinically diagnosed patients, 1 newborn and none of the mothers identified by NBS. PCD was classified as severe in all 5 clinically diagnosed patients, 3/19 newborns and 1/37 mothers; as benign in 8/19 newborns and 36/37 mothers and as unknown in 8/19 newborns. Carnitine transport activity completely separated severe phenotype from benign phenotype (median (range): 4.0% (3.5-5.0)] vs 26% (9.5-42.5), respectively). CONCLUSION The majority of mothers and a significant proportion of newborns with PCD identified through NBS are likely to remain asymptomatic without early treatment. Conversely, a small proportion of newborns with predicted severe PCD could greatly benefit from early treatment. Genetic variants and carnitine transport activity can be used to distinguish between these groups.
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Affiliation(s)
- Loek Crefcoeur
- Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Department of Pediatrics, Division of Metabolic Disorders, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam UMC Locatie Meibergdreef, Amsterdam, The Netherlands
| | - Sacha Ferdinandusse
- Department of Pediatrics, Division of Metabolic Disorders, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam UMC Locatie Meibergdreef, Amsterdam, The Netherlands
| | - Saskia N van der Crabben
- Human Genetics, Amsterdam UMC Locatie Meibergdreef, Amsterdam, The Netherlands
- United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Eugènie Dekkers
- Centre for Population Screening, RIVM, Bilthoven, The Netherlands
| | - Sabine A Fuchs
- Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Hidde Huidekoper
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mirian Janssen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janneke Langendonk
- Department of Internal Medicine, Center for Lysosomal and Metabolic Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rose Maase
- Department of Biologicals, Screening and Innovation, RIVM, Bilthoven, The Netherlands
| | - Monique de Sain
- Section Metabolic Diagnostics, Department of Genetics, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Estela Rubio
- Department of Pediatrics/Laboratory of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
| | - Francjan J van Spronsen
- Section of Metabolic Diseases, University Medical Centre Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - Frédéric Maxime Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Core Facility Metabolomics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC Locatie Meibergdreef, Amsterdam, The Netherlands
| | - Rendelien Verschoof
- Department for Vaccine Supply and Prevention Programs, RIVM, Bilthoven, The Netherlands
| | - Maaike de Vries
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frits Wijburg
- Department of Pediatrics, Division of Metabolic Disorders, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Gepke Visser
- Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Department of Pediatrics, Division of Metabolic Disorders, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Mirjam Langeveld
- Department of Endocrinology and Metabolism, Amsterdam UMC Locatie Meibergdreef, Amsterdam, The Netherlands
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Lin Y, Lin B, Chen Y, Zheng Z, Fu Q, Lin W, Zhang W. Biochemical and genetic characteristics of patients with primary carnitine deficiency identified through newborn screening. Orphanet J Rare Dis 2021; 16:503. [PMID: 34863234 PMCID: PMC8642906 DOI: 10.1186/s13023-021-02126-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/14/2021] [Indexed: 12/31/2022] Open
Abstract
Background Primary carnitine deficiency (PCD) is an autosomal recessive disorder of carnitine transportation that leads to impaired fatty acid oxidation. Large-scale studies on newborn screening (NBS) for PCD are limited. This study aimed to investigate the biochemical and genetic characteristics of patients with PCD detected through NBS. Results A total of 548 247 newborns were screened for PCD between January 2014 and June 2021; 1714 newborns with low free carnitine (C0) levels were called back and 49 patients were diagnosed with PCD. The latest incidence rate in Quanzhou, China, was estimated to be 1 in 11 189 newborns. NBS results showed that the 49 patients had varying degrees of decreased C0 levels, whereas seven patients exhibited normal C0 levels during the recall review. All patients harbored biallelic pathogenic variants of the SLC22A5 gene. Nineteen distinct SLC22A5 variants were detected in these 49 patients, and most of the detected variants were clustered in exons 1, 4, and 7. The top eight variants had an allele frequency of 86.73%. The most common variant was c.760C > T (p.R254*) with an allele frequency of 31.63%, followed by c.51C > G (p.F17L) (17.35%) and c.1400C > G (p.S467C) (16.33%). The C0 level of patients with the N/N genotype was significantly lower than that of the M/M group. The C0 levels of patients with genotypes of R254*/R254* and R254*/F17L were far lower than those of patients with the R254*/S467C genotype. Conclusions This study presented more than 500,000 NBS data with the latest incidence of 1:11 189 in the Quanzhou area. The SLC22A5 variant spectrum in the selected southern Chinese population has been updated. Patients with null variants were associated with low C0 levels. Combining NBS with genetic testing is critical to improve screening efficiency because patients with PCD may have normal C0 levels during NBS and recall review.
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Affiliation(s)
- Yiming Lin
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Bangbang Lin
- Administrative Office, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Yanru Chen
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Zhenzhu Zheng
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Qingliu Fu
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weihua Lin
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
| | - Weifeng Zhang
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
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Ziats CA, Burns WB, Tedder ML, Pollard L, Wood T, Champaigne NL. 3-Methylglutaconic aciduria in carriers of primary carnitine deficiency. Eur J Med Genet 2021; 64:104365. [PMID: 34637945 DOI: 10.1016/j.ejmg.2021.104365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/15/2021] [Accepted: 10/08/2021] [Indexed: 11/25/2022]
Abstract
The etiology of secondary 3-methylglutaconic aciduria (3-MGA-uria) is not well understood although is thought to be a marker of mitochondrial dysfunction. For this reason, suspicion for a secondary 3-MGA-uria often leads to an extensive clinical and laboratory work-up for mitochondrial disease, although in many cases evidence for mitochondrial dysfunction is never found. 3-methylglutaconic aciduria in healthy individuals without known metabolic disease has not been well described. Here, we describe clinical and biochemical features of 23 individuals evaluated at the Greenwood Genetic Center for low plasma free carnitine reported on newborn screening. Of the 23 individuals evaluated, four individuals were diagnosed with primary carnitine deficiency, 16 were identified as carriers for primary carnitine deficiency, and three individuals were determined to be unaffected non-carriers based on molecular and biochemical testing. Elevated 3-MGA (>20 mmol/mol of creatinine) was identified in nine carriers of primary carnitine deficiency, while all unaffected non carriers and all affected individuals with primary carnitine deficiency had a normal 3-MGA level (<20 mmol/mol of creatinine). Average 3-MGA among all carriers was 39.66 mmol/mol of creatinine. Average plasma free carnitine in among all carriers (n = 16) was 13.87 μm/L, and average plasma free carnitine was not significantly different between carriers with and those without elevated 3-MGA (p = 0.66). In summary, we describe elevated 3-MGA as a discriminatory feature in nine healthy carriers of primary carnitine deficiency. Our findings suggest that heterozygosity for pathogenic alterations on SLC22A5 should be considered in the differential for individuals with persistent 3-MGA-uria of unclear etiology.
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Affiliation(s)
- Catherine A Ziats
- Greenwood Genetic Center, Greenwood, SC, USA; Dell Children's Medical Group, Austin, TX, USA.
| | | | | | | | - Tim Wood
- Greenwood Genetic Center, Greenwood, SC, USA; Department of Pediatrics, Section of Genetics and Metabolism, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Neena L Champaigne
- Greenwood Genetic Center, Greenwood, SC, USA; Divsion of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
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Wojcik MH, Zhang T, Ceyhan-Birsoy O, Genetti CA, Lebo MS, Yu TW, Parad RB, Holm IA, Rehm HL, Beggs AH, Green RC, Agrawal PB. Discordant results between conventional newborn screening and genomic sequencing in the BabySeq Project. Genet Med 2021; 23:1372-1375. [PMID: 33772220 PMCID: PMC8263473 DOI: 10.1038/s41436-021-01146-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Newborn screening (NBS) is performed to identify neonates at risk for actionable, severe, early-onset disorders, many of which are genetic. The BabySeq Project randomized neonates to receive conventional NBS or NBS plus exome sequencing (ES) capable of detecting sequence variants that may also diagnose monogenic disease or indicate genetic disease risk. We therefore evaluated how ES and conventional NBS results differ in this population. METHODS We compared results of NBS (including hearing screens) and ES for 159 infants in the BabySeq Project. Infants were considered "NBS positive" if any abnormal result was found indicating disease risk and "ES positive" if ES identified a monogenic disease risk or a genetic diagnosis. RESULTS Most infants (132/159, 84%) were NBS and ES negative. Only one infant was positive for the same disorder by both modalities. Nine infants were NBS positive/ES negative, though seven of these were subsequently determined to be false positives. Fifteen infants were ES positive/NBS negative, all of which represented risk of genetic conditions that are not included in NBS programs. No genetic explanation was identified for eight infants referred on the hearing screen. CONCLUSION These differences highlight the complementarity of information that may be gleaned from NBS and ES in the newborn period.
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Affiliation(s)
- Monica H Wojcik
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Tian Zhang
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Robert C Green
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine (Genetics), Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Lin Y, Zhang W, Huang C, Lin C, Lin W, Peng W, Fu Q, Chen D. Increased detection of primary carnitine deficiency through second-tier newborn genetic screening. Orphanet J Rare Dis 2021; 16:149. [PMID: 33757571 PMCID: PMC7988980 DOI: 10.1186/s13023-021-01785-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Newborn screening for primary carnitine deficiency (NBS) is commonly implemented worldwide; however, it has poor sensitivity. This study aimed to evaluate the feasibility of improving screening by including a second-tier genetic assay. RESULTS An Agena iPLEX assay was developed to identify 17 common SLC22A5 mutations in Chinese populations and was applied in NBS as a second-tier screening. From January 2017 to December 2018, 204,777 newborns were screened for PCD using tandem mass spectrometry. A total of 316 (0.15%) residual NBS-positive specimens with low free carnitine (C0) levels were subjected to this second-tier screening. The screening identified 20 screen-positive newborns who harboured biallelic mutations in theSLC22A5 gene, 99 carriers with one mutation, and 197 screen-negative newborns with no mutations. Among the 99 carriers, four newborns were found to have a second disease-causing SLC22A5mutation by further genetic analysis. Among the 197 screen-negatives were four newborns with persistently low C0 levels, and further genetic analysis revealed that one newborn had two novel SLC22A5 pathogenic variants. In total, 25 newborns were diagnosed with PCD, for a positive predictive value of 7.91% (25/316). Based on these data, we estimate the incidence of PCD in Quanzhou is estimated to be 1:8191.Thirteen distinct SLC22A5 variants were identified, and the most common was c.760C > T, with an allelic frequency of 32% (16/50), followed by c.1400C > G (7/50, 14%), and c.51C > G (7/50, 14%). CONCLUSION Data from this study revealed that 24% (6/25) of PCD cases would have been missed by conventional NBS. This high-throughput iPLEX assay is a powerful tool for PCD genotyping. The addition of this second-tier genetic screening to the current NBS program could identify missed PCD cases, thereby increasing PCD detection. However, further studies are needed to optimise the workflow of the new screening algorithm and to evaluate the cost-effectiveness of this screening approach.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weifeng Zhang
- Department of Neonatal Intensive Care Unit, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Chenggang Huang
- Zhejiang Biosan Biochemical Technologies Co., Ltd, Hangzhou, China
| | - Chunmei Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weihua Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weilin Peng
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Qingliu Fu
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
| | - Dongmei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
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