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Lin Y, Lin C, Lin B, Zheng Z, Lin W, Chen Y, Chen D, Peng W. Newborn screening for fatty acid oxidation disorders in a southern Chinese population. Heliyon 2024; 10:e23671. [PMID: 38187300 PMCID: PMC10770602 DOI: 10.1016/j.heliyon.2023.e23671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/23/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Background and aims Fatty acid oxidation disorders (FAODs) are a group of autosomal recessive metabolic diseases included in many newborn screening (NBS) programs, but the incidence and disease spectrum vary widely between ethnic groups. We aimed to elucidate the incidence, disease spectrum, and genetic features of FAODs in a southern Chinese population. Materials and methods The FAODs screening results of 643,606 newborns from 2014 to 2022 were analyzed. Results Ninety-two patients were eventually diagnosed with FAODs, of which 61 were PCD, 20 were MADD, 5 were SCADD, 4 were VLCADD, and 2 were CPT-IAD. The overall incidence of FAODs was 1:6996 (95 % CI: 1:5814-1:8772) newborns. All PCD patients had low C0 levels during NBS, while nine patients (14.8 %) had normal C0 levels during the recall review. All but one MADD patients had elevated C8, C10, and C12 levels during NBS, while eight patients (40 %) had normal acylcarnitine levels during the recall review. The most frequent SLC22A5 variant was c.760C > T (p.R254*) with an allele frequency of 29.51 %, followed by c.51C > G (p.F17L) (17.21 %) and c.1400C > G (p.S467C) (16.39 %). The most frequent ETFDH variant was c.250G > A (p.A84T) with an allelic frequency of 47.5 %, followed by c.524G > A (R175H) (12.5 %), c.998A > G (p.Y333C) (12.5 %), and c.1657T > C (p.Y553H) (7.5 %). Conclusion The prevalence, disease spectrum, and genetic characteristics of FAODs in a southern Chinese population were clarified. PCD was the most common FAOD, followed by MADD. Hotspot variants were found in SLC22A5 and ETFDH genes, while the remaining FAODs showed great molecular heterogeneity. Incorporating second-tier genetic screening is critical for FAODs.
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Affiliation(s)
- Yiming Lin
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Chunmei Lin
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Bangbang Lin
- Administrative office, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Zhenzhu Zheng
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Weihua Lin
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Yanru Chen
- Center of Neonatal Disease Screening, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Dongmei Chen
- Department of Neonatology, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Weilin Peng
- Department of Clinical Laboratory, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
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Rossi A, Assunto A, Rosano C, Tucci S, Ruoppolo M, Caterino M, Pirozzi F, Strisciuglio P, Parenti G, Melis D. Mitochondrial reprogramming in peripheral blood mononuclear cells of patients with glycogen storage disease type Ia. GENES & NUTRITION 2023; 18:10. [PMID: 37280548 DOI: 10.1186/s12263-023-00729-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/05/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Glycogen storage disease type Ia (GSDIa) is an inborn metabolic disorder caused by the deficiency of glucose-6-phospatase-α (G6Pase-α) leading to mitochondrial dysfunction. It remains unclear whether mitochondrial dysfunction is present in patients' peripheral blood mononuclear cells (PBMC) and whether dietary treatment can play a role. The aim of this study was to investigate mitochondrial function in PBMC of GSDIa patients. METHODS Ten GSDIa patients and 10 age-, sex- and fasting-time matched controls were enrolled. Expression of genes involved in mitochondrial function and activity of key fatty acid oxidation (FAO) and Krebs cycle proteins were assessed in PBMC. Targeted metabolomics and assessment of metabolic control markers were also performed. RESULTS Adult GSDIa patients showed increased CPT1A, SDHB, TFAM, mTOR expression (p < 0.05) and increased VLCAD, CPT2 and citrate synthase activity in PBMC (p < 0.05). VLCAD activity directly correlated with WC (p < 0.01), BMI (p < 0.05), serum malonycarnitine levels (p < 0.05). CPT2 activity directly correlated with BMI (p < 0.05). CONCLUSION Mitochondrial reprogramming is detectable in PBMC of GSDIa patients. This feature may develop as an adaptation to the liver enzyme defect and may be triggered by dietary (over)treatment in the frame of G6Pase-α deficiency. PBMC can represent an adequate mean to assess (diet-induced) metabolic disturbances in GSDIa.
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Affiliation(s)
- Alessandro Rossi
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Antonia Assunto
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Carmen Rosano
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Sara Tucci
- Pharmacy, Medical Center - University of Freiburg, Hugstetterstr. 55, D-79106, Freiburg, Germany
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Francesca Pirozzi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Pietro Strisciuglio
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Giancarlo Parenti
- Department of Translational Medicine, Section of Pediatrics, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Section of Pediatrics, University of Salerno, Via Salvador Allende, 43 84081, Baronissi (Salerno), Italy.
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Li YY, Xu J, Sun XC, Li HY, Mu K. Newborn screening and genetic variation of medium chain acyl-CoA dehydrogenase deficiency in the Chinese population. J Pediatr Endocrinol Metab 2022; 35:1264-1271. [PMID: 36068006 DOI: 10.1515/jpem-2022-0394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is an autosomal recessive disorder of the fatty acid oxidative metabolism. This study aimed to investigate the epidemiological characteristics, the spectrum of variation, clinical phenotype, and prognosis of MCADD in Chinese newborns. METHODS We retrospectively analysed newborn screening (NBS) data in the Zibo area from January 2016 to March 2022 and summarized 42 cases recently reported in Chinese neonates. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and next-generation sequencing (NGS) were used to detect the concentrations of carnitine in the blood spots and for diagnosis. RESULTS A total of 183,082 newborns were detected, and six patients were diagnosed with MCADD (1/3,0514). The primary octanoylcarnitine (C8) and the octanoylcarnitine/decanoylcarnitine ratio (C8/C10) were elevated in all patients. Gene analysis revealed four known and four novel variants of the ACADM gene. Five patients were asymptomatic and developed normally under dietary guidance. One child died of vaccination-induced MCADD, presenting with hypoglycemia and elevated acylcarnitines. CONCLUSIONS The incidence of MCADD in Chinese newborns varies geographically from 1/222,903 to 1/30,514, and the most common pathogenic variant is c.449_452 del CTGA (p. T150Rfs∗4) in ACADM gene with a frequency of 27.7%. HPLC-MS/MS and genetic analysis are beneficial for early prevention and good prognosis of MCADD.
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Affiliation(s)
- Yu-Yu Li
- Medical Genetics, Zibo Maternal and Child Health Hospital, Zibo, Shandong Province, P.R. China
| | - Jia Xu
- Medical Genetics, Zibo Maternal and Child Health Hospital, Zibo, Shandong Province, P.R. China
| | - Xue-Cheng Sun
- Medical Genetics, Zibo Maternal and Child Health Hospital, Zibo, Shandong Province, P.R. China
| | - Hong-Yu Li
- Medical Genetics, Zibo Maternal and Child Health Hospital, Zibo, Shandong Province, P.R. China
| | - Kai Mu
- Medical Genetics, Zibo Maternal and Child Health Hospital, Zibo, Shandong Province, P.R. China
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Pei J, Zhao S, Yin M, Wu F, Li J, Zhang G, Wu X, Bao P, Xiong L, Song W, Ba Y, Yan P, Song R, Guo X. Differential proteomics of placentas reveals metabolic disturbance and oxidative damage participate yak spontaneous miscarriage during late pregnancy. BMC Vet Res 2022; 18:248. [PMID: 35761325 PMCID: PMC9235108 DOI: 10.1186/s12917-022-03354-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background High spontaneous miscarriage rate in yak, especially during late pregnancy, have caused a great economic loss to herdsmen living in the Qinghai-Tibet plateau. However, the mechanism underlying spontaneous miscarriage is still poorly understood. In the present study, placenta protein markers were identified to elucidate the pathological reasons for yak spontaneous miscarriage through isobaric tags for relative and absolute quantification (iTRAQ) proteomic technology and bioinformatic approaches. Results Subsequently, a total of 415 differentially expressed proteins (DEPs) were identified between aborted and normal placentas. The up-regulated DEPs in the aborted placentas were significantly associated with “spinocerebellar ataxia”, “sphingolipid signalling”, “relaxin signalling”, “protein export”, “protein digestion and absorption” and “aldosterone synthesis and secretion” pathway. While the down-regulated DEPs in the aborted placentas mainly participated in “valine, leucine and isoleucine degradation”, “PPAR signalling”, “peroxisome”, “oxidative phosphorylation”, “galactose metabolism”, “fatty acid degradation”, “cysteine and methionine metabolism” and “citrate cycle” pathway. Conclusions The results implied that the identified DEPs could be considered as placental protein markers for yak miscarriage during late pregnancy, and biomacromolecule metabolic abnormality and oxidative damage might be responsible for the high spontaneous miscarriage rate in yak. These findings provide an important theoretical basis for deciphering the pathologic mechanism of late spontaneous miscarriage in yak. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03354-w.
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Alcaide P, Ferrer-López I, Gutierrez L, Leal F, Martín-Hernández E, Quijada-Fraile P, Bellusci M, Moráis A, Pedrón-Giner C, Rausell D, Correcher P, Unceta M, Stanescu S, Ugarte M, Ruiz-Sala P, Pérez B. Lymphocyte Medium-Chain Acyl-CoA Dehydrogenase Activity and Its Potential as a Diagnostic Confirmation Tool in Newborn Screening Cases. J Clin Med 2022; 11:jcm11102933. [PMID: 35629059 PMCID: PMC9145342 DOI: 10.3390/jcm11102933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
The determination of acylcarnitines (AC) in dried blood spots (DBS) by tandem mass spectrometry in newborn screening (NBS) programs has enabled medium-chain acyl-coA dehydrogenase deficiency (MCADD) to be identified in presymptomatic newborns. Nevertheless, different confirmatory tests must be performed to confirm the diagnosis. In this work, we have collected and analyzed the NBS results and confirmatory test results (plasma AC, molecular findings, and lymphocyte MCAD activity) of forty individuals, correlating them with clinical outcomes and treatment, with the aim of obtaining useful diagnostic information that could be applied in the follow-up of the patients. Our results led us to classify patients into two groups. The first group (14 cases) had high increased octanoylcarnitine (C8) levels, biallelic pathogenic variants, and severe impaired enzyme activity (<10% of the intra-assay control (IAC)); all of these cases received nutritional therapy and required carnitine supplementation during follow-up, representing the most severe form of the disease. The second group (16 patients) was a heterogeneous group presenting moderate increases in C8, biallelic likely pathogenic/pathogenic variants, and intermediate activity (<41% IAC). All of them are currently asymptomatic and could be considered as having a milder form of the disease. Finally, eight cases presented a normal−mild increase in plasma C8, with only one pathogenic variant detected, and high−intermediate residual activity (15−100%). Based on our results, we confirm that combined evaluation of acylcarnitine profiles, genetic findings, and residual enzyme activities proves useful in predicting the risk of future metabolic decompensation, in making decisions regarding future treatment or follow-up, and also in confirming the clinical effects of unknown clinical variants.
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Affiliation(s)
- Patricia Alcaide
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
- Correspondence: ; Tel.: +34-914-974-589
| | - Isaac Ferrer-López
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
| | - Leticia Gutierrez
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
| | - Fatima Leal
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
| | - Elena Martín-Hernández
- Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (E.M.-H.); (P.Q.-F.); (M.B.)
| | - Pilar Quijada-Fraile
- Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (E.M.-H.); (P.Q.-F.); (M.B.)
| | - Marcello Bellusci
- Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain; (E.M.-H.); (P.Q.-F.); (M.B.)
| | - Ana Moráis
- Unidad de Nutrición Infantil y Enfermedades Metabólicas, Hospital Universitario Infantil La Paz, 28046 Madrid, Spain;
| | - Consuelo Pedrón-Giner
- Sección de Gastroenterología y Nutrición, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain;
| | - Dolores Rausell
- Laboratorio de Metabolopatías, Servicio de Análisis Clínicos, Hospital Universitario La Fe, 46026 Valencia, Spain; (D.R.); (P.C.)
| | - Patricia Correcher
- Laboratorio de Metabolopatías, Servicio de Análisis Clínicos, Hospital Universitario La Fe, 46026 Valencia, Spain; (D.R.); (P.C.)
| | - María Unceta
- Análisis Clínicos, Servicio de Bioquímica, Unidad de Enfermedades Metabólicas, Hospital Universitario de Cruces, 48903 Barakaldo, Spain;
| | - Sinziana Stanescu
- Servicio de Pediatría, Unidad de Enfermedades Metabólicas, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain;
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
| | - Pedro Ruiz-Sala
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma Madrid, CIBERER, IDIPAZ, 28049 Madrid, Spain; (I.F.-L.); (L.G.); (F.L.); (M.U.); (P.R.-S.); (B.P.)
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Martín‐Rivada Á, Palomino Pérez L, Ruiz‐Sala P, Navarrete R, Cambra Conejero A, Quijada Fraile P, Moráis López A, Belanger‐Quintana A, Martín‐Hernández E, Bellusci M, Cañedo Villaroya E, Chumillas Calzada S, García Silva MT, Bergua Martínez A, Stanescu S, Martínez‐Pardo Casanova M, Ruano MLF, Ugarte M, Pérez B, Pedrón‐Giner C. Diagnosis of inborn errors of metabolism within the expanded newborn screening in the Madrid region. JIMD Rep 2022; 63:146-161. [PMID: 35281663 PMCID: PMC8898721 DOI: 10.1002/jmd2.12265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
We present the results of our experience in the diagnosis of inborn errors of metabolism (IEM) since the Expanded Newborn Screening was implemented in our Region. Dried blood samples were collected 48 h after birth. Amino acids and acylcarnitines were quantitated by mass spectrometry (MS)/MS. Newborns with alterations were referred to the clinical centers for follow‐up. Biochemical and molecular genetic studies for confirmation of a disease were performed. In the period 2011 to 2019, 592 822 children were screened: 902 of them were referred for abnormal results. An IEM was confirmed in 222 (1/2670): aminoacidopathies: 89 hyperphenylalaninemia (HPA) (51 benign HPA, 32 phenylketonuria, 4 DNAJC12 defect, and 2 primapterinuria), 6 hypermethioninemia, 3 tyrosinemia type 1 (TYR‐1), 1 TYR‐3, 4 maple syrup urine disease (MSUD), 2 branched‐chain amino acid transferase 2 deficiency, 2 homocystinuria, 1 cystinuria, 2 ornithine transcarbamylase (OTC) deficiency, 2 citrullinemia type I (CTLN1); FAO defects: 43 medium‐chain acyl‐CoA dehydrogenase deficiency (MCADD), 13 very long‐chain acyl‐CoA dehydrogenase deficiency, 2 long‐chain 3‐hydroxyacyl‐CoA dehydrogenase deficiency (LCHADD), 1 multiple acyl‐coA dehydrogenation deficiency, 11 systemic primary carnitine deficiency, 2 carnitine palmitoyltransferase type 2 (CPT‐II) deficiency, 1 CPT‐I deficiency; organic acidurias: 12 glutaric aciduria type 1 (GA‐1), 4 methylmalonic acidemia (MMA), 7 MMA including combined cases with homocystinuria (MMAHC), 6 propionic acidemia (PA), 7 3‐methylcrotonyl‐CoA carboxylase, 1 3‐hydroxy‐3‐methylglutaryl‐CoA lyase deficiency lyase deficiency. Only 19 infants (8.5%) were symptomatic at newborn screening result (1 LCHADD, 5 PA, 1 CPT‐II deficiency, 1 MMA, 3 MMAHC, 2 MSUD, 2 OTC deficiency, 1 CTLN1, 1 MCADD, 2 TYR‐1). No false negative cases were identified. Genetic diagnosis was conclusive in all biochemically confirmed cases, except for two infants with HPA, identifying pathogenic variants in 32 different genes. The conditions with the highest incidence were HPA (1/6661) and MCAD deficiencies (1/13 787).
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Affiliation(s)
- Álvaro Martín‐Rivada
- Sección de Gastroenterología y Nutrición Hospital Infantil Universitario Niño Jesús Madrid Spain
| | - Laura Palomino Pérez
- Sección de Gastroenterología y Nutrición Hospital Infantil Universitario Niño Jesús Madrid Spain
| | - Pedro Ruiz‐Sala
- Centro de Diagnóstico de Enfermedades Moleculares Universidad Autónoma de Madrid, IdiPAZ, CIBERER Madrid Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares Universidad Autónoma de Madrid, IdiPAZ, CIBERER Madrid Spain
| | - Ana Cambra Conejero
- Laboratorio de Cribado Neonatal de la Comunidad de Madrid Servicio de Bioquímica Clínica, Hospital General Universitario Gregorio Marañón Madrid Spain
| | - Pilar Quijada Fraile
- Unidad de Enfermedades Mitocondriales‐Metabólicas Hereditarias Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) en Enfermedades Metabólicas, Hospital Universitario 12 de Octubre Madrid Spain
| | - Ana Moráis López
- Unidad de Nutrición Infantil y Enfermedades Metabólicas Hospital Universitario La Paz Madrid Spain
| | - Amaya Belanger‐Quintana
- Centro de Referencia Nacional (CSUR) en Enfermedades Metabólicas Hospital Universitario Ramón y Cajal Madrid Spain
| | - Elena Martín‐Hernández
- Unidad de Enfermedades Mitocondriales‐Metabólicas Hereditarias Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) en Enfermedades Metabólicas, Hospital Universitario 12 de Octubre Madrid Spain
| | - Marcello Bellusci
- Unidad de Enfermedades Mitocondriales‐Metabólicas Hereditarias Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) en Enfermedades Metabólicas, Hospital Universitario 12 de Octubre Madrid Spain
| | - Elvira Cañedo Villaroya
- Sección de Gastroenterología y Nutrición Hospital Infantil Universitario Niño Jesús Madrid Spain
| | - Silvia Chumillas Calzada
- Unidad de Enfermedades Mitocondriales‐Metabólicas Hereditarias Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) en Enfermedades Metabólicas, Hospital Universitario 12 de Octubre Madrid Spain
| | - María Teresa García Silva
- Unidad de Enfermedades Mitocondriales‐Metabólicas Hereditarias Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) en Enfermedades Metabólicas, Hospital Universitario 12 de Octubre Madrid Spain
| | - Ana Bergua Martínez
- Unidad de Nutrición Infantil y Enfermedades Metabólicas Hospital Universitario La Paz Madrid Spain
| | - Sinziana Stanescu
- Centro de Referencia Nacional (CSUR) en Enfermedades Metabólicas Hospital Universitario Ramón y Cajal Madrid Spain
| | | | - Miguel L. F. Ruano
- Laboratorio de Cribado Neonatal de la Comunidad de Madrid Servicio de Bioquímica Clínica, Hospital General Universitario Gregorio Marañón Madrid Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares Universidad Autónoma de Madrid, IdiPAZ, CIBERER Madrid Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares Universidad Autónoma de Madrid, IdiPAZ, CIBERER Madrid Spain
| | - Consuelo Pedrón‐Giner
- Sección de Gastroenterología y Nutrición Hospital Infantil Universitario Niño Jesús Madrid Spain
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Miller DB, Robison R, Piccolo SR. Toward a methodology for evaluating DNA variants in nuclear families. PLoS One 2021; 16:e0258375. [PMID: 34624066 PMCID: PMC8500447 DOI: 10.1371/journal.pone.0258375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022] Open
Abstract
The genetic underpinnings of most pediatric-cancer cases are unknown. Population-based studies use large sample sizes but have accounted for only a small proportion of the estimated heritability of pediatric cancers. Pedigree-based studies are infeasible for most human populations. One alternative is to collect genetic data from a single nuclear family and use inheritance patterns within the family to filter candidate variants. This approach can be applied to common and rare variants, including those that are private to a given family or to an affected individual. We evaluated this approach using genetic data from three nuclear families with 5, 4, and 7 children, respectively. Only one child in each nuclear family had been diagnosed with cancer, and neither parent had been affected. Diagnoses for the affected children were benign low-grade astrocytoma, Wilms tumor (stage 2), and Burkitt’s lymphoma, respectively. We used whole-genome sequencing to profile normal cells from each family member and a linked-read technology for genomic phasing. For initial variant filtering, we used global minor allele frequencies, deleteriousness scores, and functional-impact annotations. Next, we used genetic variation in the unaffected siblings as a guide to filter the remaining variants. As a way to evaluate our ability to detect variant(s) that may be relevant to disease status, the corresponding author blinded the primary author to affected status; the primary author then assigned a risk score to each child. Based on this evidence, the primary author predicted which child had been affected in each family. The primary author’s prediction was correct for the child who had been diagnosed with a Wilms tumor; the child with Burkitt’s lymphoma had the second-highest risk score among the seven children in that family. This study demonstrates a methodology for filtering and evaluating candidate genomic variants and genes within nuclear families that may merit further exploration.
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Affiliation(s)
- Dustin B. Miller
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Reid Robison
- Department of Biology, Brigham Young University, Provo, UT, United States of America
- Department of Psychiatry, University of Utah, Salt Lake City, UT, United States of America
| | - Stephen R. Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States of America
- * E-mail:
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