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Children
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Human Genetics and Bioinformatics in Pediatric Diseases
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Human Genetics and Bioinformatics in Pediatric Diseases

A special issue of Children (ISSN 2227-9067). This special issue belongs to the section "Translational Pediatrics".

Deadline for manuscript submissions: 1 February 2025 | Viewed by 13350

Special Issue Editors

Prof. Dr. Wenhao Zhou

E-Mail Website
Guest Editor
Children's Hospital and Institutes of Biomedical Sciences, Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
Interests: diagnosis and prevention of birth defects in the neonatal nervous system; neonatal encephalopathy; neonatal hereditary disease
Dr. Mingbang Wang

E-Mail Website
Guest Editor
Microbiome Therapy Center, South China of Shenzhen University, Shenzhen, China
Interests: ediatric disorders; perinatal risk; machine learning; gut microbiota; the role and mechanism of genetic and perinatal risk factors and their interactions in the occurrence of pediatric and psychiatric diseases; application of machine learning, deep learning and other artificial intelligence technology in metagenomics and metabolomics; the role of gut microbiota and metabolites in the perinatal period, newborns, children, and neuropsychiatric diseases
Prof. Dr. Hongfang Jin

E-Mail Website
Guest Editor
Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
Interests: pediatric cardiovascular disease; pediatric syncope

Special Issue Information

Dear Colleagues,

At present, next-generation sequencing (NGS) technologies such as whole exome sequencing (WES) and whole genome sequencing (WGS) have played an important role in the genetic testing of children. Radpid WES/WGS tests significantly shorten the turnaround time, and the results help to adjust the treatment regimen in a timely manner. In recent years, metagenomic next-generation sequencing(mNGS) has been widely used for the diagnosis of infectious diseases and has achieved significantly higher sensitivity than conventional methods. In severe infections, alongside the testing of conventional methods, mNGS is also used as a first-line test for the diagnosis of infections in children.

This Special Issue aims to provide a comprehensive overview of how the gut microbiota plays a role in pediatric diseases. In this Special Issue, we welcome all papers, including original research, systematic reviews, and meta-analyses. We also welcome clinical and preclinical research and basic research on humans and/or animals.

  • Application of metagenomic sequencing /16s rRNA gene sequencing technology in pediatric diseases.
  • The application of LC-MS/MS metabolome technology in pediatric diseases.
  • Multi-omics technologies, such as metagenomic sequencing, transcriptome sequencing, metabolomics, and other NGS technologies used for the assessment of pediatric diseases.
  • Metagenomics NGS technology (mNGS) studies on life-threatening infections in newborns and children caused by opportunistic pathogens.
  • Research on new genetics, proteins (cytokines, signal molecules), and metabolite markers involving the occurrence, development, and clinical manifestations of pediatric diseases.

Prof. Dr. Wenhao Zhou
Dr. Mingbang Wang
Prof. Dr. Hongfang Jin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Children is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pediatric diseases
  • birth defects
  • genome sequencing
  • gut microbiota
  • metagenomics next-generation sequencing (mngs)

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Published Papers (5 papers)

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Research

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18 pages, 3692 KiB  
Article
The Association of Neonatal Gut Microbiota Community State Types with Birth Weight
by Wanling Chen, Kaiping Guo, Xunbin Huang, Xueli Zhang, Xiaoxia Li, Zimiao Chen, Yanli Wang, Zhangxing Wang, Rongtian Liu, Huixian Qiu, Mingbang Wang and Shujuan Zeng
Children 2024, 11(7), 770; https://doi.org/10.3390/children11070770 - 25 Jun 2024
Viewed by 1353
Abstract
Background: while most gut microbiota research has focused on term infants, the health outcomes of preterm infants are equally important. Very-low-birth-weight (VLBW) or extremely-low-birth-weight (ELBW) preterm infants have a unique gut microbiota structure, and probiotics have been reported to somewhat accelerate the maturation [...] Read more.
Background: while most gut microbiota research has focused on term infants, the health outcomes of preterm infants are equally important. Very-low-birth-weight (VLBW) or extremely-low-birth-weight (ELBW) preterm infants have a unique gut microbiota structure, and probiotics have been reported to somewhat accelerate the maturation of the gut microbiota and reduce intestinal inflammation in very-low preterm infants, thereby improving their long-term outcomes. The aim of this study was to investigate the structure of gut microbiota in ELBW neonates to facilitate the early identification of different types of low-birth-weight (LBW) preterm infants. Methods: a total of 98 fecal samples from 39 low-birth-weight preterm infants were included in this study. Three groups were categorized according to different birth weights: ELBW (n = 39), VLBW (n = 39), and LBW (n = 20). The gut microbiota structure of neonates was obtained by 16S rRNA gene sequencing, and microbiome analysis was conducted. The community state type (CST) of the microbiota was predicted, and correlation analysis was conducted with clinical indicators. Differences in the gut microbiota composition among ELBW, VLBW, and LBW were compared. The value of gut microbiota composition in the diagnosis of extremely low birth weight was assessed via a random forest-machine learning approach. Results: we briefly analyzed the structure of the gut microbiota of preterm infants with low birth weight and found that the ELBW, VLBW, and LBW groups exhibited gut microbiota with heterogeneous compositions. Low-birth-weight preterm infants showed five CSTs dominated by Enterococcus, Staphylococcus, Klebsiella, Streptococcus, Pseudescherichia, and Acinetobacter. The birth weight and clinical indicators related to prematurity were associated with the CST. We found the composition of the gut microbiota was specific to the different types of low-birth-weight premature infants, namely, ELBW, VLBW, and LBW. The ELBW group exhibited significantly more of the potentially harmful intestinal bacteria Acinetobacter relative to the VLBW and LBW groups, as well as a significantly lower abundance of the intestinal probiotic Bifidobacterium. Based on the gut microbiota’s composition and its correlation with low weight, we constructed random forest model classifiers to distinguish ELBW and VLBW/LBW infants. The area under the curve of the classifiers constructed with Enterococcus, Klebsiella, and Acinetobacter was found to reach 0.836 by machine learning evaluation, suggesting that gut microbiota composition may be a potential biomarker for ELBW preterm infants. Conclusions: the gut bacteria of preterm infants showed a CST with Enterococcus, Klebsiella, and Acinetobacter as the dominant genera. ELBW preterm infants exhibit an increase in the abundance of potentially harmful bacteria in the gut and a decrease in beneficial bacteria. These potentially harmful bacteria may be potential biomarkers for ELBW preterm infants. Full article
(This article belongs to the Special Issue Human Genetics and Bioinformatics in Pediatric Diseases)
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17 pages, 1554 KiB  
Article
Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon
by Sonal Gupta, Praveen Mathur, Ashwani Kumar Mishra, Krishna Mohan Medicherla, Obul Reddy Bandapalli and Prashanth Suravajhala
Children 2023, 10(5), 902; https://doi.org/10.3390/children10050902 - 19 May 2023
Cited by 2 | Viewed by 2600
Abstract
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants [...] Read more.
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies. Full article
(This article belongs to the Special Issue Human Genetics and Bioinformatics in Pediatric Diseases)
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13 pages, 741 KiB  
Article
Breaking Barriers to Rapid Whole Genome Sequencing in Pediatrics: Michigan’s Project Baby Deer
by Caleb P. Bupp, Elizabeth G. Ames, Madison K. Arenchild, Sara Caylor, David P. Dimmock, Joseph D. Fakhoury, Padmani Karna, April Lehman, Cristian I. Meghea, Vinod Misra, Danielle A. Nolan, Jessica O’Shea, Aditi Sharangpani, Linda S. Franck and Andrea Scheurer-Monaghan
Children 2023, 10(1), 106; https://doi.org/10.3390/children10010106 - 4 Jan 2023
Cited by 12 | Viewed by 4751
Abstract
The integration of precision medicine in the care of hospitalized children is ever evolving. However, access to new genomic diagnostics such as rapid whole genome sequencing (rWGS) is hindered by barriers in implementation. Michigan’s Project Baby Deer (PBD) is a multi-center collaborative effort [...] Read more.
The integration of precision medicine in the care of hospitalized children is ever evolving. However, access to new genomic diagnostics such as rapid whole genome sequencing (rWGS) is hindered by barriers in implementation. Michigan’s Project Baby Deer (PBD) is a multi-center collaborative effort that sought to break down barriers to access by offering rWGS to critically ill neonatal and pediatric inpatients in Michigan. The clinical champion team used a standardized approach with inclusion and exclusion criteria, shared learning, and quality improvement evaluation of the project’s impact on the clinical outcomes and economics of inpatient rWGS. Hospitals, including those without on-site geneticists or genetic counselors, noted positive clinical impacts, accelerating time to definitive treatment for project patients. Between 95–214 hospital days were avoided, net savings of $4155 per patient, and family experience of care was improved. The project spurred policy advancement when Michigan became the first state in the United States to have a Medicaid policy with carve-out payment to hospitals for rWGS testing. This state project demonstrates how front-line clinician champions can directly improve access to new technology for pediatric patients and serves as a roadmap for expanding clinical implementation of evidence-based precision medicine technologies. Full article
(This article belongs to the Special Issue Human Genetics and Bioinformatics in Pediatric Diseases)
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12 pages, 984 KiB  
Article
Dendritic Spine in Autism Genetics: Whole-Exome Sequencing Identifying De Novo Variant of CTTNBP2 in a Quad Family Affected by Autism Spectrum Disorder
by Yingmei Xie, Hui Wang, Bing Hu, Xueli Zhang, Aiping Liu, Chunquan Cai, Shijun Li, Cheng Chen, Zhangxing Wang, Zhaoqing Yin and Mingbang Wang
Children 2023, 10(1), 80; https://doi.org/10.3390/children10010080 - 30 Dec 2022
Cited by 4 | Viewed by 2393
Abstract
Autism spectrum disorder (ASD) affects around 1% of children with no effective blood test or cure. Recent studies have suggested that these are neurological disorders with a strong genetic basis and that they are associated with the abnormal formation of dendritic spines. Chromosome [...] Read more.
Autism spectrum disorder (ASD) affects around 1% of children with no effective blood test or cure. Recent studies have suggested that these are neurological disorders with a strong genetic basis and that they are associated with the abnormal formation of dendritic spines. Chromosome microarray (CMA) together with high-throughput sequencing technology has been used as a powerful tool to identify new candidate genes for ASD. In the present study, CMA was first used to scan for genome-wide copy number variants in a proband, and no clinically significant copy number variants were found. Whole-exome sequencing (WES) was used further for genetic testing of the whole quad family affected by ASD, including the proband, his non-autistic sister, and his parents. Sanger sequencing and MassARRAY-based validation were used to identify and confirm variants associated with ASD. WES yielded a 151-fold coverage depth for each sample. A total of 98.65% of the targeted whole-exome region was covered at >20-fold depth. A de novo variant in CTTNBP2, p.M115T, was identified. The CTTNBP2 gene belongs to a family of ankyrin repeat domain-containing proteins associated with dendritic spine formation. Although CTTNBP2 has been associated with ASD, limited studies have been developed to identify clinically relevant de novo mutations of CTTNBP2 in children with ASD; family-based WES successfully identified a clinically relevant mutation in the CTTNBP2 gene in a quad family affected by ASD. Considering the neuron-specific expression of CTTNBP2 and its role in dendritic spine formation, our results suggest a correlation between the CTTNBP2 mutation and ASD, providing genetic evidence for ASD spine pathology. Although the present study is currently insufficient to support the assertion that the de novo mutation M115T in CTTNBP2 directly causes the autism phenotype, our study provides support for the assertion that this mutation is a candidate clinically relevant variant in autism. Full article
(This article belongs to the Special Issue Human Genetics and Bioinformatics in Pediatric Diseases)
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Review

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16 pages, 264 KiB  
Review
Prospective Genetic Screening in Multiple Endocrine Neoplasia Syndromes
by Diana Paun, Dana Tilici, Sorin Paun and Alexandra Mirica
Children 2024, 11(8), 1012; https://doi.org/10.3390/children11081012 - 20 Aug 2024
Viewed by 743
Abstract
Multiple endocrine neoplasia syndromes are a rare but potentially fatal pathology due to the lack of early diagnosis. We have performed a narrative review of the medical literature, summarizing the main clinical concepts useful in current clinical practice, showing the importance of screening [...] Read more.
Multiple endocrine neoplasia syndromes are a rare but potentially fatal pathology due to the lack of early diagnosis. We have performed a narrative review of the medical literature, summarizing the main clinical concepts useful in current clinical practice, showing the importance of screening and early diagnosis during childhood. Full article
(This article belongs to the Special Issue Human Genetics and Bioinformatics in Pediatric Diseases)
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