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Madritsch S, Arnold V, Haider M, Bosenge J, Pfeifer M, Weil B, Zechmeister M, Hengstschläger M, Neesen J, Laccone F. Aneuploidy detection in pooled polar bodies using rapid nanopore sequencing. J Assist Reprod Genet 2024; 41:1261-1271. [PMID: 38642269 PMCID: PMC11143085 DOI: 10.1007/s10815-024-03108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 04/22/2024] Open
Abstract
PURPOSE Various screening techniques have been developed for preimplantation genetic testing for aneuploidy (PGT-A) to reduce implantation failure and miscarriages in women undergoing in vitro fertilisation (IVF) treatment. Among these methods, the Oxford nanopore technology (ONT) has already been tested in several tissues. However, no studies have applied ONT to polar bodies, a cellular material that is less restrictively regulated for PGT-A in some countries. METHODS We performed rapid short nanopore sequencing on pooled first and second polar bodies of 102 oocytes from women undergoing IVF treatment to screen for aneuploidy. An automated analysis pipeline was developed with the expectation of three chromatids per chromosome. The results were compared to those obtained by array-based comparative genomic hybridisation (aCGH). RESULTS ONT and aCGH were consistent for 96% (98/102) of sample ploidy classification. Of those samples, 36 were classified as euploid, while 62 were classified as aneuploid. The four discordant samples were assessed as euploid using aCGH but classified as aneuploid using ONT. The concordance of the ploidy classification (euploid, gain, or loss) per chromosome was 92.5% (2169 of 2346 of analysed chromosomes) using aCGH and ONT and increased to 97.7% (2113/2162) without the eight samples assessed as highly complex aneuploid using ONT. CONCLUSION The automated detection of the ploidy classification per chromosome and shorter duplications or deletions depending on the sequencing depth demonstrates an advantage of the ONT method over standard, commercial aCGH methods, which do not consider the presence of three chromatids in pooled polar bodies.
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Affiliation(s)
- Silvia Madritsch
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria.
| | - Vivienne Arnold
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Martha Haider
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Julia Bosenge
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Mateja Pfeifer
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
| | - Beatrix Weil
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | | | - Markus Hengstschläger
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Jürgen Neesen
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
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Afsar T, Fu H, Khan H, Ali Z, Zehri Z, Zaman G, Abbas S, Mahmood A, Alam Q, Hu J, Razak S, Umair M. Loss-of-function variant in the LRR domain of SLITRK2 implicated in a neurodevelopmental disorder. Front Genet 2024; 14:1308116. [PMID: 38283150 PMCID: PMC10813200 DOI: 10.3389/fgene.2023.1308116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
Background: Neurodevelopmental disorders are characterized by different combinations of intellectual disability (ID), communication and social skills deficits, and delays in achieving motor or language milestones. SLITRK2 is a postsynaptic cell-adhesion molecule that promotes neurite outgrowth and excitatory synapse development. Methods and Results: In the present study, we investigated a single patient segregating Neurodevelopmental disorder. SLITRK2 associated significant neuropsychological issues inherited in a rare X-linked fashion have recently been reported. Whole-exome sequencing and data analysis revealed a novel nonsense variant [c.789T>A; p.(Cys263*); NM_032539.5; NP_115928.1] in exon 5 of the SLITRK2 gene (MIM# 300561). Three-dimensional protein modeling revealed substantial changes in the mutated SLITRK2 protein, which might lead to nonsense-medicated decay. Conclusion: This study confirms the role of SLITRK2 in neuronal development and highlights the importance of including the SLITRK2 gene in the screening of individuals presenting neurodevelopmental disorders.
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Affiliation(s)
- Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Hongxia Fu
- Department of Neurology, Dongguan Songshan Lake Central Hospital, Dongguan, China
| | - Hammal Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zain Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zamrud Zehri
- Department of Gynecology, Civil Hospital, Quetta, Pakistan
| | - Gohar Zaman
- Department of Computer Science, Abbottabad University of Science and Technology, Havelian, Abbottabad, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, United States
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Qamre Alam
- Molecular Genomics and Precision Department, ExpressMed Diagnostics and Research, Zinj, Bahrain
| | - Junjian Hu
- Department of Central Laboratory, Dongguan Songshan Lake Central Hospital, Dongguan, China
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Muhammad Umair
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
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Zheng K, Lin S, Gao J, Chen S, Su J, Liu Z, Duan S. Novel compound heterozygous MYO15A splicing variants in autosomal recessive non-syndromic hearing loss. BMC Med Genomics 2024; 17:4. [PMID: 38167320 PMCID: PMC10763153 DOI: 10.1186/s12920-023-01777-4] [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: 08/25/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Hereditary hearing loss is a highly heterogeneous disorder. This study aimed to identify the genetic cause of a Chinese family with autosomal recessive non-syndromic sensorineural hearing loss (ARNSHL). METHODS Clinical information and peripheral blood samples were collected from the proband and its parents. Two-step high-throughput next-generation sequencing on the Ion Torrent platform was applied to detect variants as follows. First, long-range PCR was performed to amplify all the regions of the GJB2, GJB3, SLC26A4, and MT-RNR1 genes, followed by next-generation sequencing. If no candidate pathogenetic variants were found, the targeted exon sequencing with AmpliSeq technology was employed to examine another 64 deafness-associated genes. Sanger sequencing was used to identify variants and the lineage co-segregation. The splicing of the MYO15A gene was assessed by in silico bioinformatics prediction and minigene assays. RESULTS Two candidate MYO15A gene (OMIM, #602,666) heterozygous splicing variants, NG_011634.2 (NM_016239.3): c.6177 + 1G > T and c.9690 + 1G > A, were identified in the proband, and these two variants were both annotated as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Further bioinformatic analysis predicted that the c.6177 + 1G > T variant might cause exon skipping and that the c.9690 + 1G > A variant might activate a cryptic splicing donor site in the downstream intronic region. An in vitro minigene assay confirmed the above predictions. CONCLUSIONS We identified a compound heterozygous splicing variant in the MYO15A gene in a Han Chinese family with ARNSHL. Our results broaden the spectrum of MYO15A variants, potentially benefiting the early diagnosis, prevention, and treatment of the disease.
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Affiliation(s)
- Kaifeng Zheng
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Sheng Lin
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Jian Gao
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Shiguo Chen
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jindi Su
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Zhiqiang Liu
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Shan Duan
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China.
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Akbar W, Ullah A, Haider N, Suleman S, Khan FU, Shah AA, Sikandar MA, Basit S, Ahmad W. Identification of novel homozygous variants in FOXE3 and AP4M1 underlying congenital syndromic anophthalmia and microphthalmia. J Gene Med 2024; 26:e3601. [PMID: 37758467 DOI: 10.1002/jgm.3601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/14/2023] [Accepted: 09/13/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Anophthalmia and microphthalmia are severe developmental ocular disorders that affect the size of the ocular globe and can be unilateral or bilateral. The disease is found in syndromic as well as non-syndromic forms. It is genetically caused by chromosomal aberrations, copy number variations and single gene mutations, along with non-genetic factors such as viral infections, deficiency of vitamin A and an exposure to alcohol or drugs during pregnancy. To date, more than 30 genes having different modes of inheritance patterns are identified as causing anophthalmia and microphthalmia. METHODS In the present study, a clinical and genetic analysis was performed of six patients with anophthalmia and microphthalmia and/or additional phenotypes of intellectual disability, developmental delay and cerebral palsy from a large consanguineous Pakistani family. Whole exome sequencing followed by data analysis for variants prioritization and validation through Sanger sequencing was performed to identify the disease causing variant(s). American College of Medical Genetics and Genomics (ACMG) guidelines were applied to classify clinical interpretation of the prioritized variants. RESULTS Clinical investigations revealed that the affected individuals are afflicted with anophthalmia. Three of the patients showed additional phenotype of intellectual disability, developmental delays and other neurological symptoms. Whole exome sequencing of the DNA samples of the affected members in the family identified a novel homozygous stop gain mutation (NM_012186: c.106G>T: p.Glu36*) in Forkhead Box E3 (FOXE3) gene shared by all affected individuals. Moreover, patients segregating additional phenotypes of spastic paraplegia, intellectual disability, hearing loss and microcephaly showed an additional homozygous sequence variant (NM_004722: c.953G>A: p.Arg318Gln) in AP4M1. Sanger sequencing validated the correct segregation of the identified variants in the affected family. ACMG guidelines predicted the variants to be pathogenic. CONCLUSIONS We have investigated first case of syndromic anophthalmia caused by variants in the FOXE3 and AP4M1. The present findings are helpful for understanding pathological role of the mutations of the genes in syndromic forms of anophthalmia. Furthermore, the study signifies searching for the identification of second variant in families with patients exhibiting variable phenotypes. In addition, the findings will help clinical geneticists, genetic counselors and the affected family with respect to prenatal testing, family planning and genetic counseling.
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Affiliation(s)
- Warda Akbar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asmat Ullah
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Nighat Haider
- Shaheed Zulfiqar Ali Bhutto Medical University, Department of Pediatrics, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Sufyan Suleman
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Fati Ullah Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abid Ali Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Sulman Basit
- College of Medicine, Taibah University, Medina, Saudi Arabia
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Peng Y, Zhou L, Chen J, Huang X, Pang J, Liu J, Tang W, Yang S, Liang C, Xie W. Clinical features and genetic analysis of a case series of skeletal ciliopathies in a prenatal setting. BMC Med Genomics 2023; 16:318. [PMID: 38062428 PMCID: PMC10704717 DOI: 10.1186/s12920-023-01753-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Short-rib polydactyly syndrome (SRPS) refers to a group of lethal skeletal dysplasias that can be difficult to differentiate between subtypes or from other non-lethal skeletal dysplasias such as Ellis-van Creveld syndrome and Jeune syndrome in a prenatal setting. We report the ultrasound and genetic findings of four unrelated fetuses with skeletal dysplasias. METHODS Systemic prenatal ultrasound examination was performed in the second or third trimester. Genetic tests including GTG-banding, single nucleotide polymorphism (SNP) array and exome sequencing were performed with amniocytes or aborted fetal tissues. RESULTS The major and common ultrasound anomalies for the four unrelated fetuses included short long bones of the limbs and narrow thorax. No chromosomal abnormalities and pathogenic copy number variations were detected. Exome sequencing revealed three novel variants in the DYNC2H1 gene, namely NM_001080463.2:c.6809G > A p.(Arg2270Gln), NM_001080463.2:3133C > T p.(Gln1045Ter), and NM_001080463.2:c.337C > T p.(Arg113Trp); one novel variant in the IFT172 gene, NM_015662.3:4540-5 T > A; and one novel variant in the WDR19 gene, NM_025132.4:c.2596G > C p.(Gly866Arg). The genotypes of DYNC2H1, IFT172 and WDR19 and the phenotypes of the fetuses give hints for the diagnosis of short-rib thoracic dysplasia (SRTD) with or without polydactyly 3, 10, and 5, respectively. CONCLUSION Our findings expand the mutation spectrum of DYNC2H1, IFT172 and WDR19 associated with skeletal ciliopathies, and provide useful information for prenatal diagnosis and genetic counseling on rare skeletal disorders.
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Affiliation(s)
- Ying Peng
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road.
| | - Lin Zhou
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Jing Chen
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Xiaoliang Huang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Jialun Pang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Jing Liu
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Wanglan Tang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Shuting Yang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Changbiao Liang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road
| | - Wanqin Xie
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China, No. 53 Xiangchun Road.
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Khodaeian M, Bitarafan F, Garrousi F, Sardehie EA, Pak N, Hosseinpour S, Shakiba M, Falah M, Garshasbi M, Tavasoli AR. Expanding phenotype heterogeneity of NARS2 by presenting subdural hematoma and parenchymal hemorrhage. J Clin Lab Anal 2023; 37:e24983. [PMID: 37950505 PMCID: PMC10749492 DOI: 10.1002/jcla.24983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 10/12/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND NARS2 encodes mitochondrial Asparaginyl-tRNA Synthetase 2, which catalyzes the aminoacylation of tRNA-Asn in the mitochondria. To date, 24 variants have been reported in NARS2 gene in 35 patients. The phenotypic variability of NARS2-associated disorder is broad, ranging from neurodevelopmental disorders to hearing loss. In this study, we report some novel imaging findings in an Iranian patient suffering from epileptic encephalopathy, caused by a previously reported variant, c.500A > G; p.(His167Arg), in NARS2. METHODS The spectrum of clinical manifestations of two Iranian patients was investigated and genetic analysis was performed by Whole-exome sequencing (WES). Additionally, we also reviewed the literature and summarized the phenotypes of previously reported patients with variants in the NARS2 gene. RESULTS Here, we present the phenotypic and genetic features of 2 unrelated Iranian infants presented with neurodevelopmental delay, seizures, hearing impairment, feeding problems, elevated serum lactate levels in addition to subdural hematoma and cerebral parenchymal hemorrhage in the brain magnetic resonance imaging (MRI) of one of the patients. Genetic analysis revealed a biallelic missense variant in NARS2: c.500A > G; p.(His167Arg). We described the subdural hematoma and cerebral parenchymal hemorrhage of the brain for the first time. CONCLUSIONS Our study provides new clinical findings, subdural hematoma, and parenchymal hemorrhage, in NARS2-related disorders. Our findings along with previous studies provide more evidence of the clinical presentation of the disease caused by pathogenic variants in NARS2. Expanding the clinical spectrum increases the diagnostic rate of molecular testing and improves the quality of counseling for at-risk couples.
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Affiliation(s)
| | - Fatemeh Bitarafan
- Department of Medical GeneticsOslo University Hospital and University of Oslo0450OsloNorway
| | | | | | - Neda Pak
- Pediatric Radiology Division, Children's Medical Center, Pediatrics Center of ExcellenceTehran University of Medical SciencesTehranIran
| | - Sareh Hosseinpour
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of ExcellenceTehran University of Medical SciencesTehranIran
| | - Marjan Shakiba
- Department of Pediatric Endocrinology and Metabolism, Mofid Children's HospitalShahid Beheshti University of Medical SciencesTehranIran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Hazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical SciencesTarbiat Modares UniversityTeheranIran
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of ExcellenceTehran University of Medical SciencesTehranIran
- Department of Neurology, Barrow Neurological InstitutePhoenix Children's HospitalPhoenixArizonaUSA
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Khan S, Umair M, Abbas S, Ali U, Zaman G, Ansar M, Wang R, Zhang X, Houlden H, Harlalka GV, Gul A. Overlapping neurological phenotypes in two extended consanguineous families with novel variants in the CNTNAP1 and ADGRG1 genes. J Gene Med 2023; 25:e3513. [PMID: 37178061 DOI: 10.1002/jgm.3513] [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: 01/05/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations. METHODS The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease-causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals. RESULTS The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood. CONCLUSIONS In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.
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Affiliation(s)
- Shazia Khan
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Hafeez Institute of Medical Sciences, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
| | - Uroba Ali
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Gohar Zaman
- Department of Computer Science, Abbottabad University of Science and Technology, Havelian, Abbottabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Henry Houlden
- Department of Neuromuscular Disorder, UCL Institute of Neurology, London, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Department of Pharmacology, Samarth College of Pharmacy, Deulgaon Raja, Dist. Buldana, Maharashtra, India
| | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
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8
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Zaman Q, Iftikhar A, Rehman G, Khan Q, Najumuddin, Jan A, Khan J, Anas M, Laiba, Umair M, Muthaffar OY, Abdulkareem AA, Bibi F, Naseer MI, Jelani M. Two novel homozygous variants of ATP6V0A2 and ALDH18A1 lead to autosomal recessive cutis laxa type 2 and 3 in two Pakistani families. J Gene Med 2023; 25:e3522. [PMID: 37119015 DOI: 10.1002/jgm.3522] [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: 02/17/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Autosomal recessive cutis laxa type 2A (ARCL2A; OMIM: 219200) is characterized by neurovegetative, developmental and progeroid elastic skin anomalies. It is caused by biallelic variation in ATPase, H+ transporting V0 subunit A2 (ATP6V0A2; OMIM: 611716) located on chromosome 12q24.31. Autosomal recessive cutis laxa type 3A (ARCL3A; OMIM: 219150) is another subclinical type characterized by short stature, ophthalmological abnormalities and a progeria-like appearance. The ARCL3A is caused by loss of function alterations in the aldehyde dehydrogenase 18 family member A1 (ALDH18A1; OMIM: 138250) gene located at chromosome 10q24.1. METHODS Whole-exome sequencing (WES), and Sanger sequencing were performed for molecular diagnosis. 3D protein modeling was performed to investigate the deleterious effect of the variant on protein structure. RESULTS In this study, clinical and molecular diagnosis were performed for two families, ED-01 and DWF-41, which displayed hallmark features of ARCL2A and ARCL3A, respectively. Three affected individuals in the ED-01 family (IV-4, IV-5 and V-3) displayed sagging loose skin, down-slanting palpebral fissures, excessive wrinkles on the abdomen, hands and feet, and prominent veins on the trunk. Meanwhile the affected individuals in the DWF-41 family (V-2 and V-3) had progeroid skin, short stature, dysmorphology, low muscle tone, epilepsy, lordosis, scoliosis, delayed puberty and internal genitalia. WES in the index patient (ED-01: IV-4) identified a novel homozygous deletion (NM_012463.3: c.1977_1980del; p.[Val660LeufsTer23]) in exon 16 of the ATP6V0A2 while in DWF-41 a novel homozygous missense variant (NM_001323413.1:c.1867G>A; p.[Asp623Asn]) in exon 15 of the ALDH18A1 was identified. Sanger validation in all available family members confirmed the autosomal recessive modes of inheritances in each family. Three dimensional in-silico protein modeling suggested deleterious impact of the identified variants. Furthermore, these variants were assigned class 1 or "pathogenic" as per guidelines of American College of Medical Genetics 2015. Screening of ethnically matched healthy controls (n = 200 chromosomes), excluded the presence of these variations in general population. CONCLUSIONS To the best of our knowledge, this is the first report of ATP6V0A2 and ALDH18A1 variations in the Pakhtun ethnicity of Pakistani population. The study confirms that WES can be used as a first-line diagnostic test in patients with cutis laxa, and provides basis for population screening and premarital testing to reduce the diseases burden in future generations.
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Affiliation(s)
- Qaiser Zaman
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
- Higher Education Department, Peshawar, Khyber Pakhunkhwa, Pakistan
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Aiman Iftikhar
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
| | - Gauhar Rehman
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Qadeem Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
| | - Najumuddin
- National Center for Bioinformatics, Quaid-I-Azam University, Islamabad, Pakistan
| | - Amin Jan
- Department of Physiology, North-West School of Medicine Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Jamshid Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
| | - Muhammad Anas
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
| | - Laiba
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Dargai, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Osama Yousef Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angham Abdulrhman Abdulkareem
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Science, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Musharraf Jelani
- Rare Diseases Genetics and Genomics, Centre for Omic Sciences, Islamia College Peshawar, Khyber Pakhtunkhwa, Pakistan
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Liang L, Wu H, Cai Z, Zhao J. Genetic and molecular dynamics analysis of two variants of the COL4A5 gene causing Alport syndrome. BMC Med Genomics 2023; 16:192. [PMID: 37596645 PMCID: PMC10436629 DOI: 10.1186/s12920-023-01623-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 07/31/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Alport syndrome (AS; OMIM#308,940) is a hereditary kidney disease that progresses over time and is distinguished by hearing loss and ocular irregularities. The syndrome has three subtypes, namely X-linked (XL; OMIM#301,050), autosomal recessive (AR; OMIM#203,780), and autosomal dominant (AD; OMIM#104,200), which are categorized based on their respective modes of inheritance. XLAS is attributed to a pathogenic variant in the COL4A5 (OMIM*303,630) gene, which encodes the α5(IV) chain of type IV collagen (Col-IV). In contrast, ADAS and ARAS are the result of variants in the COL4A3 (OMIM*120,070) and COL4A4 (OMIM*120,131) genes, which encode the α3(IV) and α4(IV) chains of Col-IV, respectively. Typically, the diagnosis of AS necessitates hereditary or pathological assessments. The determination of splicing variants as pathogenic or non-pathogenic based on gene sequencing outcomes is challenging. METHODS In this study, we conducted exome sequencing and Sanger sequencing on two unrelated Chinese patients with AS. We identified a deletion variant c.4414delG in the COL4A5 gene and a splicing variant c.4298-20T > A in the same gene. In order to ascertain the impact of c.4298-20T > A on the synthesis of COL4A5 mRNA, we performed experiments involving minigene splicing. Additionally, we predicted the ability of these two variants to affect triple helix formation of α345(IV) using molecular dynamics methods. RESULTS The c.4414delG deletion variant caused a change in the genetic code of the COL4A5 gene. Specifically, it caused a shift in codon 1472 from encoding aspartate to encoding methionine. This shift resulted in a change of 75 amino acids in the protein sequence, ultimately leading to an early stop codon. This premature stop codon caused the production of a truncated α5(IV) chain with a predicted protein effect of p.D1472Mfs. The mRNA of the COL4A5 gene experienced intron 46 retention due to the splicing variant c.4298-20T > A, leading to the inclusion of six additional amino acids between amino acids 1432 and 1433 of the α5(IV) chain. This variant is predicted to have a protein effect of p.(P1432_G1433insDYFVEI). The impact of two variants, c.4414delG and c.4298-20T > A, on the aggregation region for α3(IV), α4(IV), and α5(IV) trimerisation were studied using molecular dynamics simulations. Results showed that the deletion variant c.4414delG had a significantly stronger disruption on NC1, compared to the splicing variant c.4298-20T > A. This difference in impact is consistent with the varying clinical phenotypes observed in the two patients. Based on the American College of Medical Genetics and Genomics (ACMG) classification criteria and guidelines for genetic variants, the deletion variant c.4414delG was rated as pathogenic while the splicing variant c.4298-20T > A was rated as likely-pathogenic. CONCLUSION Our study has identified two novel pathogenic loci, the deletion variant c.4414delG and the splicing variant c.4298-20T > A, associated with XLAS. This finding expands the genetic spectrum of XLAS. We suggest that molecular dynamics can effectively model the effect of genetic variation on α345(IV) trimerization, which may offer valuable insights into the mechanisms of XLAS pathogenesis.
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Affiliation(s)
- Lei Liang
- Center for Prenatal Diagnosis and Medical Genetics, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010015, PR China
| | - Haotian Wu
- School of Public Health, Inner Mongolia Medical University, Hohhot, 010015, PR China
| | - Zeyu Cai
- Department of Nephrology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010015, PR China
| | - Jianrong Zhao
- Department of Nephrology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010015, PR China.
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Ma Q, Che L, Chen Y, Gu Z. Identification of five novel variants of ADAR1 in dyschromatosis symmetrica hereditaria by next-generation sequencing. Front Pediatr 2023; 11:1161502. [PMID: 37476031 PMCID: PMC10354868 DOI: 10.3389/fped.2023.1161502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Background Dyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant inherited pigmentary dermatosis characterized by a mixture of hyperpigmented and hypopigmented freckles on the dorsal aspect of the distal extremities. To date, pathogenic mutations causing DSH have been identified in the adenosine deaminase acting on RNA1 gene (ADAR1), which is mapped to chromosome 1q21. Objective The present study aimed to investigate the underlying pathological mechanism in 14 patients with DSH from five unrelated Chinese families. Next-generation sequencing (NGS) and direct sequencing were performed on a proband with DSH to identify causative mutations. All coding, adjacent intronic, and 5'- and 3'-untranslated regions of ADAR1 were screened, and variants were identified. Result These mutations consisted of three missense mutations (NM_001025107: c.716G>A, NM_001111.5: c.3384G>C, and NM_001111.5: c.3385T>G), one nonsense mutation (NM_001111.5:c.511G>T), and one splice-site mutation (NM_001111.5: c.2080-1G>T) located in exon 2, exon 14, and the adjacent intronic region according to recommended Human Genome Variation Society (HGVS) nomenclature. Moreover, using polymerase chain reaction and Sanger sequencing, we identified five novel ADAR1 variants, which can be predicted to be pathogenic by in silico genome sequence analysis. Among the mutations, the missense mutations had no significant effect on the spatial structure of the protein, while the stop codon introduced by the nonsense mutation truncated the protein. Conclusion Our results highlighted that the advent of NGS has facilitated high-throughput screening for the identification of disease-causing mutations with high accuracy, stability, and specificity. Five novel genetic mutations were found in five unrelated families, thereby extending the pathogenic mutational spectrum of ADAR1 in DSH and providing new insights into this complex genetic disorder.
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Affiliation(s)
- Qian Ma
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingyi Che
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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11
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Abdulkareem AA, Zaman Q, Khan H, Khan S, Rehman G, Tariq N, Ahmad M, Owais M, Najumuddin, Muthaffar OY, Bibi F, Khang R, Ryu SW, Naseer MI, Jelani M. Whole exome sequencing identified five novel variants in CNTN2, CARS2, ARSA, and CLCN4 leading to epilepsy in consanguineous families. Front Genet 2023; 14:1185065. [PMID: 37359369 PMCID: PMC10285458 DOI: 10.3389/fgene.2023.1185065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/26/2023] [Indexed: 11/20/2023] Open
Abstract
Introduction: Epilepsy is a group of neurological disorders characterized by recurring seizures and fits. The Epilepsy genes can be classified into four distinct groups, based on involvement of these genes in different pathways leading to Epilepsy as a phenotype. Genetically the disease has been associated with various pathways, leading to pure epilepsy-related disorders caused by CNTN2 variations, or involving physical or systemic issues along with epilepsy caused by CARS2 and ARSA, or developed by genes that are putatively involved in epilepsy lead by CLCN4 variations. Methods: In this study, five families of Pakistani origin (EP-01, EP-02, EP-04, EP-09, and EP-11) were included for molecular diagnosis. Results: Clinical presentations of these patients included neurological symptoms such as delayed development, seizures, regression, myoclonic epilepsy, progressive spastic tetraparesis, vision and hearing impairment, speech problems, muscle fibrillation, tremors, and cognitive decline. Whole exome sequencing in index patients and Sanger sequencing in all available individuals in each family identified four novel homozygous variants in genes CARS2: c.655G>A p.Ala219Thr (EP-01), ARSA: c.338T>C: p.Leu113Pro (EP-02), c.938G>T p.Arg313Leu (EP-11), CNTN2: c.1699G>T p.Glu567Ter (EP-04), and one novel hemizygous variant in gene CLCN4: c.2167C>T p.Arg723Trp (EP-09). Conclusion: To the best of our knowledge these variants were novel and had not been reported in familial epilepsy. These variants were absent in 200 ethnically matched healthy control chromosomes. Three dimensional protein analyses revealed drastic changes in the normal functions of the variant proteins. Furthermore, these variants were designated as "pathogenic" as per guidelines of American College of Medical Genetics 2015. Due to overlapping phenotypes, among the patients, clinical subtyping was not possible. However, whole exome sequencing successfully pinpointed the molecular diagnosis which could be helpful for better management of these patients. Therefore, we recommend that exome sequencing be performed as a first-line molecular diagnostic test in familial cases.
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Affiliation(s)
- Angham Abdulrhman Abdulkareem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qaiser Zaman
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
- Higher Education Department, Peshawar, Khyber Pakhtunkhwa, Pakistan
- Department of Zoology, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Sabar Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Gauhar Rehman
- Department of Zoology, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Nabeel Tariq
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Mashal Ahmad
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Owais
- Mardan College of Medical Technologies, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Najumuddin
- Programme of Biotechnology, Department of Applied Sciences, Faculty of Engineering, Science and Technology (FEST), Hamdard University, Karachi, Pakistan
| | - Osama Yousef Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rin Khang
- 3Billion Inc., Seoul, Republic of Korea
| | | | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Musharraf Jelani
- Rare Diseases Genetics and Genomics, Centre for Omic Sciences, Islamia College, Peshawar, Khyber Pakhtunkhwa, Pakistan
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12
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Younus M, Rasheed M, Lin Z, Asiri SA, Almazni IA, Alshehri MA, Shafiq S, Iqbal I, Khan A, Ullah H, Umair M, Waqas A. Homozygous Missense Variant in the N-Terminal Region of ANK3 Gene Is Associated with Developmental Delay, Seizures, Speech Abnormality, and Aggressive Behavior. Mol Syndromol 2023; 14:11-20. [PMID: 36777705 PMCID: PMC9912002 DOI: 10.1159/000526381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction Intellectual disability (ID) is a lifelong disability that affects an individual‧s learning capacity and adaptive behavior. Such individuals depend on their families for day-to-day survival and pose a significant challenge to the healthcare system, especially in developing countries. ID is a heterogeneous condition, and genetic studies are essential to unravel the underlying cellular pathway for brain development and functioning. Methods Here we studied a female index patient, born to a consanguineous Pakistani couple, showing clinical symptoms of ID, ataxia, hypotonia, developmental delay, seizures, speech abnormality, and aggressive behavior. Whole exome sequencing (WES) coupled with Sanger sequencing was performed for molecular diagnosis. Further, 3D protein modeling was performed to see the effect of variant on protein structure. Results WES identified a novel homozygous missense variant (c.178T>C; p.Tyr60His) in the ANK3 gene. In silico analysis and 3-dimensional (3D) protein modeling supports the deleterious impact of this variant on the encoding protein, which compromises the protein‧s overall structure and function. Conclusion Our finding supports the clinical and genetic diversity of the ANK3 gene as a plausible candidate gene for ID syndrome. Intelligence is a complex polygenic human trait, and understanding molecular and biological pathways involved in learning and memory can solve the complex puzzle of how cognition develops. Intellectual disability (ID) is defined as a deficit in an individual‧s learning and adaptive behavior at an early age of onset [American Psychiatric Association, 2013]. It is one of the major medical, and cognitive disorders with a prevalence of 1-3% in the population worldwide [Leonard and Wen, 2002]. ID often exists with other disabling mental conditions such as autism, attention deficit hyperactivity disorder, epilepsy, schizophrenia, bipolar disorder, or depression. Almost half of the cases appear to have a genetic explanation that ranges from cytogenetically visible abnormalities to monogenic defects [Flint, 2001; Ropers, 2010; Tucker-Drob et al., 2013]. Intellectual disability is a genetically heterogeneous condition, and more than 700 genes have been identified to cause ID alone or as a part of the syndrome. Research in X-linked ID has identified more than 100 disease-causing genes on the X chromosome that play a role in cognition; however, research into autosomal causes of ID is still ongoing [Vissers et al., 2016].
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Affiliation(s)
- Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Memoona Rasheed
- Department of Pathology, Islamabad Medical and Dental College, Islamabad, Pakistan
| | - Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ibrahim A. Almazni
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Imran Iqbal
- Department of PLR, Institute of Active Polymers, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences (Zoology), University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Hanif Ullah
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,*Muhammad Umair,
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education Lahore, Lahore, Pakistan,**Ahmed Waqas,
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Rafeeq MM, Murad HAS, Najumuddin, Ullah S, Ahmed Z, Alam Q, Bilal M, Habib AH, Sain ZM, Khan MJ, Umair M. Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia. Front Genet 2023; 13:1117500. [PMID: 36733940 PMCID: PMC9888409 DOI: 10.3389/fgene.2022.1117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands. Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation. Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD). Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families.
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Affiliation(s)
- Misbahuddin M. Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najumuddin
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad, Pakistan
| | - Zaheer Ahmed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Bahrain
| | - Muhammad Bilal
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziaullah M. Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
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Alfadhel M, Umair M, Al Tuwaijri A, Al Mutairi F. A Patient with Coarse Facial Features and Molecular Odyssey: Lessons Learned and Best Practice. Clin Chem 2023; 69:17-20. [PMID: 36598549 DOI: 10.1093/clinchem/hvac187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/09/2022] [Indexed: 01/05/2023]
Affiliation(s)
- Majid Alfadhel
- Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 14611, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh 11426, Saudi Arabia
| | - Fuad Al Mutairi
- Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 14611, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia
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Chen W, Li Y, Zhang J, Yuan Y, Sun D, Yuan J, Yang K, Liang Y, Guo Q. Genetic variations in the DYNC2H1 gene causing SRTD3 (short-rib thoracic dysplasia 3 with or without polydactyly). Front Genet 2023; 14:1125473. [PMID: 37091781 PMCID: PMC10116042 DOI: 10.3389/fgene.2023.1125473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Background and aims: Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) represents a type of severe fetal skeletal dysplasia (SD) characterized by shortened limbs, narrow thorax with or without polydactyly, which is caused by the homozygous or compound heterozygous mutations in the DYNC2H1 gene. SRTD3 is a recessive disorder, identification of the responsible genetic variation would be beneficial to an accurate prenatal diagnosis and well-grounded counseling for the affected families. Material and methods: Two families having experienced recurrent fetal SDs were recruited and submitted to a multiplatform genetic investigation. Whole-exome sequencing (WES) was performed with samples collected from the probands. Sanger sequencing and fluorescent quantitative PCR (qPCR) were conducted as validation assays for suspected variations. Results: WES identified two compound heterozygous variations in the DYNC2H1(NM_001080463.2) gene, namely c.2386C>T (p.Arg796Trp) and c.7289T>C (p.Ile2430Thr) for one; and exon (64-83)del and c.8190G>T (p.Leu2730Phe) for the other, respectively. One variant in them, exon (64-83)del, was novelly identified. Conclusion: The study detected two compound heterozygous variation in DYNC2H1 including one novel deletion: exon (64-83) del. Our findings clarified the cause of fetal skeletal dysplasia in the subject families, provided guidance for their future pregnancies, and highlighted the value of WES in diagnosis of skeletal dysplasia with unclear prenatal indications.
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Affiliation(s)
- Wenqi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Yazhou Li
- Department of Pediatric Orthopaedic, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Yufan Yuan
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Donglan Sun
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
| | - Jiayu Yuan
- Department of Pediatric Orthopaedic, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Kai Yang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Healthcare Hospital, Capital Medical University, Beijing, China
| | - Ying Liang
- Reproductive Medicine Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
- *Correspondence: Qing Guo, ; Ying Liang,
| | - Qing Guo
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Key Laboratory of Maternal and Fetal Medicine of Hebei Province, Shijiazhuang, Hebei, China
- *Correspondence: Qing Guo, ; Ying Liang,
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16
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Ahmad Z, Liaqat R, Palander O, Bilal M, Zeb S, Ahmad F, Jawad Khan M, Umair M. Genetic overview of postaxial polydactyly: Updated classification. Clin Genet 2023; 103:3-15. [PMID: 36071556 DOI: 10.1111/cge.14224] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022]
Abstract
Polydactyly or polydactylism, also known as a hyperdactyly, is a congenital limb defect with various morphologic phenotypes. Apart from physical and functional impairments, the presence of polydactyly is an indication of an underlying syndrome in the newborn. Usually, it follows as an autosomal dominant/recessive inheritance pattern with defects in the limb development's anteroposterior patterning. Although mutations in several genes have been associated with polydactyly; however, the exact underlying cause, pathways, and disease mechanisms are still unexplored, thus making it of multi-factorial origin. Polydactyly is divided into three subtypes; radial, ulnar, and central polydactyly. So far, 11 loci (PAPA1-PAPA11) and seven human genes have been reported to cause non-syndromic postaxial polydactyly in humans, including the ZNF141, GLI3, IQCE, GLI1, FAM92A1, KIAA0825, and DACH1. In this review, we discuss emerging evidences of clinical and molecular characterization of polydactyly types in term of the involvement of newly associated genes and loci for non-syndromic postaxial polydactyly, and how these might impact our understanding of the genetic mechanisms and molecular etiology involved in the cause of polydactyly.
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Affiliation(s)
- Zaheer Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Romana Liaqat
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Oliva Palander
- Faculty of Medicine, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shah Zeb
- Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China.,College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, People's Republic of China
| | - Farooq Ahmad
- Department of Biochemistry, Women University Swabi, Swabi, Pakistan
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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17
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Waqas A, Liaqat R, Shaheen S, Khan AZ, Habib AH, Binothman N, Aljadani M, Zehri Z, Shaheen S, Alkathiri A, Naz R, Umair M, Abbas S. A novel homozygous truncating variant in PPFIBP1 further delineates PPFIBP1-associated neurodevelopmental disorder. Int J Dev Neurosci 2022; 83:191-200. [PMID: 36527195 DOI: 10.1002/jdn.10247] [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: 08/24/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are classified as a group of disorders affecting function and development of the brain and having wide clinical variability. Herein, we describe two affected individuals segregating a recessive NDD. The affected individuals exhibited phenotypes such as global developmental delay (GDD), intellectual disability (ID), microcephaly and speech delay. Whole-exome sequencing (WES) followed by bidirectional Sanger sequencing techniques identified a homozygous nonsense variant (c.466C > T; p.Gln156*) in the PPFIBP1 gene (NM_003622.4) that segregated with the disease phenotype. Further, to elucidate the effect of the variant on protein structure, 3D protein modelling was performed for the mutant and normal protein that suggested substantial reduction of the mutant protein. Our data support the evidence that PPFIBP1 has a pivotal role in neurodevelopment in humans, and loss-of-function variants cause clinically variable neurodevelopmental phenotypes.
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Affiliation(s)
- Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education, Lahore, Punjab, Pakistan
| | - Romana Liaqat
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sidrah Shaheen
- Department of Higher Education, Government Girls degree College No. 1, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Ali Zaman Khan
- Department of Surgery, Surgical Ward 'A', Khyber Teaching Hospital, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Zamrud Zehri
- Shaheed Nawab Ghous Bakhsh Raisani Memorial Hospital, Mastung, Balochistan, Pakistan
| | - Shabnam Shaheen
- Department of Higher Education, Government Girls Degree College, Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - Afnan Alkathiri
- Medical Genetics, Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Rubina Naz
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
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18
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Umair M, Younus M, Shafiq S, Nayab A, Alfadhel M. Clinical genetics of spondylocostal dysostosis: A mini review. Front Genet 2022; 13:996364. [PMID: 36506336 PMCID: PMC9732429 DOI: 10.3389/fgene.2022.996364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Spondylocostal dysostosis is a genetic defect associated with severe rib and vertebrae malformations. In recent years, extensive clinical and molecular diagnosis advancements enabled us to identify disease-causing variants in different genes for such severe conditions. The identification of novel candidate genes enabled us to understand the developmental biology and molecular and cellular mechanisms involved in the etiology of these rare diseases. Here, we discuss the clinical and molecular targets associated with spondylocostal dysostosis, including clinical evaluation, genes, and pathways involved. This review might help us understand the basics of such a severe disorder, which might help in proper clinical characterization and help in future therapeutic strategies.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, Ministry of National Guard Health Affairs (MNGH), King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
| | - Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Anam Nayab
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Majid Alfadhel
- Medical Genomics Research Department, Ministry of National Guard Health Affairs (MNGH), King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia,Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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19
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Abu Raya YS, Srebnik N, Rubinstein E, Schonberger O, Broza YY, Suschinel R, Haick H, Ionescu R. Noninvasive Pregestational Genetic Testing of Embryos Using Smart Sensors Array. ACS Sens 2022; 7:3265-3271. [PMID: 36374562 DOI: 10.1021/acssensors.2c01492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pregestational genetic testing of embryos is the conventional tool in detecting genetic disorders (fetal aneuploidy and monogenic disorders) for in vitro fertilization (IVF) procedures. The accepted clinical practice for genetic testing still depends on biopsy, which has the potential to harm the embryo. Noninvasive genetic prenatal testing has not yet been achieved. In this study, embryos with common genetic disorders created through IVF were tested with an artificially intelligent nanosensor array. Volatile organic compounds emitted by the culture fluid of embryos were analyzed with chemical gas sensors. The obtained results showed significant discrimination between the embryos with different genetic diseases and their wild-types. Embryos were obtained from the same clinical center for avoiding differences based on clinical and demographical characteristics. The achieved discrimination accuracy was 81% for PKD disease, 90% for FRAX disease, 85% for HOCM disease, 90% for BRCA disease, and 100% for HSCR disease. These proof-of-concept findings might launch the development of a noninvasive approach for early assessment of embryos by examining the culture fluid of the embryos, potentially enabling noninvasive diagnosis and screening of genetic diseases for IVF.
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Affiliation(s)
- Yasmin Shibli Abu Raya
- Department of Chemical Engineering and Russel Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
| | - Naama Srebnik
- In Vitro Fertilization Unit, Shaare Zedek Medical Center, Hebrew University Medical School, 9112102 Jerusalem, Israel
| | - Esther Rubinstein
- In Vitro Fertilization Unit, Shaare Zedek Medical Center, Hebrew University Medical School, 9112102 Jerusalem, Israel
| | - Oshrat Schonberger
- In Vitro Fertilization Unit, Shaare Zedek Medical Center, Hebrew University Medical School, 9112102 Jerusalem, Israel
| | - Yoav Y Broza
- Department of Chemical Engineering and Russel Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
| | - Raluca Suschinel
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Hossam Haick
- Department of Chemical Engineering and Russel Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
| | - Radu Ionescu
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
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20
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Al Tuwaijri A, Alyafee Y, Umair M, Alsubait A, Alharbi M, AlEidi H, Ballow M, Aldrees M, Alam Q, Al Abdulrahman A, Alrifai MT, Alfadhel M. Congenital disorder of glycosylation with defective fucosylation 2 (
FCSK
gene defect): The third report in the literature with a mild phenotype. Mol Genet Genomic Med 2022; 11:e2117. [PMID: 36426412 PMCID: PMC10094070 DOI: 10.1002/mgg3.2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Congenital disorders of glycosylation (CDG) are a group of heterogeneous disorders caused by abnormal lipid or protein glycosylation. Variants in the FCSK gene have been reported to cause CDG. Defective FCSK-induced CDG (FCSK-CDG) has only been reported previously in three unrelated children. METHODS In this study, we genetically and clinically examined a 3-year-old proband with resolved infantile spasms and normal development. Standard whole-exome sequencing (WES) and Sanger sequencing were performed to identify the functional impact of the variant. RESULTS WES revealed a rare biallelic missense variant (c.3013G>C; p.Val1005Leu) in FCSK. RT-qPCR showed a significant depletion in FCSK gene expression in the affected individual. Western blotting revealed reduced FCSK expression at the protein level compared to that in the control. Furthermore, 3D protein modeling suggested changes in the secondary structure, which might affect the overall FCSK protein function. CONCLUSION This study broadens the mutation and phenotypic spectrum of FCSK-associated developmental disorders.
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Affiliation(s)
- Abeer Al Tuwaijri
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
- Clinical Laboratory Sciences Department College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS) Riyadh Saudi Arabia
| | - Yusra Alyafee
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Arwa Alsubait
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
- Medical Research Core Facilities and Platforms King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Hamad AlEidi
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Mariam Ballow
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Mohammed Aldrees
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Abdulkareem Al Abdulrahman
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
| | - Muhammad Talal Alrifai
- Neurology Division, Department of Pediatrics King Abdulaziz Medical City, Ministry of National Guard Health Affairs (NGHA) Riyadh Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department King Abdullah International Medical Research Center (KAIMRC) Riyadh Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG‐HA) Riyadh Saudi Arabia
- Genetics and Precision Medicine Department (GPM) King Abdullah Specialized Children's Hospital Riyadh Saudi Arabia
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21
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Alfadhel M, Umair M, Alghamdi MA, Al Fakeeh K, Al Qahtani AT, Farahat A, Shalaby MA, Kari JA, Raina R, Cochat P, Alhasan KA. Clinical and molecular characterization of a large primary hyperoxaluria cohort from Saudi Arabia: a retrospective study. Pediatr Nephrol 2022; 38:1801-1810. [PMID: 36409364 PMCID: PMC10154271 DOI: 10.1007/s00467-022-05784-y] [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: 04/27/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Primary hyperoxalurias (PHs) constitute rare disorders resulting in abnormal glyoxalate metabolism. PH-associated phenotypes range from progressive nephrocalcinosis and/or recurrent urolithiasis to early kidney failure. METHODS A retrospective study was conducted for patients with confirmed PH diagnoses from three tertiary centers in Saudi Arabia. Detailed clinical molecular diagnosis was performed for 25 affected individuals. Whole exome sequencing (WES)-based molecular diagnosis was performed for all affected individuals. RESULTS The male:female ratio was 52% male (n = 13) and 48% female (n = 12), and consanguinity was present in 88%. Nephrolithiasis and/or nephrocalcinosis were present in all patients. Kidney stones were present in 72%, nephrocalcinosis in 60%, hematuria in 32%, proteinuria in 16%, abdominal pain in 36%, developmental delay in 8%, and chronic kidney disease stage 5 (CKD stage 5) was observed in 28% of the patients. The most common PH disorder was type I caused by variants in the AGXT gene, accounting for 56%. The GRHPR gene variants were identified in 4 patients, 16% of the total cases. Seven patients did not reveal any associated variants. Missense variants were the most commonly observed variants (48%), followed by frame-shift duplication variants (28%). CONCLUSIONS Characterization of the genetic and clinical aspects of PH in this unique population provides direction for improved patient management and further research. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Majid Alfadhel
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia. .,Medical Genomic Research Department, King Abdullah International Medical Research Center(KAIMRC), King Saud Bin Abdulaziz University for Health Sciences(KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia.
| | - Muhammad Umair
- Medical Genomic Research Department, King Abdullah International Medical Research Center(KAIMRC), King Saud Bin Abdulaziz University for Health Sciences(KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Malak A Alghamdi
- Medical Genetic Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Al Fakeeh
- Nephrology Division, Department of Pediatrics, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Abdullah T Al Qahtani
- Nephrology Division, Department of Pediatrics, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Afrah Farahat
- Division of Nephrology, Department of Pediatrics, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed A Shalaby
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rupesh Raina
- Department of Nephrology, Cleveland Clinic Akron General and Akron Childrens Hospital, Akron, OH, USA
| | - Pierre Cochat
- Centre de Référence Des Maladies Rénales Rares Néphrogones, Hospices Civils de Lyon & Université Claude-Bernard Lyon 1, Lyon, France
| | - Khalid A Alhasan
- Division of Nephrology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Division of Pediatric Kidney Transplant, Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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22
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Alyafee Y, Al Tuwaijri A, Umair M, Alharbi M, Haddad S, Ballow M, Alayyar L, Alam Q, Althenayyan S, Al Ghilan N, Al Khaldi A, Faden MS, Al Sufyan H, Alfadhel M. Non-invasive prenatal testing for autosomal recessive disorders: A new promising approach. Front Genet 2022; 13:1047474. [PMID: 36406136 PMCID: PMC9669374 DOI: 10.3389/fgene.2022.1047474] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background: In pregnant women at risk of autosomal recessive (AR) disorders, prenatal diagnosis of AR disorders primarily involves invasive procedures, such as chorionic villus sampling and amniocentesis. Methods: We collected blood samples from four pregnant women in their first trimester who presented a risk of having a child with an AR disorder. Cell-free DNA (cfDNA) was extracted, amplified, and double-purified to reduce maternal DNA interference. Additionally, whole-genome amplification was performed for traces of residual purified cfDNA for utilization in subsequent applications. Results: Based on our findings, we detected the fetal status with the family corresponding different genes, i.e., LZTR1, DVL2, HBB, RNASEH2B, and MYO7A, as homozygous affected, wild-type, and heterozygous carriers, respectively. Results were subsequently confirmed by prenatal amniocentesis. The results of AmpFLSTR™ Identifiler™ presented a distinct profile from the corresponding mother profile, thereby corroborating the result reflecting the genetic material of the fetus. Conclusion: Herein, we detected AR disease mutations in the first trimester of pregnancy while surmounting limitations associated with maternal genetic material interference. Importantly, such detection strategies would allow the screening of pregnant women for common AR diseases, especially in highly consanguineous marriage populations. This technique would open avenues for the early detection and prevention of recessive diseases among the population.
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Affiliation(s)
- Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shahad Haddad
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Maryam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Latifah Alayyar
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Saleh Althenayyan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nadia Al Ghilan
- Maternal Fetal Medicine Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Aziza Al Khaldi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Majid S. Faden
- Department of Obstetrics and Gynaecology, Maternal Fetal Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamad Al Sufyan
- Assisted Reproductive Technology Laboratories, Thuriah Medical Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNG-HA, Riyadh, Saudi Arabia
- *Correspondence: Majid Alfadhel,
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Al Hawsawi K, Al Jabri M, Dajam MS, Almahdi B, Alhawsawi WK, Abbas S, Al Tuwaijri A, Umair M, Alfadhel M, Al-Khenaizan S. Case Report: Bi-allelic missense variant in the desmocollin 3 gene causes hypotrichosis and recurrent skin vesicles. Front Genet 2022; 13:994509. [PMID: 36061207 PMCID: PMC9428628 DOI: 10.3389/fgene.2022.994509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hypotrichosis with Recurrent Skin Vesicles (HYPTSV) is an extremely rare condition, having autosomal recessive inheritance. Here in we report a 4-years- old Saudi boy who presented with a history of recurrent skin blisters that are localized to the extremities and hypotrichosis since birth.Methods: The present study describes a consanguineous Saudi family segregating HYPTSV in an autosomal recessive fashion. A single proband (II-1) exhibited features such as diffused non-scarring alopecia on the scalp, intraepidermal blister, post-inflammatory hyperpigmented macules, and follicular hyperkeratosis. DNA of the index was subjected to whole-genome sequencing (WGS). Furthermore, 3D protein modeling was performed for the mutated and normal protein.Results: WGS revealed a novel bi-allelic missense variant (c.154G>C; p. Val52Leu) in the DSC3 gene, which segregated perfectly using Sanger sequencing. In addition, 3D protein modeling revealed a substantial change in the mutated DSC3 protein as compared to the normal DSC3 protein.Conclusion: This is the 3rd novel variant reported in the DSC3 gene associated with the HYPTSV phenotype. This report further strengthens the evidence that bi-allelic variants in the DSC3 cause severe HYPTSV in humans.
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Affiliation(s)
- Khalid Al Hawsawi
- Dermatology Department, King Abdulaziz Hospital, Makkah, Saudi Arabia
| | - Mazin Al Jabri
- Dermatology Department, Hera General Hospital, Makkah, Saudi Arabia
| | - Mazen S Dajam
- Dermatology Department, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Bashaer Almahdi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Waseem K Alhawsawi
- Dermatology Department, King Fahad Hospital of The University, Al Khobar, Saudi Arabia
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, United States
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Sultan Al-Khenaizan
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- Department of Dermatology, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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Chen C, Li W, Yin M, Li M, Wu L, Si J, Zhao L, Li B, Yan Z, Lyu Q. Does the cell number of 0PN embryos on day 3 affect pregnancy and neonatal outcomes following single blastocyst transfer? BMC Pregnancy Childbirth 2022; 22:200. [PMID: 35279109 PMCID: PMC8918324 DOI: 10.1186/s12884-022-04492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background 0PN zygotes have a low cleavage rate, and the clinical outcomes of cleavage-stage embryo transfers are unsatisfactory. Blastocyst culturing is used to screen 0PN embryos, but whether the cell number of 0PN embryos on day 3 affects the clinical outcomes following single blastocyst transfer is unknown and would be helpful in evaluating the clinical value of these embryos. Methods This retrospective study compared 46,804 0PN zygotes, 242 0PN frozen-thawed single blastocyst transfers, and 92 corresponding 0PN singletons with 232,441 2PN zygotes, 3563 2PN frozen-thawed single blastocyst transfers, and 1250 2PN singletons from January 2015 to October 2019 at a tertiary-care academic medical centre. The 0PN and 2PN embryos were divided into two groups: the group with < 6 cells on day 3 and that with ≥ 6 cells. Embryo development, subsequent pregnancy and neonatal outcomes were compared between the two groups. Results The cleavage and available blastocyst rates of the 0PN zygotes were much lower than those of the 2PN zygotes (25.9% vs. 97.4%, P < 0.001; 13.9% vs. 23.4%, P < 0.001). In the < 6 cells group, the available blastocyst rate of the cleaved 0PN embryos was significantly lower than that of the 2PN embryos (2.5% vs. 12.7%, P < 0.001). However, in the ≥ 6 cells group, the available blastocyst rate of the 0PN cleaved embryos significantly improved, although it was slightly lower than that of the 2PN embryos (33.9% vs. 35.7%, P = 0.014). Importantly, compared to those of the 2PN single blastocyst transfers, the clinical pregnancy rate, live birth rate, Z-score and malformation rate of the 0PN single blastocyst transfers were not significantly different in either the < 6 cells group (30.4% vs. 39.8%, P = 0.362; 30.4% vs. 31.3%, P = 0.932; 0.89 ± 0.90 vs. 0.42 ± 1.02, P = 0.161; 0% vs. 2.6%, P = 1.000) or the ≥ 6 cells group (50.7% vs. 46.6%, P = 0.246; 39.7% vs. 38.3%, P = 0.677; 0.50 ± 1.23 vs. 0.47 ± 1.11, P = 0.861; 2.4% vs. 1.8%, P = 1.000). Conclusions The cell number on day 3 of 0PN embryos affected the subsequent formation of blastocysts but did not influence the subsequent pregnancy and neonatal outcomes of 0PN single blastocyst transfers, which may be beneficial to clinicians counselling patients on the clinical value of 0PN embryos. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-022-04492-7.
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