scholarly journals Case report: a de-novo 7p12.3 microduplication detected in an infant with perineal hamartoma and imperforate anus

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ayca Kocaaga ◽  
Sevgi Yimenicioglu ◽  
Cigdem Arslan Alıcı
Keyword(s):  
Imperforate Anus ◽  
De Novo ◽  
Neonatal Period ◽  
Wide Spectrum ◽  
Anorectal Malformations ◽  
Sacrococcygeal Teratoma ◽  
Anal Atresia ◽  
Whole Exome ◽  
Laboratory Investigations ◽  
Magnetic Resonance Imaging Mri

Abstract Background Anorectal malformations (ARM) represent a wide spectrum of defects. Caudal and genitourinary malformations can associate with anorectal malformations. Genetic factors may play role in the development of anorectal malformations. Perineal masses like sacrococcygeal teratoma, rectal prolapse, or duplication cysts were reported before, but their association with perineal hamartoma and anal atresia is extremely rare. Case presentation Here, we report an 11-month-old female infant. She had 551 kb duplication at 7p12.3 with perineal hamartoma and anal atresia consisting a cystic lesion with a diameter of 4 mm at the filum terminale (L2 vertebra) on lumbar magnetic resonance imaging (MRI) in neonatal period. She presented with hypotonia. She had anorectal anomaly and external perineal mass bulging from left major labium extending across anal region with imperforate anus. There was 1 × 1 cm polyp-like protrusion on it. She was operated in neonatal period. Genetic laboratory investigations showed karyotype 46, XX. The microduplication of the chromosome 7p12.3 was detected by microarray analysis. There were not any significant homozygous or heterozygous variants determined  by whole-exome sequencing. Conclusions To the best of our knowledge, this is the first report of a patient with a microduplication of the chromosome 7p12.3, and second case with perineal hamartoma and imperforate anus. Clinicians should pay attention to microdeletions and microduplications while giving genetic counseling to patients with urogenital and anorectal abnormalities.

CNV Analysis in Monozygotic Twin Pairs Discordant for Urorectal Malformations

2013 ◽  
Vol 16 (4) ◽  
pp. 802-807 ◽  
Author(s):  
Friederike Baudisch ◽  
Markus Draaken ◽  
Enrika Bartels ◽  
Eberhard Schmiedeke ◽  
Soyhan Bagci ◽  
...  
Keyword(s):  
De Novo ◽  
Bladder Exstrophy ◽  
Anorectal Malformations ◽  
Monozygotic Twin ◽  
Regulatory Elements ◽  
Copy Number Variations ◽  
Molecular Karyotyping ◽  
Genetic Changes ◽  
Coding Regions ◽  
Whole Exome

Early post-twinning mutational events can account for discordant phenotypes in monozygotic (MZ) twin pairs. Such mutational events may comprise genomic alterations of different sizes, ranging from single nucleotides to large copy-number variations (CNVs). Anorectal malformations (ARM) and the bladder exstrophy-epispadias complex (BEEC) represent the most severe end of the urorectal malformation spectrum. Recently, CNV studies in patients with sporadic ARM and the BEEC have identified de novo events that occur in specific chromosomal regions. We hypothesized that early arising, post-twinning CNVs might contribute to discordance in MZ twin pairs with ARM or the BEEC; knowledge of such CNVs might help to identify additional chromosomal regions involved in the development of these malformations. We investigated four discordant MZ twin pairs (three ARM and one BEEC) using molecular karyotyping arrays comprising 1,140,419 markers with a median marker spacing of 1.5 kb. Filtering the coding regions for possible disease-causing post-twinning de novo CNVs present only in the affected twin, but not in the unaffected twin or the parents, identified a total of 136 CNVs. These 136 CNVs were then filtered against publicly available databases and finally re-evaluated visually. No potentially causative CNV remained after applying these filter criteria. Our results suggest that post-twinning CNV events that affect coding regions of the genome did not contribute to the discordant phenotypes in MZ twin pairs that we investigated. Possible causes for the discordant phenotypes include changes in regulatory elements or smaller genetic changes within coding regions which may be detectable by whole-exome sequencing.

scholarly journals Whole exome sequencing reveals a wide spectrum of ciliary gene mutations in nonsyndromic biliary atresia

2020 ◽  
Author(s):  
Wai-Yee Lam ◽  
Man-Ting So ◽  
Jacob Shujui Hsu ◽  
Patrick Ho-Yu Chung ◽  
Diem Ngoc Ngo ◽  
...  
Keyword(s):  
Biliary Atresia ◽  
Exome Sequencing ◽  
De Novo ◽  
Wide Spectrum ◽  
Gene Mutations ◽  
Compound Heterozygous ◽  
Genetic Contribution ◽  
Whole Exome ◽  
Compound Heterozygous Variants ◽  
End Stage

ABSTRACTBiliary atresia (BA) is the most common obstructive cholangiopathy in neonates, often progressing to end-stage cirrhosis. BA pathogenesis is believed to be multifactorial, but the genetic contribution remains poorly defined. We conducted exome sequencing on 89 nonsyndromic BA trios. In 31.5% of the patients, rare and deleterious de novo, homozygous recessive and/or compound heterozygous variants were detected in liver-expressed ciliary genes of diverse ciliary functions. Enrichment of deleterious mutations in liver-expressed ciliary geneset was significant compared to 148 control trios (OR 2.58, 95% CI 1.15-6.07). KIF3B, PCNT and TTC17 are essential for ciliogenesis. Reduced ciliary proteins expression were detected in the BA livers with KIF3B and TTC17 mutations. CRISPR/Cas9-engineered zebrafish knockouts of KIF3B, PCNT and TTC17 displayed reduced biliary flow. Our findings support a larger genetic contribution to nonsyndromic BA risk than expected. Ciliary gene mutations leading to cholangiocyte cilia malformation and dysfunction could be a key biological mechanism in BA pathogenesis.

scholarly journals Whole exome-trio analysis reveals rare variants associated with Congenital Pouch Colon

2019 ◽  
Author(s):  
Sonal Gupta ◽  
Praveen Mathur ◽  
Ashwani Kumar Mishra ◽  
Krishna Mohan Medicherla ◽  
Prashanth Suravajhala
Keyword(s):  
Rare Variants ◽  
De Novo ◽  
Anorectal Malformations ◽  
Open Reading Frames ◽  
Missense Mutations ◽  
Clinical Genetic ◽  
Variants Of Unknown Significance ◽  
Whole Exome ◽  
Congenital Pouch Colon ◽  
Pouch Colon

AbstractAnorectal malformations (ARM) are individually common but Congenital Pouch Colon (CPC), a rare anorectal anomaly causes a dilated pouch in genitourinary tract. We have earlier attempted to understand the clinical genetic makeup of CPC and identified genes responsible for the disease using whole exome sequencing (WES). Here we report our studies of CPC, by identifying de novo heterozygous missense mutations in 16 proband-parent trios and further discover variants of unknown significance which could provide insights into CPC manifestation and its etiology. Our study confirms candidate mutations in genes, viz. C7orf57, C10orf120, C9orf84 and MUC16, CTC1 particularly emphasizing the role of hypothetical genes or open reading frames causing this developmental disorder. Variant validation revealed disease causing mutations associated with CPC and genitourinary diseases which could close the gaps of surgery in bringing intervention in therapies.

scholarly journals Identification of a de novo splicing mutation in the CSF1R gene in a Chinese patient with hereditary diffuse leukoencephalopathy with spheroids

2021 ◽  
Author(s):  
Xinwei Wu ◽  
Congcong Sun ◽  
Xingbang Wang ◽  
Ying Liu ◽  
Wei Wu ◽  
...  
Keyword(s):  
Family History ◽  
Bioinformatics Analysis ◽  
De Novo ◽  
Clinical Phenotype ◽  
Brain Magnetic Resonance Imaging ◽  
Chinese Patient ◽  
Splicing Mutation ◽  
Left Lower Extremity ◽  
Whole Exome ◽  
Magnetic Resonance Imaging Mri

Abstract Objective To report a de novo splicing mutation in the CSF1R gene in a patient with hereditary diffuse leukoencephalopathy with spheroids (HDLS). Methods A 42-year-old Chinese woman with constant weakness on her left lower extremity was recruited in the current study. Detail medical history and clinical characteristics were reviewed. Brain magnetic resonance imaging (MRI), whole-exome sequencing, and Sanger sequencing were performed with bioinformatics analysis. Results The Chinese HDLS patient with no HDLS family history exhibited a de novo splicing mutation (c.1754-10 T > A) in the CSF1R gene. This mutation was located at the splice site of intron 12 and resulted in the skipping of exon 13 from the CSF1R mRNA. This finding constitutes the first de novo splicing mutation ever reported in HDLS. Furthermore, MRI abnormalities had been reported at least 6 months prior to the onset of the patient’s clinical phenotype. Conclusion Our study indicates that the diagnosis of HDLS should be considered even in the absence of a family history and can help deepen the clinical and genetic understanding of HDLS.

scholarly journals A case report of atypical hemiplegic migraine with nonheadache onset in a Chinese child

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Chen ◽  
Xiaolan Sun ◽  
Ruiyan Wang ◽  
Zhaoshi Yi ◽  
Zhixin Huang ◽  
...  
Keyword(s):  
De Novo ◽  
Chinese Child ◽  
Hemiplegic Migraine ◽  
Motor Weakness ◽  
Alternating Hemiplegia Of Childhood ◽  
Whole Exome ◽  
Initial Stage ◽  
Atp1a2 Gene ◽  
Magnetic Resonance Imaging Mri ◽  
Core Symptoms

Abstract Background Hemiplegic migraine (HM) is an uncommon subtype of migraine with aura including motor weakness. The core symptoms of HM are headache and motor weakness. However, we report a rare case of atypical HM with nonheadache onset in a Chinese child who was misdiagnosed several times. Case presentation We report a Chinese boy whose onset was sudden when he was 3 years old. He presented with a variety of phenotypes, including fever, vomiting, alternating hemiplegia, and drowsiness, but no headache in the initial stages. Magnetic resonance imaging (MRI) demonstrated unilateral cerebral oedema during the initial episode of hemiplegia. These symptoms recurred many times. As the disease progressed, the patient developed episodic headache. The patient was misdiagnosed several times with encephalitis, alternating hemiplegia of childhood (AHC) and mitochondrial encephalopathy. Whole-exome next-generation sequencing revealed a de novo heterozygous missense mutation in the ATP1A2 gene(p.Gly715Arg) classified as pathogenic and eventually led to a diagnosis of HM when he was 11 years old. Flunarizine was subsequently administered, and no recurrence was found during follow-up. Conclusions HM in children may be atypical in the initial stage of the disease, which could manifest as fever, alternating hemiplegia and drowsiness but no headache at the onset. This could easily lead to misdiagnosis. With age, it may eventually manifest as typical HM. Therefore, attention should be given to differentiation in clinical practice.When similar clinical cases appear, gene detection is particularly important, which is conducive to early diagnosis and treatment.

scholarly journals Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures

2021 ◽  
Author(s):  
Adam L. Numis ◽  
Gilberto da Gente ◽  
Elliott H. Sherr ◽  
Hannah C. Glass
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
List Type ◽  
Sequencing Analysis ◽  
Neonatal Seizures ◽  
Pathogenic Variants ◽  
Targeted Analysis ◽  
Whole Exome ◽  
Epilepsy Gene

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.

scholarly journals Analysis workflow to assess de novo genetic variants from human whole-exome sequencing

2021 ◽  
Vol 2 (1) ◽  
pp. 100383
Author(s):  
Nicholas S. Diab ◽  
Spencer King ◽  
Weilai Dong ◽  
Garrett Allington ◽  
Amar Sheth ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Variants ◽  
De Novo ◽  
Whole Exome ◽  
Analysis Workflow

scholarly journals Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 65
Author(s):  
Patricia Haug ◽  
Samuel Koller ◽  
Jordi Maggi ◽  
Elena Lang ◽  
Silke Feil ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Screening ◽  
De Novo ◽  
Efficient Tool ◽  
Sequencing Technologies ◽  
Whole Exome ◽  
Screening And Identification ◽  
High Throughput Dna Sequencing ◽  
New Mutations

Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.

scholarly journals Novel Dominant KCNQ2 Exon 7 Partial In-Frame Duplication in a Complex Epileptic and Neurodevelopmental Delay Syndrome

2020 ◽  
Vol 21 (12) ◽  
pp. 4447
Author(s):  
Pedro A. Lazo ◽  
Juan L. García ◽  
Paulino Gómez-Puertas ◽  
Íñigo Marcos-Alcalde ◽  
Cesar Arjona ◽  
...  
Keyword(s):  
Protein Function ◽  
De Novo ◽  
3D Structure ◽  
Unknown Origin ◽  
Unknown Etiology ◽  
Neurodevelopmental Delay ◽  
Calmodulin Binding ◽  
Whole Exome ◽  
Dynamics Simulations ◽  
Frame Duplication

Complex neurodevelopmental syndromes frequently have an unknown etiology, in which genetic factors play a pathogenic role. This study utilizes whole-exome sequencing (WES) to examine four members of a family with a son presenting, since birth, with epileptic-like crises, combined with cerebral palsy, severe neuromotor and developmental delay, dystonic tetraparexia, axonal motor affectation, and hyper-excitability of unknown origin. The WES study detected within the patient a de novo heterozygous in-frame duplication of thirty-six nucleotides within exon 7 of the human KCNQ2 gene. This insertion duplicates the first twelve amino acids of the calmodulin binding site I. Molecular dynamics simulations of this KCNQ2 peptide duplication, modelled on the 3D structure of the KCNQ2 protein, suggest that the duplication may lead to the dysregulation of calcium inhibition of this protein function.

scholarly journals A novel TSC1 variant associated with tuberous sclerosis and sacrococcygeal teratoma

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Saba Ahmad ◽  
Luis Manon ◽  
Gifty Bhat ◽  
Jerry Machado ◽  
Alice Zalan ◽  
...  
Keyword(s):  
Tuberous Sclerosis ◽  
Tuberous Sclerosis Complex ◽  
Cellular Differentiation ◽  
Autosomal Dominant ◽  
De Novo ◽  
Autosomal Dominant Disease ◽  
Sacrococcygeal Teratoma ◽  
Dominant Disease ◽  
The Brain

AbstractTuberous sclerosis complex (TSC) is an autosomal dominant disease associated with tumors and malformed tissues in the brain and other vital organs. We report a novel de novo frameshift variant of the TSC1 gene (c.434dup;p. Ser146Valfs*8) in a child with TSC who initially presented with a sacral teratoma. This previously unreported association between TSC and teratoma has broad implications for the pathophysiology of embryonic tumors and mechanisms underlying cellular differentiation.

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