&lt;p&gt;A Homozygous Truncating Mutation in &lt;em&gt;NALCN&lt;/em&gt; Causing IHPRF1: Detailed Clinical Manifestations and a Review of Literature&lt;/p&gt;

Karimi, Amir Hossein; Karimi, Mohammad Reza; Farnia, Poopak; Parvini, Farshid; Foroutan, Majid

doi:10.2147/tacg.s261781

Cited by 12 publications

(8 citation statements)

References 40 publications

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“…The impact of novel variants with unknown significance can be predicted in silico using bioinformatics tools such as MutationTaster [ 43 ], SIFT [ 44 ], Polyphen [ 45 ] and VEP [ 46 ]. This is common practice in clinical diagnosis to predict the impact of novel variants before co-segregation and functional confirmation [ 47 ]. Moreover, there are algorithms such as CHASM [ 48 ] and PrimateAI [ 49 ] that are specifically developed to predict functional effects of mutations in the cancer context and distinguish driver mutations from passengers.…”

Section: Single-layer Approachesmentioning

confidence: 99%

Prospects and challenges of cancer systems medicine: from genes to disease networks

Karimi

Abolmaali

et al. 2021

Briefings in Bioinformatics

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It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.

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Section: Single-layer Approachesmentioning

confidence: 99%

Prospects and challenges of cancer systems medicine: from genes to disease networks

Karimi

Abolmaali

et al. 2021

Briefings in Bioinformatics

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“…A review of the literature with focusing on common/uncommon manifestations of affected siblings is also provided. Such studies shows the diagnostic power of high throughout sequencing for more accurate and less expensive diagnosis of rare inherited disorders (11)(12)(13)(14).…”

Section: Introductionmentioning

confidence: 99%

Cohen syndrome due to a novel stop-gain mutation in VPS13B gene: A case report and comparative study in affected siblings worldwide

Saeediye,

Parvini

2024

Preprint

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Background Cohen syndrome (CS) is a highly rare heterogeneous disorder associated with mutations in the vacuolar protein sorting 13 homolog B (VPS13B) gene. CS is mainly characterized by intellectual disability, microcephaly, progressive retinopathy, hypotonia, obesity, neutropenia and dysmorphic facial features. Case presentation : Here, we report two affected siblings suspicious to CS. Our objectives were the delineation of gene mutation causing this rare condition and comparison of observed manifestations with symptoms reported in other CS affected siblings worldwide. Whole exome sequencing (WES) in combination with Sanger sequencing were utilized to identify the disease-causing mutation in the affected siblings. Subsequently, to elucidate the effects of the mutation found, clinical data of patients were collected. Moreover, the possible impact of the identified mutation on the corresponding protein was analyzed using bioinformatics tools. A novel homozygous stop-gain mutation NM_015243: c.1043G > A: p.W348X in the VPS13B gene was identified in the proband. This mutation was confirmed by Sanger sequencing in the affected siblings and segregated with the autosomal recessive (AR) inheritance pattern of CS. Moreover, in-silico approaches highly confirmed the disease-causing nature of the identified mutation. Conclusion Our findings could expand the mutations spectrum of CS and the comparative study of all reported manifestations in CS affected siblings throughout the world, clearly shed light the common and uncommon manifestations of CS in different affected siblings with different VPS13B gene mutations. These results could be also useful in genetic diagnosis and counseling in CS affected patients.

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“…A review of the literature is also provided. Beyond any doubt, such studies show that rapid progress in the eld of high throughout sequencing allows more accurate and less expensive diagnosis of rare inherited disorders (15)(16)(17).…”

Section: Introductionmentioning

confidence: 99%

A novel de novo nonsense mutation in SALL4 causing duane radial ray syndrome: A case report and expanding the phenotypic spectrum

Ajam-Hosseini

Parvini

Angaji

2023

Preprint

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Background: SALL4, a member of the SALL genes family, encodes a zinc-finger transcriptional factor that either activates or represses gene transcription depending on cell type during embryonic development. SALL4 mutations cause extremely variable conditions including Duane-radial ray (DRR), Okihiro, Holt-oram, Acro-renal ocular (ARO) and IVIC syndromes, all with autosomal dominant inheritance pattern. However, all these syndromes with different terminologies are actually the same entity termed SALL4 related disorders. Case presentation: Herein, we examine an Iranian patient suspected to DRR syndrome which has not been previously described in the population. Whole-exome sequencing (WES) was performed to examine pathogenic genes in the proband. Subsequently, Sanger sequencing was used to confirm the mutation found. To elucidate the effects of the identified mutation, clinical data of patient was collected. Morever, the possible impact of the mutation found on the corresponding protein was evaluated using bioinformatics tools. WES identifed a novel de novo heterozygous nonsense mutation in exon 2 of SALL4 gene (c.712C>T:p.Q238X). Subsequently, segregation and phenotype-genotype correlation analysis as well as in-silicoapproaches confirmed the autosomal dominance inheritance and disease-causing nature of the identified mutation. In addition, studied patient had features not described previously, including kyphoscoliosis, dimple presacral sinus, barrel chest and artric disc (C6-C7). These manifestations could be additional characteristics of the growing phenotypic spectrum of SALL4 related disorders. Conclusion: Our findings could extend the pathogenic mutations and phenotypic spectrum of SALL4 related disorders. Such reports can also aid to conduct genetic counseling, prenatal diagnosis and clinical management for individuals at high risk of SALL4 related disorders.

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<p>A Homozygous Truncating Mutation in <em>NALCN</em> Causing IHPRF1: Detailed Clinical Manifestations and a Review of Literature</p>

Cited by 12 publications

References 40 publications

Prospects and challenges of cancer systems medicine: from genes to disease networks

Prospects and challenges of cancer systems medicine: from genes to disease networks

Cohen syndrome due to a novel stop-gain mutation in VPS13B gene: A case report and comparative study in affected siblings worldwide

A novel de novo nonsense mutation in SALL4 causing duane radial ray syndrome: A case report and expanding the phenotypic spectrum

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