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1.
BMC Genomics ; 23(1): 35, 2022 Jan 07.
Article En | MEDLINE | ID: mdl-34996359

BACKGROUND: Gene expression is regulated by transcription factors, cofactors, and epigenetic mechanisms. Coexpressed genes indicate similar functional categories and gene networks. Detecting gene-gene coexpression is important for understanding the underlying mechanisms of cellular function and human diseases. A common practice of identifying coexpressed genes is to test the correlation of expression in a set of genes. In single-cell RNA-seq data, an important challenge is the abundance of zero values, so-called "dropout", which results in biased estimation of gene-gene correlations for downstream analyses. In recent years, efforts have been made to recover coexpressed genes in scRNA-seq data. Here, our goal is to detect coexpressed gene pairs to reduce the "dropout" effect in scRNA-seq data using a novel graph-based k-partitioning method by merging transcriptomically similar cells. RESULTS: We observed that the number of zero values was reduced among the merged transcriptomically similar cell clusters. Motivated by this observation, we leveraged a graph-based algorithm and develop an R package, scCorr, to recover the missing gene-gene correlation in scRNA-seq data that enables the reliable acquisition of cluster-based gene-gene correlations in three independent scRNA-seq datasets. The graphically partitioned cell clusters did not change the local cell community. For example, in scRNA-seq data from peripheral blood mononuclear cells (PBMCs), the gene-gene correlation estimated by scCorr outperformed the correlation estimated by the nonclustering method. Among 85 correlated gene pairs in a set of 100 clusters, scCorr detected 71 gene pairs, while the nonclustering method detected only 4 pairs of a dataset from PBMCs. The performance of scCorr was comparable to those of three previously published methods. As an example of downstream analysis using scCorr, we show that scCorr accurately identified a known cell type (i.e., CD4+ T cells) in PBMCs with a receiver operating characteristic area under the curve of 0.96. CONCLUSIONS: Our results demonstrate that scCorr is a robust and reliable graph-based method for identifying correlated gene pairs, which is fundamental to network construction, gene-gene interaction, and cellular omic analyses. scCorr can be quickly and easily implemented to minimize zero values in scRNA-seq analysis and is freely available at https://github.com/CBIIT-CGBB/scCorr .


Gene Expression Profiling , Single-Cell Analysis , Humans , Leukocytes, Mononuclear , Sequence Analysis, RNA , Software , Whole Exome Sequencing
2.
Neurosciences (Riyadh) ; 27(1): 45-49, 2022 Jan.
Article En | MEDLINE | ID: mdl-35017290

Homozygous or compound heterozygous pathogenic variants of the RBCK1 gene can result in a systemic disorder characterized by the accumulation of complex carbohydrate molecules, namely polyglucosan bodies in the muscular tissues. The role of this gene in the pathophysiology of the disorder at the molecular level remains unclear. Being a very rare disorder, the medical knowledge is based on just a few reported cases. Here we report a 7-year-old girl who presented with exercise intolerance and hepatosplenomegaly. Her liver profile was constantly raised. The genetic investigation has revealed a variant of the RBCK1 gene of unknown significance, which has later been confirmed as pathogenic via a variety of clinical, genetic, and histopathological approaches. More importantly, it is evident that the availability of sophisticated genetic testing, such as whole-exome sequencing, has significantly improved the knowledge of and diagnosis of many rare metabolic disorders.


Muscular Diseases , Child , Female , Glucans , Humans , Transcription Factors/genetics , Ubiquitin-Protein Ligases , Whole Exome Sequencing
3.
In Vivo ; 36(1): 251-257, 2022.
Article En | MEDLINE | ID: mdl-34972722

BACKGROUND/AIM: It is estimated that nonmelanoma skin cancer (NMSC), including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), affects more than 3 million Americans each year. Translation of next-generation sequencing (NGS) data into identification of new potential targets for therapeutic applications may be helpful. Whole-exome sequencing (WES) is a widely used NGS method that involves sequencing the protein-coding regions of the genome. CASE REPORT: We report a case of a 65-year-old female smoker who was found to have two 6 mm lesions in her left nasal vestibule. Biopsies demonstrated synchronous BCC and SCC. The patient underwent surgical excision of both cancers with safe margins followed by plastic reconstruction. WES was performed on both cancers and 16 alterations including BRCA2 (p.P389S), FAM5C (S420L), KMT2A (P855L), and SMO (L412F), as unique for BCC, and 4 alterations including TP53 (p.H179Q) and CDKN2A (p.P114L), as unique for SCC, were identified. CONCLUSION: We report the first documented case with unique genetic alterations in two distinct and synchronous skin BCC and SCC arising from the same nasal vestibule of a patient. This adds to the growing field of data regarding genetic variants in characterizing malignancies and potentially for targeted therapies.


Carcinoma, Basal Cell , Carcinoma, Squamous Cell , Skin Neoplasms , Aged , Carcinoma, Basal Cell/genetics , Carcinoma, Squamous Cell/diagnosis , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/surgery , Female , Humans , Mutation , Skin Neoplasms/diagnosis , Skin Neoplasms/genetics , United States , Whole Exome Sequencing
4.
Arq Bras Oftalmol ; 85(1): 85-87, 2022.
Article En | MEDLINE | ID: mdl-34468556

This is a case report of a 2-year-old male patient with cognitive delay, facial abnormalities, and microcornea in the right eye, who was referred for ophthalmological investigation. The initial ophthalmological examination revealed hypertelorism, epicanthus, nystagmus, esotropia, and microcornea in the right eye. The examination under anesthesia revealed microphthalmia in the right eye, and iris, retina, and optic nerve coloboma in both eyes. Whole exome sequencing revealed evidence of a heterozygotic pathogenic variant in PACS1. The PACS1 pathogenic variant in association with the clinical findings confirmed the diagnosis of Schuurs-Hoeijmakers syndrome. To our knowledge, this is the first report to describe microcornea and microphthalmia as additional ocular manifestations of Schuurs-Hoeijmakers syndrome.


Coloboma , Eye Abnormalities , Child, Preschool , Coloboma/diagnosis , Coloboma/genetics , Humans , Iris , Male , Syndrome , Vesicular Transport Proteins/genetics , Whole Exome Sequencing
5.
Gene ; 807: 145934, 2022 Jan 10.
Article En | MEDLINE | ID: mdl-34478820

Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein-protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.


Eating/genetics , Energy Metabolism/genetics , Liver/metabolism , Animal Feed/analysis , Animals , Cattle , Databases, Genetic , Insulin-Like Growth Factor I/genetics , Lipid Metabolism/genetics , Liver/physiology , Phospholipid Hydroperoxide Glutathione Peroxidase/genetics , Protein Interaction Maps/genetics , Signal Transduction/genetics , Src Homology 2 Domain-Containing, Transforming Protein 1/genetics , Transcriptome/genetics , Ubiquitination/genetics , Whole Exome Sequencing/methods
6.
Gene ; 812: 146099, 2022 Feb 20.
Article En | MEDLINE | ID: mdl-34906645

Nasopharyngeal Carcinoma (NPC) found to be dependent on geographical and racial variation and is more prevalent in Northeast (NE) India. WES-based study was conducted in three states (tribes); Nagaland (Naga), Mizoram (Mizo) and Manipur (Manipuri), which provided an overview of germline variants involved inthemajor signaling pathways. Validation and recurrence assessment of WES data confirmed the risk effect of STEAP3_rs138941861 and JAG1_rs2273059, and the protective role of PARP4_rs17080653 and TGFBR1_rs11568778 variants, where STEAP3_rs138941861conferring Arg290His substitution was the only exonic non-synonymous variant and to be located in proximity to the linking region between the transmembrane and oxidoreductasedomainsof STEAP3 protein, andaffectedits structural and functional dynamics by altering the Electrostatic Potential around this connecting region. Moreover, these significantly associated variants having deleterious effect were observed to have interactions in p53 signaling pathway which emphasizes the importance of this pathway in the causation of NPC.


Cell Cycle Proteins/genetics , Jagged-1 Protein/genetics , Nasopharyngeal Carcinoma/genetics , Nasopharyngeal Neoplasms/genetics , Nuclear Proteins/genetics , Oxidoreductases/genetics , Receptor, Transforming Growth Factor-beta Type I/genetics , Whole Exome Sequencing/methods , Adult , Amino Acid Substitution , Case-Control Studies , Cell Cycle Proteins/chemistry , Female , Genetic Predisposition to Disease , High-Throughput Nucleotide Sequencing , Humans , India , Male , Middle Aged , Models, Molecular , Oxidoreductases/chemistry , Polymorphism, Single Nucleotide , Protein Conformation , Protein Domains
7.
Gene ; 808: 146000, 2022 Jan 15.
Article En | MEDLINE | ID: mdl-34626719

Hearing loss is a common disease, of which genetic factors are the main cause. The incidence of mild or moderate postlingual deafness in children is not high, and the impact on life and learning is not as severe as that of prelingual deafness. This leads to insufficient attention to the disorder in the clinic. To date, only a few disease-causing genes have been reported. This report describe a case of novel heterozygous mutations in OTOGL that causes nonsyndromic mild sensorineural hearing loss. Basic information, imaging examinations, audiological examination, and vestibular function tests of the proband were collected. Blood samples of the proband's family were collected and analyzed by whole exome sequencing and Sanger sequencing. A pedigree diagram was drawn and the genetic patterns were analyzed. The proband is a 16-year-old female student with mild sensorineural hearing loss. High-resolution CT of the inner ear and vestibular function tests showed no abnormalities. The age of onset was approximately 4 years old. Except for hearing loss, no lesions were seen in other organs. The parents of the proband were not close relatives and had normal hearing. Two novel heterozygous mutations were found in the OTOGL gene. The c.5038del (p.D1680Ifs*6) variant was inherited from the father, and the c.2770C > T (p.R924X) variant from the mother. They enriched the mutation spectrum of OTOGL, which provides the basis for gene function research and genetic consultation.


Hearing Loss, Sensorineural/genetics , Membrane Proteins/genetics , Adolescent , Adult , China , Family , Female , Genotype , Heterozygote , Humans , Male , Membrane Proteins/metabolism , Mutation , Pedigree , Phenotype , Whole Exome Sequencing
8.
Methods Mol Biol ; 2391: 45-54, 2022.
Article En | MEDLINE | ID: mdl-34686975

Changes in the surrounding environment are mirrored by changes in the transcript profile of an organism. In the case of a plant pathogen, host colonization would be a challenge that triggers changes in transcript expression patterns. Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pathogen colonizes its host. Several robust data analysis methods and pipelines are available that can identify these differentially expressed transcripts. In this chapter we outline the steps and other caveats that are needed to run one such pipeline.


Gene Expression Profiling , Sequence Analysis, RNA , Data Analysis , RNA-Seq , Transcriptome , Whole Exome Sequencing
9.
Pediatr Pulmonol ; 57(1): 264-272, 2022 01.
Article En | MEDLINE | ID: mdl-34585851

INTRODUCTION: Rubinstein-Taybi syndrome (RSTS) is a rare genetic syndrome caused primarily by a mutation in the CREBBP gene found on chromosome 16. Patients with RSTS are at greater risk for a variety of medical problems, including upper airway obstruction and aspiration. Childhood interstitial lung disease (ILD) thus far has not been definitively linked to RSTS. Here we present three patients with RSTS who developed ILD and discuss possible mechanisms by which a mutation in CREBBP may be involved in the development of ILD. METHODS: Routine hematoxylin and eosin staining was performed on lung biopsy tissue for histological analysis. Immunofluorescent staining was performed on lung biopsy tissue for markers of fibrosis, surfactant deficiency and histone acetylation. Cases 1 and 2 had standard clinical microarray analysis. Case 3 had whole exome sequencing. Bioinformatics analyses were performed to identify possible causative genes using ToppGene. RESULTS: Computed tomography images in all cases showed consolidated densities overlying ground glass opacities. Lung histopathology revealed accumulation of proteinaceous material within alveolar spaces, evidence of fibrosis, and increased alveolar macrophages. Immunofluorescent staining showed increase in surfactant protein C staining, patchy areas of increased anti-smooth muscle antibody staining, and increased staining for acetylated histone 2 and histone 3 lysine 9. DISCUSSION: Clinical characteristics, radiographic imaging, lung histopathology, and immunofluorescent staining results shared by all cases demonstrated findings consistent with ILD. Immunofluorescent staining suggests two possible mechanisms for the development of ILD: abnormal surfactant metabolism and/or persistent activation of myofibroblasts. These two pathways could be related to dysfunctional CREBBP protein.


Lung Diseases, Interstitial , Rubinstein-Taybi Syndrome , CREB-Binding Protein/genetics , Child , Humans , Lung Diseases, Interstitial/etiology , Lung Diseases, Interstitial/genetics , Mutation , Rubinstein-Taybi Syndrome/complications , Rubinstein-Taybi Syndrome/diagnosis , Rubinstein-Taybi Syndrome/genetics , Whole Exome Sequencing
10.
Clin Dysmorphol ; 31(1): 6-10, 2022 Jan 01.
Article En | MEDLINE | ID: mdl-34866617

Epilepsy, progressive myoclonic 3, with or without intracellular inclusions (MIM# 611726) is a rare autosomal recessive condition associated with pathogenic variants in KCTD7, which encodes the BR-C,ttk and bab/pox virus and zinc finger domain-containing KCTD7 protein. We report four individuals from three Indian families presenting with an initial period of normal development, progressive myoclonic seizures followed by neuroregression and an abnormal electroencephalogram. We identified two novel missense variants, c.458G>C p.(Arg153Pro) and c.205C>G p.(Leu69Val) and one known disease-causing variant, c.280C>T p.(Arg94Trp) in KCTD7 by exome sequencing. We review the literature of 67 individuals with variants in KCTD7. Our study expands the molecular spectrum of KCTD7-related progressive myoclonic epilepsy.


Myoclonic Epilepsies, Progressive , Potassium Channels , Humans , Mutation, Missense , Myoclonic Epilepsies, Progressive/genetics , Potassium Channels/genetics , Whole Exome Sequencing
11.
Pac Symp Biocomput ; 27: 199-210, 2022.
Article En | MEDLINE | ID: mdl-34890149

Inferring the cell types in single-cell RNA-sequencing (scRNA-seq) data is of particular importance for understanding the potential cellular mechanisms and phenotypes occurring in complex tissues, such as the tumor-immune microenvironment (TME). The sparsity and noise of scRNA-seq data, combined with the fact that immune cell types often occur on a continuum, make cell typing of TME scRNA-seq data a significant challenge. Several single-label cell typing methods have been put forth to address the limitations of noise and sparsity, but accounting for the often overlapped spectrum of cell types in the immune TME remains an obstacle. To address this, we developed a new scRNA-seq cell-typing method, Cell-typing using variance Adjusted Mahalanobis distances with Multi-Labeling (CAMML). CAMML leverages cell type-specific weighted gene sets to score every cell in a dataset for every potential cell type. This allows cells to be labelled either by their highest scoring cell type as a single label classification or based on a score cut-off to give multi-label classification. For single-label cell typing, CAMML performance is comparable to existing cell typing methods, SingleR and Garnett. For scenarios where cells may exhibit features of multiple cell types (e.g., undifferentiated cells), the multi-label classification supported by CAMML offers important benefits relative to the current state-of-the-art methods. By integrating data across studies, omics platforms, and species, CAMML serves as a robust and adaptable method for overcoming the challenges of scRNA-seq analysis.


Computational Biology , Single-Cell Analysis , RNA/genetics , Sequence Analysis, RNA , Whole Exome Sequencing
12.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 43-47, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964965

OBJECTIVE: To explore the clinical features and genetic basis for a Chinese pedigree diagnosed with congenital glycosylation disease (CGD). METHODS: Clinical manifestations of two brothers were analyzed. Whole exome sequencing was carried out for the sib pair. Suspected variants were verified by Sanger sequencing. RESULTS: Both the proband and her younger brother were found to carry compound heterozygous variants of the PMM2 gene, which included a known pathogenic mutation of c.395T>C (p.I132T) and a previously unreported c.448-1(delAG) in the 5' end of exon 6 of the gene. CONCLUSION: The compound heterozygous variants of the PMM2 gene probably underlay the CGD in the sib pair.


/genetics , China , Female , Glycosylation , Humans , Male , Mutation , Pedigree , Whole Exome Sequencing
13.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 52-55, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964967

OBJECTIVE: To explore the genetic basis for a Chinese patient with retinitis pigmentosa (RP). METHODS: Whole exome sequencing (WES) was carried out to screen potential variant in the proband. Candidate variants were determined by taking consideration of clinical phenotype. Sanger sequencing was used to verify the variant in the proband and his parents. RESULTS: The proband was found to harbor compound heterozygous variants of c.8G>A (p.Cys3Tyr) and c.958_959insA (p.Arg320Glnfs*29) in the C2ORF71 gene, which has derived from his father and mother, respectively. Both variants were unreported previously. Based on the ACMG guidelines, they were predicted to be likely pathogenic and pathogenic, respectively. CONCLUSION: The novel compound heterozygous variants of the C2ORF71 gene probably underlay the pathogenesis of RP in the proband. Above finding has enriched the spectrum of C2ORF71 gene mutations and facilitated genetic counseling for the family.


Retinitis Pigmentosa , /genetics , China , Humans , Mutation , Pedigree , Retinitis Pigmentosa/genetics , Whole Exome Sequencing
14.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 26-30, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964961

OBJECTIVE: To analyze the clinical characteristics and pathogenic gene in a Chinese pedigree affected with mitochondrial DNA depletion syndrome 8A (MTDPS8A). METHODS: Whole exome sequencing was carried out for the patient. Sanger sequencing was used to verify the results, and PolyPhen-2 and PROVEAN software were used to predict the impact of amino acid changes on the function of the protein. RESULTS: The patient, a two-month-old female, was admitted to the hospital for poor milk intake and poor mental response. Her clinical manifestations included feeding difficulty, shortness of breath and low muscle tone. Auxiliary laboratory test indicated that the infant was underdeveloped with abnormal liver, kidney, and heart functions accompanied by hyperlacticacidemia. She responded poorly to treatment and eventually died. Sequencing revealed that the child has carried compound heterozygous missense variants of the RRM2B gene, namely c.16delA (p.R6Gfs*22) and c.175G>C (p.A59P), which were respectively inherited from her father and mother, and both were newly discovered pathologic variants. CONCLUSION: The c.16delA and c.175G>C compound heterozygous variants of the RRM2B gene probably underlay the pathogenesis of MTDPS8A. Above finding has strengthened the understanding of the clinical feature and genetic etiology of this disease and expanded the mutation spectrum of the RRM2B gene.


Genetic Testing , Ribonucleotide Reductases , Cell Cycle Proteins , Child , China , DNA, Mitochondrial/genetics , Female , Humans , Infant , Mutation , Pedigree , Whole Exome Sequencing
15.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 31-34, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964962

OBJECTIVE: To explore the genetic basis for a child with Rothmund-Thomson syndrome (RTS). METHODS: The child has featured poikeloderma, short stature, cataract, sparse hair and skeletal malformation. Peripheral blood samples of the child and her family members were collected and subjected to whole exome sequencing. Candidate variants were verified by Sanger sequencing. RESULTS: The child was found to harbor compound heterozygous variants of the RECQL4 gene, namely c.1048_1049delAG and c.2886-1G>A, among which c.2886-1G>A was unreported previously. According to the ACMG guidelines, the c.1048_1049delAG was predicted to be pathogenic (PVS1+PM3_Strong+PM2), while the c.2886-1G>A was predicted to be likely pathogenic (PVS1+PM2). CONCLUSION: The compound heterozygous variants of the RECQL4 gene probably underlay the pathogenesis of RTS in this patient. Above finding has enriched the mutational spectrum of the RECQL4 gene.


Rothmund-Thomson Syndrome , Child , Family , Female , Humans , Mutation , RecQ Helicases/genetics , Rothmund-Thomson Syndrome/genetics , Whole Exome Sequencing
16.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 35-38, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964963

OBJECTIVE: To investigate the clinical characteristics and genetic basis for a child with Keppen-Lubinsky syndrome (KPLBS). METHODS: Trio-whole exome sequencing (Trio-WES) was carried out for the proband and her parents. Candidate variant was verified by Sanger sequencing and bioinformatic analysis. RESULTS: The child has featured peculiar facies including large eyes, alar hypoplasia, microretrognathia, premature aging appearance in addition with growth delay and mental retardation. Trio-WES has identified that she has carried a de novo variant of the KCNJ6 gene, namely c.460G>C (p.Gly154Arg). The variant has not been recorded in the database. Prediction of protein structure indicated that the variant may affect the potassium ion selective filtration structure channel in the transmembrane region of KCNJ6 protein, which may result in up regulation of the function of the channel. CONCLUSION: The de novo c.460G>C (p.Gly154Arg) variant of the KCNJ6 gene probably underlay the KPLBS in this child. Above finding has enriched the genotypic and phenotype spectrum of this syndrome.


Intellectual Disability , Cataract , China , Female , G Protein-Coupled Inwardly-Rectifying Potassium Channels/genetics , Humans , Hypogonadism/congenital , Intellectual Disability/genetics , Mutation , Whole Exome Sequencing
17.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 48-51, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964966

OBJECTIVE: To analyze the clinical phenotype and genetic characteristics of a child with Perlman syndrome. METHODS: Genomic DNA was extracted from peripheral blood samples from the patient and her parents. Whole exome sequencing (WES) was carried out to detect potential variant in the proband. Candidate variant was verified by Sanger sequencing. The pathogenicity of candidate variants was evaluated according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). RESULTS: The results of WES showed that the proband has harbored compound heterozygous variants of the DIS3L2 gene, namely c.2109delC and c.1829.c.1830insC, which were respectively inherited from her mother and father. The results were confirmed by Sanger sequencing. Based on the ACMG guidelines, the two novel variants were both predicted to be pathogenic (PVS1+PS2+PM2). CONCLUSION: The compound heterozygous variants of the DIS3L2 gene probably underlay the Perlman syndrome in this patient. Above finding has enriched the spectrum of DIS3L2 gene mutations.


Genetic Testing , Genomics , Exoribonucleases , Female , Fetal Macrosomia , Humans , Mutation , Whole Exome Sequencing , Wilms Tumor
18.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 56-59, 2022 Jan 10.
Article Zh | MEDLINE | ID: mdl-34964968

OBJECTIVE: To explore the genotype-phenotype correlation of a Chinese pedigree affected with Lowe syndrome. METHODS: Whole exome sequencing (WES) and Sanger sequencing were carried out for the proband and members of his pedigree. RESULTS: The proband, a 3-year-and-5-month-old male, presented with multiple anomalies including congenital cataract, glaucoma, brain dysplasia, renal dysfunction and cognitive impairment. WES revealed that he has harbored a novel hemizygous missense variant of the OCRL gene, namely NM_000276.3: c.1255T>C (p.Trp419Arg) (GRCh37/hg19), which was derived from his unaffected mother. The same variant was not found in his elder brother who was healthy. The variant was predicted to be pathogenic according to ACMG/AMP guideline. Compared with previously reported cases of Lowe syndrome, our patient has displayed rare features including corpus callosum dysplasia, reduction of white matter, cerebral hypoplasia, laryngomalacia, sebaceous cyst, recurrent eczema, cryptorchidism, hypoglycemia and irritability. CONCLUSION: Above finding has expanded the mutational spectrum of the OCRL gene, enriched clinical features of Lowe syndrome, and enabled genetic counseling for this pedigree.


Oculocerebrorenal Syndrome , Aged , China , Genetic Association Studies , Humans , Infant , Male , Mutation , Pedigree , Phosphoric Monoester Hydrolases/genetics , Whole Exome Sequencing
19.
Zhonghua Nan Ke Xue ; 27(10): 899-903, 2021 10 20.
Article Zh | MEDLINE | ID: mdl-34914268

Objective: To compare the efficiency of the target gene panel method and whole-exome sequencing (WES) in detecting idiopathic hypogonadotropic hypogonadism (IHH), and select a more suitable gene detection method. METHODS: We selected 24 genes closely related to the molecular pathogenesis of IHH to make up the gene panel, detected the mutation sites in 73 patients with IHH using the panel method, and verified the results of sequencing with the Sanger method. Using the key words "idiopathic hypogonadotropic hypogonadism", we searched databases for relevant literature, calculated the positive rate of IHH detected by WES and compared it with that detected with the panel method. RESULTS: Of the 73 cases of IHH detected with the panel method, 7 were found with pathogenic mutations, including 2 cases of FGFR1, 2 cases of CHD7, 2 cases of KISS1R, and 1 case of NR5A1 mutation. Sanger sequencing showed that the positive rate of the panel method was 9.7%. Of the 1 336 articles retrieved, 5 met the inclusion criteria and were included, in which WES revealed a positive rate of about 30%. CONCLUSIONS: For detection of the diseases with clear mutated genes, the panel method is relatively inexpensive and has a high sequencing depth, while for detection of the diseases with complicated genetic patterns and unclear mutated genes, WES is more efficient. Further studies are needed for choice of the two methods for different purpose of detection./.


Hypogonadism , Humans , Hypogonadism/diagnosis , Hypogonadism/genetics , Male , Whole Exome Sequencing
20.
Nat Commun ; 12(1): 7348, 2021 12 22.
Article En | MEDLINE | ID: mdl-34937871

Surgery for locoregionally advanced head and neck squamous cell carcinoma (HNSCC) results in 30‒50% five-year overall survival. In IMCISION (NCT03003637), a non-randomized phase Ib/IIa trial, 32 HNSCC patients are treated with 2 doses (in weeks 1 and 3) of immune checkpoint blockade (ICB) using nivolumab (NIVO MONO, n = 6, phase Ib arm A) or nivolumab plus a single dose of ipilimumab (COMBO, n = 26, 6 in phase Ib arm B, and 20 in phase IIa) prior to surgery. Primary endpoints are feasibility to resect no later than week 6 (phase Ib) and primary tumor pathological response (phase IIa). Surgery is not delayed or suspended for any patient in phase Ib, meeting the primary endpoint. Grade 3‒4 immune-related adverse events are seen in 2 of 6 (33%) NIVO MONO and 10 of 26 (38%) total COMBO patients. Pathological response, defined as the %-change in primary tumor viable tumor cell percentage from baseline biopsy to on-treatment resection, is evaluable in 17/20 phase IIa patients and 29/32 total trial patients (6/6 NIVO MONO, 23/26 COMBO). We observe a major pathological response (MPR, 90‒100% response) in 35% of patients after COMBO ICB, both in phase IIa (6/17) and in the whole trial (8/23), meeting the phase IIa primary endpoint threshold of 10%. NIVO MONO's MPR rate is 17% (1/6). None of the MPR patients develop recurrent HSNCC during 24.0 months median postsurgical follow-up. FDG-PET-based total lesion glycolysis identifies MPR patients prior to surgery. A baseline AID/APOBEC-associated mutational profile and an on-treatment decrease in hypoxia RNA signature are observed in MPR patients. Our data indicate that neoadjuvant COMBO ICB is feasible and encouragingly efficacious in HNSCC.


Head and Neck Neoplasms/drug therapy , Immunotherapy , Ipilimumab/therapeutic use , Neoadjuvant Therapy , Nivolumab/therapeutic use , Squamous Cell Carcinoma of Head and Neck/drug therapy , Aged , Biomarkers, Tumor/metabolism , Female , Fluorodeoxyglucose F18/chemistry , Head and Neck Neoplasms/diagnostic imaging , Head and Neck Neoplasms/pathology , Head and Neck Neoplasms/surgery , Humans , Immune Checkpoint Inhibitors/therapeutic use , Male , Middle Aged , Positron-Emission Tomography , Squamous Cell Carcinoma of Head and Neck/diagnostic imaging , Squamous Cell Carcinoma of Head and Neck/pathology , Squamous Cell Carcinoma of Head and Neck/surgery , Whole Exome Sequencing
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