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1.
Braz. j. med. biol. res ; 54(11): e11396, 2021. graf
Article in English | LILACS | ID: biblio-1339444

ABSTRACT

Current understanding of the genetic factors contributing to the etiology of non-syndromic craniosynostosis (NSC) remains scarce. The present work investigated the presence of variants in ALX4, EFNA4, and TWIST1 genes in children with NSC to verify if variants within these genes may contribute to the occurrence of these abnormal phenotypes. A total of 101 children (aged 45.07±40.94 months) with NSC participated in this cross-sectional study. Parents and siblings of the probands were invited to participate. Medical and family history of craniosynostosis were documented. Biological samples were collected to obtain genomic DNA. Coding exons of human TWIST1, ALX4, and EFNA4 genes were amplified by polymerase chain reaction and Sanger sequenced. Five missense variants were identified in ALX4 in children with bilateral coronal, sagittal, and metopic synostosis. A de novo ALX4 variant, c.799G>A: p.Ala267Thr, was identified in a proband with sagittal synostosis. Three missense variants were identified in the EFNA4 gene in children with metopic and sagittal synostosis. A TWIST1 variant occurred in a child with unilateral coronal synostosis. Variants were predicted to be among the 0.1% (TWIST1, c.380C>A: p. Ala127Glu) and 1% (ALX4, c.769C>T: p.Arg257Cys, c.799G>A: p.Ala267Thr, c.929G>A: p.Gly310Asp; EFNA4, c.178C>T: p.His60Tyr, C.283A>G: p.Lys95Glu, c.349C>A: Pro117Thr) most deleterious variants in the human genome. With the exception of ALX4, c.799G>A: p.Ala267Thr, all other variants were present in at least one non-affected family member, suggesting incomplete penetrance. Thus, these variants may contribute to the development of craniosynostosis, and should not be discarded as potential candidate genes in the diagnosis of this condition.


Subject(s)
Humans , Child , Craniosynostoses/genetics , Transcription Factors/genetics , Base Sequence , Family , Cross-Sectional Studies , Mutation, Missense/genetics , DNA-Binding Proteins/genetics
2.
Clinics ; 76: e2052, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153974

ABSTRACT

OBJECTIVES: Single nucleotide variants (SNVs) are the most common type of genetic variation among humans. High-throughput sequencing methods have recently characterized millions of SNVs in several thousand individuals from various populations, most of which are benign polymorphisms. Identifying rare disease-causing SNVs remains challenging, and often requires functional in vitro studies. Prioritizing the most likely pathogenic SNVs is of utmost importance, and several computational methods have been developed for this purpose. However, these methods are based on different assumptions, and often produce discordant results. The aim of the present study was to evaluate the performance of 11 widely used pathogenicity prediction tools, which are freely available for identifying known pathogenic SNVs: Fathmn, Mutation Assessor, Protein Analysis Through Evolutionary Relationships (Phanter), Sorting Intolerant From Tolerant (SIFT), Mutation Taster, Polymorphism Phenotyping v2 (Polyphen-2), Align Grantham Variation Grantham Deviation (Align-GVGD), CAAD, Provean, SNPs&GO, and MutPred. METHODS: We analyzed 40 functionally proven pathogenic SNVs in four different genes associated with differences in sex development (DSD): 17β-hydroxysteroid dehydrogenase 3 (HSD17B3), steroidogenic factor 1 (NR5A1), androgen receptor (AR), and luteinizing hormone/chorionic gonadotropin receptor (LHCGR). To evaluate the false discovery rate of each tool, we analyzed 36 frequent (MAF>0.01) benign SNVs found in the same four DSD genes. The quality of the predictions was analyzed using six parameters: accuracy, precision, negative predictive value (NPV), sensitivity, specificity, and Matthews correlation coefficient (MCC). Overall performance was assessed using a receiver operating characteristic (ROC) curve. RESULTS: Our study found that none of the tools were 100% precise in identifying pathogenic SNVs. The highest specificity, precision, and accuracy were observed for Mutation Assessor, MutPred, SNP, and GO. They also presented the best statistical results based on the ROC curve statistical analysis. Of the 11 tools evaluated, 6 (Mutation Assessor, Phanter, SIFT, Mutation Taster, Polyphen-2, and CAAD) exhibited sensitivity >0.90, but they exhibited lower specificity (0.42-0.67). Performance, based on MCC, ranged from poor (Fathmn=0.04) to reasonably good (MutPred=0.66). CONCLUSION: Computational algorithms are important tools for SNV analysis, but their correlation with functional studies not consistent. In the present analysis, the best performing tools (based on accuracy, precision, and specificity) were Mutation Assessor, MutPred, and SNPs&GO, which presented the best concordance with functional studies.


Subject(s)
Humans , Computational Biology , Mutation, Missense/genetics , Virulence , Polymorphism, Single Nucleotide , Sexual Development , Mutation
3.
Journal of Experimental Hematology ; (6): 1917-1922, 2021.
Article in Chinese | WPRIM | ID: wpr-922224

ABSTRACT

OBJECTIVE@#To analyze the different subtypes caused by c.721C>T substitution in the exon 7 of the ABO gene, and to investigate the related molecular mechanism of different antigens expression.@*METHODS@#ABO subtypes in 7 samples were identified by standard serological methods. The exons 6, 7, and adjacent intron of ABO gene were amplified by Polymerase Chain Reaction (PCR), and the PCR products were analyzed by direct DNA sequencing and cloning sequencing.@*RESULTS@#ABO subtypes phenotypes were A@*CONCLUSION@#c.721C>T substitution in the ABO gene causes p.Arg241Trp exchange resulting in the decreasing of GTA or GTB activities and weaker antigen expression. O.01.07 is a null allele which cannot form a functional catalytic enzyme has no effect on A


Subject(s)
ABO Blood-Group System/genetics , Alleles , Exons , Genotype , Mutation, Missense
4.
Article in Chinese | WPRIM | ID: wpr-922030

ABSTRACT

OBJECTIVE@#To study the genetic variants of a child with Autism Spectrum Disorder (ASD) combined with epilepsy, and explore its possible pathogenic mechanism.@*METHODS@#Clinical data of the child were collected and evaluated, whole-exome sequencing (WES) technology was used to explore the genetic variants sites of the child and his parents and candidate genes were filtered out. Sanger sequencing were performed to verify the variants identified by WES and PolyPhen2 was utilized to predict the function of these variants. qPCR was carry out to determine the expression of the variant gene.@*RESULTS@#The proband carried a compound heterozygous mutation in the SIK3 gene (Chr11 q23.3, NM_025164.6), which contains a missense mutation c.1295A>G (p.N432S) inherited from the father and a deletion [c.2389_2391del(p.797del)] inherited from the mother. Both mutation sites are highly conservative, and PolyPhen2 predicted (c.1295A>G [p.N432S]) to be harmful. Compared to the mother, expression of SIK3in mRNA level in the peripheral blood of the proband and his father were both significantly decreased; compared to normal child, SIK3 expression in the peripheral blood of the proband and two other children with ASD were all decreased significantly too. In addition, studies on mice found that Sik3 gene has a marked higher level of expression in the brain.@*CONCLUSION@#The SIK3 gene variants may probably be associated with ASD. The detailed mechanism needs to be studied further, which may involve lipid metabolism dysfunction in the brain.


Subject(s)
Animals , Autism Spectrum Disorder/genetics , Epilepsy/genetics , Male , Mice , Mutation , Mutation, Missense , Protein Kinases , /genetics , Whole Exome Sequencing
5.
Article in Chinese | WPRIM | ID: wpr-888396

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a sib pair featuring 17beta-hydroxysteroid dehydrogenase type 3 deficiency.@*METHODS@#Genomic DNA was extracted from the proband, her sister, and their parents, and was subjected to sequencing analysis with a gene panel for sexual development. Suspected variant was verified by Sanger sequencing and bioinformatic analysis.@*RESULTS@#Both the proband and her sister were found to harbor novel compound heterozygous missense variants of the HSD17B3 gene, namely c.839T>C (p.Leu280Pro) and c.239G>T (p.Arg80Leu), which were derived respectively from their mother and father. The variants were unreported previously and predicted to be deleterious by PolyPhen2, MutationTaster and other online software. Based on the American College of Medical Genetics and Genomics standards and guidelines, both c.839T>C(p.Leu280Pro) and c.239G>T (p.Arg80Leu) were predicted to be likely pathogenic (PM2+PP1+PP2+PP3+PP4, PM2+PM5+PP1+PP2+PP3+PP4).@*CONCLUSION@#The compound heterogeneous variants of the HSD17B3 gene probably underlay the disease in this sib pair. 17beta-hydroxysteroid dehydrogenase type 3 deficiency may lack specific clinical features and laboratory index, genetic testing can facilitate a definitive diagnosis.


Subject(s)
17-Hydroxysteroid Dehydrogenases/genetics , Female , Genetic Testing , Genomics , Humans , Mutation , Mutation, Missense
6.
Article in Chinese | WPRIM | ID: wpr-888360

ABSTRACT

OBJECTIVE@#To analyze the pathogenic variants of the KIF1A gene and its corresponding protein structure in an autism spectrum disorder (ASD) family trio carrying harmful missense variants in the KIF1A gene.@*METHODS@#The peripheral blood DNA of the patient and his parents was extracted and sequenced using whole exome sequencing (WES) technology and verified by Sanger sequencing. Bioinformatics software SIFT, PolyPhen-2, Mutation Taster, and CADD software were used to analyze the harmfulness and conservation of variants. The Human Brain Transcriptome (HBT) database was used to analyze the expression of the KIF1A gene in the brain. PredictProtein and SWISS-MODEL were further used to predict the secondary structure and tertiary structure of KIF1A wild-type protein and variant protein. PyMOL V2.4 was utilized to investigate the change of hydrogen bond connection after protein variant.@*RESULTS@#The WES sequencing revealed a missense variant c.664A>C (p.Asn222His) in the child's KIF1A gene, and this variant was a de novo variant. The harmfulness prediction results suggest that this variant is harmful. By analyzing expression level of KIF1A gene in the brain. It is found that KIF1A gene widely expressed in various brain regions during embryonic development. By analyzing the variant protein structure, the missense variant of KIF1A will cause many changes in the secondary structure of protein, such as alpha-helix, beta-strand, and protein binding domain. The connection of hydrogen bond and spatial structure will also change, thereby changing the original biological function.@*CONCLUSION@#The KIF1A gene may be a risk gene for ASD.


Subject(s)
Autism Spectrum Disorder/genetics , Child , Female , Humans , Kinesin/genetics , Mutation , Mutation, Missense , Pregnancy , Protein Domains , Whole Exome Sequencing
7.
Article in Chinese | WPRIM | ID: wpr-879564

ABSTRACT

OBJECTIVE@#To detect pathogenic variants in a pedigree affected with propionic acidemia (PA).@*METHODS@#The proband was subjected to high-throughput next-generation sequencing. Suspected variants were validated by Sanger sequencing of his family members. mRNA was extracted from peripheral blood lymphocytes from the proband's father in order to verify the impact of the splicing variant by RT-PCR combined with Sanger sequencing. The pathogenicity of the missense variant was predicted by using PolyPhen-2, Mutation Taster, SIFT, COBALT and HOPE software.@*RESULTS@#The proband was found to harbor compound heterozygous variants of the PCCB gene, namely c.184-2A>G and c.733G>A (p.G245S), which were respectively inherited from his father and mother. RT-PCR combined with Sanger sequencing confirmed skipping of exon 2 during transcription. Bioinformatic analysis indicated the c.733G>A (p.G245S) variant to be damaging.@*CONCLUSION@#The two variants of the PCCB gene probably underlay the disease in this patient. Above findings have enriched the spectrum of PCCB gene variants.


Subject(s)
Exons , Humans , Mutation , Mutation, Missense , Pedigree , Propionic Acidemia/genetics
8.
Article in Chinese | WPRIM | ID: wpr-879528

ABSTRACT

OBJECTIVE@#To detect variant of the CD40L gene and infection of Jamestown Canyon virus (JCV) in a 7-year-and-9-month-old boy with co-commitment progressive multifocal leukoencephalopathy (PML) and X-linked hyper IgM syndrome (XHIGM).@*METHODS@#Peripheral blood samples of the child and his parents were collected for the extraction of genomic DNA. The 5 exons and exon/intronic boundaries of the CD40L gene were subjected to PCR amplification and sequencing. Suspected variants were analyzed by using bioinformatic software. The JCV gene was amplified from genomic DNA by nested PCR and sequenced.@*RESULTS@#The child was found to harbor a hemizygous c.506 A>C (p.Y169S) missense variant in exon 5 of the CD40L gene. The variant may affect the TNFH domain of the CD40L protein and result in structural instability and loss of hydrophobic interaction between CD40L and CD40. As predicted by PolyPhen2 and SIFT software, the variant was probably damaging (score = 1.00) and deleterious (score= -8.868). His mother was found to be a heterozygous carrier, while the same variant was not found in his father. Gel electrophoresis of the nested PCR product revealed presence of target JCV band, which was confirmed to be 99% identical with the JCV gene by sequencing.@*CONCLUSION@#The patient was diagnosed with co-commitment XHIGM and PML based on the testing of the CD40L gene and JCV infection.


Subject(s)
Adult , CD40 Ligand/genetics , Child , Exons/genetics , Female , Humans , Hyper-IgM Immunodeficiency Syndrome, Type 1/genetics , Leukoencephalopathy, Progressive Multifocal/genetics , Male , Mutation, Missense , Polymerase Chain Reaction
9.
Article in Chinese | WPRIM | ID: wpr-879527

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a child with clinically suspected 3-methylcrotonyl-coenzyme A carboxylase deficiency (MCCD).@*METHODS@#Genomic DNA was extracted from peripheral blood samples of the proband and her parents. Whole exome sequencing was used to screen pathogenic variant in the proband. Suspected variant was verified by Sanger sequencing. Impact of the variant on the structure and function of protein product was analyzed by using bioinformatic software.@*RESULTS@#Sanger sequencing showed that the proband has carried homozygous missense c.1342G>A (p.Gly448Ala) variant of the MCCC2 gene, for which her mother was a heterozygous carrier. The same variant was not detected in her father. The variant was predicted to be pathogenic by PolyPhen-2 and Mutation Taster software, and the site was highly conserved among various species. Based on the American College of Medical Genetics and Genomics standards and guidelines, the c.1342G>A (p.Gly448Ala) variant of MCCC2 gene was predicted to be likely pathogenic(PM2+PP2-PP5).@*CONCLUSION@#The homozygous missense variant of the MCCC2 gene c.1342G>A (p.Gly448Ala) probably underlay the molecular pathogenesis of the proband. Genetic testing has confirmed the clinical diagnosis.


Subject(s)
Carbon-Carbon Ligases/genetics , Child , Female , Humans , Male , Mutation, Missense/genetics , Pedigree , Urea Cycle Disorders, Inborn/genetics
10.
Article in Chinese | WPRIM | ID: wpr-879521

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a Chinese pedigree affected with non-syndromic cleft lip and cleft palate (NSCLP).@*METHODS@#With informed consent obtained, members of the pedigree were subjected to clinical examination and history taking to exclude syndromic cleft lip and palate. One affected member was subjected to whole-exome sequencing and bioinformatics analysis. Candidate variant was verified by Sanger sequencing and co-segregation analysis of her family members and 100 unrelated healthy individuals.@*RESULTS@#Whole-exome sequencing and co-segregation analysis showed that all affected members of this pedigree have carried a heterozygous missense c.253A>G (p.Cys85Arg) variant in exon 4 of the IRF6 gene, which has co-segregated with the phenotype and was not found among the 100 unrelated healthy individuals.@*CONCLUSION@#The missense c.253A>G variant in exon 4 of the IRF6 gene probably underlay the NSCLP in this pedigree.


Subject(s)
Brain/abnormalities , China , Cleft Lip/genetics , Cleft Palate/genetics , Female , Humans , Interferon Regulatory Factors/genetics , Mutation, Missense , Pedigree , Whole Exome Sequencing
11.
Article in Chinese | WPRIM | ID: wpr-879514

ABSTRACT

OBJECTIVE@#To explore the molecular basis for an individual suspected as AwB subtype through DNA sequencing.@*METHODS@#ABO serology was carried out with the standard tube method. To identify the ABO gene haplotype, the amplicons of exon 7 were cloned and sequenced.@*RESULTS@#Serological results showed that the forward typing was AwB and the reverse typing was B. Sequencing analysis revealed that the sample has contained an O01 allele in addition with c.297A>G, c.657C>T, c.796C>A, c.803G>C, c.930G>A variants as compared with the A101 allele.@*CONCLUSION@#Through sequencing analysis, the sample with an AwB subtype by serological testing was identified as a novel B(A) phenotype, which was unreported previously.


Subject(s)
ABO Blood-Group System/genetics , Alleles , Base Sequence , Exons/genetics , Humans , Mutation, Missense , Phenotype
12.
Rev. chil. pediatr ; 91(5): 761-766, oct. 2020. tab
Article in Spanish | LILACS | ID: biblio-1144276

ABSTRACT

INTRODUCCIÓN: La asociación de casos familiares de epilepsia y discapacidad intelectual (DI) en mujeres fue reportada en 1971. El año 2008, se identificó el rol de variantes patogénicas del gen PCDH19 en algunas familias. La enfermedad se presenta con crisis febriles en cluster, DI y rasgos autistas. La mayoría se debe a variantes de novo, pero hay algunos casos heredados por un modo peculiar de transmisión ligada X. OBJETIVO: Comunicar el caso de una paciente con epilepsia portadora de una variante patogénica en el gen PCDH1 9, revisando la historia natural de la enfermedad y la evidencia disponible para su manejo. CASO CLÍNICO: Paciente femenina, con antecedentes de embarazo y período perinatal normal. A los 6 meses, estando febril, presentó crisis focales motoras en cluster que repitieron a los 14, 18, 21 meses y 3 años siempre asociadas a fiebre, presentando incluso estatus epiléptico. Mantiene biterapia con topiramato y ácido valproico, completando 13 años sin crisis. El estudio del gen SCN1A no mostró anomalías y el estudio del gen PCDH19 reveló una variante patogénica en heterocigosis, "de novo". La paciente ha evolucionado con DI y alteraciones conductuales severas que requieren aten ción de salud mental. CONCLUSIONES: Las variantes patogénicas PCDH19 tienen expresión fenotípica variada. El diagnóstico genético debe sospecharse con la clínica. La morbilidad psiquiátrica a largo plazo puede ser incapacitante.


INTRODUCTION: The association of family cases of epilepsy and intellectual disability in women was reported in 1971. In 2008, the role of pathogenic variants of the PCDH19 gene in some families were identified. The disease presents with febrile seizure clusters, intellectual disability, and autistic features. Most cases are due to de novo variants, however, there are some inherited cases, with an atypical way of X-linked transmission. OBJECTIVE: To report the case of a patient with epilepsy carrier of a pathogenic variant of the PCDH19 gene, reviewing the natural history of this condition and the available evidence for its management. CLINICAL CASE: Female patient, with normal history of pregnancy and perinatal period. At 6 months, while febrile, she presented focal motor seizure clusters that repeated at 14, 18, 21 months and 3 years old, always associated with fever, even presenting status epilepticus. She is on therapy with topiramate and valproic acid, achieving 13 seizure-free years. The analysis of the SCN1A gene showed no abnormalities and the study of the PCDH19 gene revealed a de novo heterozygous pathogenic variant. The patient evolved with intellectual disability and severe behavioral disorders that require mental health team support. CONCLUSIONS: PCDH19 pathogenic variants have varied phenotypic expression. The genetic diagnosis should be guided with the clinical features. Long-term psychiatric morbidity can be disabling.


Subject(s)
Humans , Female , Adolescent , Cadherins/genetics , Mutation, Missense , Epilepsy/genetics , Intellectual Disability/genetics , Genetic Markers , Diagnosis, Differential , Epilepsy/complications , Epilepsy/diagnosis , Heterozygote , Intellectual Disability/complications , Intellectual Disability/diagnosis
13.
Article in Chinese | WPRIM | ID: wpr-826539

ABSTRACT

OBJECTIVE@#To detect pathogenic variant in a juvenile with severe type Cornelia de Lange syndrome (CdLS).@*METHODS@#A 12-year-old female presented with comprehensive developmental retardation and deformity of lower limbs. Genomic DNA was extracted from peripheral blood sample of the patient. Whole exome sequencing was performed to identify pathogenic variants. Putative variant was verified by Sanger sequencing. The impact of variants was predicted and validated by bioinformatic analysis.@*RESULTS@#A de novo missense variant, c.1507A>G (p. Lys503Glu), was found in the NIPBL gene of the proband. The variant was unreported previously and predicted to be pathogenic by PolyPhen-2, MutationTaster and SIFT. Using HomoloGene system, the 503 loci in the NIPBL protein are highly conserved. The change of amino acid (Glu), locating in 503 locus, was found to cause the Neuromodulin_N superfamily domain destroyed, resulting in severe damage to the function of NIPBL protein.@*CONCLUSION@#The de novo missense variant c.1507A>G (p. Lys503Glu) of the NIPBL gene probably underlies the disease in this patient.


Subject(s)
Cell Cycle Proteins , Genetics , Child , De Lange Syndrome , Genetics , Developmental Disabilities , Genetics , Female , Humans , Mutation, Missense , Phenotype
15.
Article in Chinese | WPRIM | ID: wpr-879497

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a pedigree affected with X-linked recessive mental retardation Claes-Jensen type.@*METHODS@#Genomic DNA was extracted from peripheral blood samples of the patient, his parents (phenotypically normal) and two elder brothers with similar clinical manifestations. Whole exome sequencing was carried out for the proband, and the result was verified by Sanger sequencing.@*RESULTS@#The proband was found to harbor a hemizygous c.1565C>T missense variant in exon 11 of the KDM5C gene. The transition has resulted in replacement of serine by phenylalanine at position 522 (p.Ser522Phe). Sanger sequencing showed that the patient's two elder brothers and mother carried the same variant, which was predicted to be probably damaging by SIFT, PolyPhen2 and Mutation_Taster. The three affected brothers presented with similar clinical phenotypes characterized by mental retardation, speech delay, behavioral problem, self-limited epilepsy responsible to medication, short stature and microcephaly. The mother only had mild cognitive impairment and learning disability. The same variant was not found in their father and was unreported previously.@*CONCLUSION@#The c.1565C>T (p.Ser522Phe) of the KDM5C gene probably underlay the X-linked recessive mental retardation Claes-Jensen type in this pedigree.


Subject(s)
Aged , Female , Histone Demethylases/genetics , Humans , Male , Mental Retardation, X-Linked/pathology , Mutation, Missense/genetics , Pedigree , Phenotype , Whole Exome Sequencing
16.
Pesqui. bras. odontopediatria clín. integr ; 19(1): 4709, 01 Fevereiro 2019. ilus
Article in English | LILACS, BBO | ID: biblio-998221

ABSTRACT

Objective: To determine the DUSP6 gene mutation in three generations of Malaysian Malay subjects having Class III malocclusion. Material and Methods: Genetic analyses of DUSP6 gene were carried out in 30 subjects by selecting three individuals representing three generations, respectively, from ten Malaysian Malay families having Class III malocclusion and 30 healthy controls. They were submitted Clinical Evaluation to clinical examination, lateral cephalometric radiographs, dental casts, and/ or facial and intra-oral photographs. Buccal cell was taken from each participant of Class III malocclusion and control groups. DNA extractions from buccal cell were carried out using Gentra puregene buccal cell kit. Bio Edit Sequence Alignment Editor software was used to see the sequencing result. Results: A heterozygous missense mutation c.1094C>T (p. Thr 365 Ile) was identified in DUSP6 gene in three members of one family with Class III malocclusion, whereas no mutation was found in the control group. Conclusion: Current study successfully identified a missense mutation in DUSP6 gene among one Malaysian Malay family affected by Class III malocclusion. The outcome of this study broadened the mutation spectrum of Class III malocclusion and the importance of DUSP6 gene in skeletal functions.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Genetic Variation/genetics , Cephalometry/methods , Mutation, Missense , Malocclusion , Arabia , Case-Control Studies , Photography, Dental/instrumentation
17.
Article in English | WPRIM | ID: wpr-763180

ABSTRACT

PURPOSE: Partner and localizer of BRCA2 (PALB2) is a breast cancer susceptibility gene that plays an important role in DNA repair. This is the first study assessing the prevalence of PALB2 mutations in early-onset and familial breast/ovarian cancer patients from Pakistan. MATERIALS AND METHODS: PALB2 mutation screening was performed in 370 Pakistani patients with early-onset and familial breast/ovarian cancer, who were negative for BRCA1, BRCA2, TP53, CHEK2, and RAD51C mutations, using denaturing high-performance liquid chromatography analysis. Mutations were confirmed by DNA sequencing. Novel PALB2 alterations were analyzed for their potential effect on protein function or splicing using various in silico prediction tools. Three-hundred and seventy-two healthy controls were screened for the presence of the identified (potentially) functional mutations. RESULTS: A novel nonsense mutation, p.Y743*, was identified in one familial breast cancer patient (1/127, 0.8%). Besides, four in silico-predicted potentially functional mutations including three missense mutations and one 5' untranslated region mutation were identified: p.D498Y, novel p.G644R, novel p.E744K, and novel c.-134_-133delTCinsGGGT. The mutations p.Y743* and p.D498Y were identified in two familial patients diagnosed with unilateral or synchronous bilateral breast cancer at the ages of 29 and 39, respectively. The other mutations were identified in an early-onset (≤ 30 years of age) breast cancer patient each. All five mutations were absent in 372 healthy controls suggesting that they are disease associated. CONCLUSION: Our findings show that PALB2 mutations account for a small proportion of early-onset and hereditary breast/ovarian cancer cases in Pakistan.


Subject(s)
5' Untranslated Regions , Breast Neoplasms , Chromatography, Liquid , Codon, Nonsense , Computer Simulation , DNA Repair , Germ-Line Mutation , Humans , Mass Screening , Mutation, Missense , Pakistan , Prevalence , Sequence Analysis, DNA
18.
Article in English | WPRIM | ID: wpr-761870

ABSTRACT

Concomitant Loeys-Dietz syndrome (LDS) and hematologic malignancies are exceptionally rare. This is the first report of a patient operated on for aortic root dilation who had been previously diagnosed with LDS and B-cell-lymphoma. After completion of chemotherapy and complete remission, an elective valve-sparing aortic root replacement (using the David-V method) was performed. Due to the positive family history, pre-operative genetic counseling was conducted, and revealed LDS with a TGFBR1 (transforming growth factor beta receptor type I) mutation in 6 probands of the family, albeit in 1 of them posthumously. This missense mutation has been previously described in relation to aortic dissection, but a causative relationship to malignancy has so far neither been proposed nor proven.


Subject(s)
Aortic Aneurysm, Thoracic , Drug Therapy , Genetic Counseling , Hematologic Neoplasms , Humans , Loeys-Dietz Syndrome , Lymphoma, B-Cell , Mutation, Missense
19.
Article in Korean | WPRIM | ID: wpr-766770

ABSTRACT

Congenital fiber type disproportion (CFTD) has been related with mutations in ACTA1, SEPN1, RYR1 and tropomyosin 3 (TPM3) genes. Particularly, TPM3 mutation was identified as one of the most frequent cause of CFTD and was also detected in cap myopathy and nemaline myopathy. Herein we report patients of autosomal dominant TPM3 missense mutations with CFTD in a Korean family over twogenerations. Two of our patients, who developed mild muscle weakness in infancy, presented with altered mentality and respiratory distress despite relatively mild limb weakness.


Subject(s)
Extremities , Humans , Muscle Weakness , Muscular Diseases , Mutation, Missense , Myopathies, Nemaline , Myopathies, Structural, Congenital , Respiratory Insufficiency , Ryanodine Receptor Calcium Release Channel , Tropomyosin
20.
Article in English | WPRIM | ID: wpr-766018

ABSTRACT

BACKGROUND: Most triple-negative breast cancers (TNBCs) have a high histologic grade, are associated with high endoplasmic stress, and possess a high frequency of TP53 mutations. TP53 missense mutations lead to the production of mutant p53 protein and usually show high levels of p53 protein expression. Tumor-infiltrating lymphocytes (TILs) accumulate as part of the anti-tumor immune response and have a strong prognostic and predictive significance in TNBC. We aimed to elucidate the association between p53 expression and the amount of TILs in TNBC. METHODS: In 678 TNBC patients, we evaluated TIL levels and expression of endoplasmic stress molecules. Immunohistochemical examination of p53 protein expression was categorized into three groups: no, low, and high expression. RESULTS: No, low, and high p53 expression was identified in 44.1% (n = 299), 20.1% (n = 136), and 35.8% (n = 243) of patients, respectively. Patients with high p53 expression showed high histologic grade (p < .001), high TIL levels (p = .009), and high expression of endoplasmic reticulum stress-associated molecules (p-eIF2a, p = .013; XBP1, p = .007), compared to patients with low p53 expression. There was no significant difference in disease-free (p = .406) or overall survival rates (p = .444) among the three p53 expression groups. CONCLUSIONS: High p53 expression is associated with increased expression of endoplasmic reticulum stress molecules and TIL influx.


Subject(s)
Breast Neoplasms , Endoplasmic Reticulum , Endoplasmic Reticulum Stress , Humans , Lymphocytes, Tumor-Infiltrating , Mutation, Missense , Survival Rate , Triple Negative Breast Neoplasms
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