Read by QxMD icon Read

In silico analysis missense mutation

Gabrielle Bradshaw, Robbie R Lualhati, Cassie L Albury, Neven Maksemous, Deidre Roos-Araujo, Robert A Smith, Miles C Benton, David A Eccles, Rod A Lea, Heidi G Sutherland, Larisa M Haupt, Lyn R Griffiths
Background: We investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood. Aim: To identify causative functional genetic variants related to an undiagnosed primary immunodeficiency. Method: Whole genome microarray copy number variant (CNV) analysis was performed on the proband followed by whole exome sequencing (WES) and trio analysis of the proband and family members...
2018: Frontiers in Immunology
Paolo Miotto, Andrea M Cabibbe, Emanuele Borroni, Massimo Degano, Daniela M Cirillo
Low-level rifampicin resistance associated with specific rpoB mutations (referred as "disputed") in Mycobacterium tuberculosis is easily missed by some phenotypic methods. To understand the mechanism by which some mutations are systematically missed by MGIT phenotypic testing we performed an in silico analysis of their effect on the structural interaction between the RpoB protein and rifampicin. We also characterized 24 representative clinical isolates by determining minimum inhibitory concentrations (MICs) on 7H10 agar, and testing them by an extended MGIT protocol...
March 14, 2018: Journal of Clinical Microbiology
Masoud Tajamolian, Parisa Kolahdouz, Parvaneh Nikpour, Seyed Khalil Forouzannia, Mohammad Hasan Sheikhha, Ehsan Farashahi Yazd
Background: Familial hypercholesterolemia (FH) is a disorder that is inherited by autosomal dominant pattern. The main cause of FH disease is the occurrence of mutations in low-density lipoprotein receptor (LDLR) gene sequence, as well as apolipoprotein B and proprotein convertase subtilisin/kexin type 9 genes, located in the next ranks, respectively. Materials and Methods: Forty-five unrelated Iranian patients with FH were screened using a high-resolution melting (HRM) method for exon 9 along with intron/exon boundaries of LDLR gene...
2018: Advanced Biomedical Research
Maria Carolina Costa Melo Svidnicki, Andrey Santos, Jhonathan Angel Araujo Fernandez, Ana Paula Hitomi Yokoyama, Isis Quezado Magalhães, Vitoria Regia Pereira Pinheiro, Silvia Regina Brandalise, Paulo Augusto Achucarro Silveira, Fernando Ferreira Costa, Sara Teresinha Olalla Saad
BACKGROUND: Pyruvate kinase deficiency is a hereditary disease that affects the glycolytic pathway of the red blood cell, causing nonspherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait and shows a marked variability in clinical expression. This study reports on the molecular characterization of ten Brazilian pyruvate kinase-deficient patients and the genotype-phenotype correlations. METHOD: Sanger sequencing and in silico analysis were carried out to identify and characterize the genetic mutations...
January 2018: Revista Brasileira de Hematologia e Hemoterapia
Isabella Tabaro, Giuseppe Reimondo, Giangiacomo Osella, Caterina Aurizi, Pasquale Caraci, Luca Barbieri, Daniela Francesca Giachino, Fabio Sirchia, Massimo Terzolo
PURPOSE: Acute porphyrias are metabolic disorders of heme biosynthesis characterized by acute life-threatening attacks. The diagnosis is often missed since clinical presentation is aspecific mimicking other medical and surgical conditions. Variegate porphyria (VP) is an autosomal dominant inherited disease with incomplete penetrance due to decreased activity of the Protoporphyrinogen Oxydase (PPOX) gene; most VP mutations are family specific. We report the case of a 40 year-old woman who presented many times to the emergency department complaining of unexplained abdominal pain and laboratory investigations showed repeatedly hyponatremia...
March 7, 2018: Endocrine
Hwal Rim Jeong, Hae Sang Lee, Jin Soon Hwang
BACKGROUND: Luteinizing hormone (LH) is a useful parameter in diagnosing precocious puberty. The pubertal response of serum LH to a GnRH stimulation test is varied, and clinical symptoms of precocious puberty are sometimes disproportionate with serum LH concentrations. Many patients present in a state of precocious puberty that advances rapidly, but the post-GnRH peak LH remains prepubertal. LH receptor mutations are suspected of involvement in the non-classic type of central precocious puberty (CPP)...
March 5, 2018: Experimental and Clinical Endocrinology & Diabetes
Rhonda Flores, Peng Zhang, Wei Wu, Xu Wang, Peiying Ye, Pan Zheng, Yang Liu
A recent meta-analysis revealed the contribution of the SIGLEC6 locus to the risk of developing systemic lupus erythematosus (SLE). However, no specific Siglec (sialic acid-binding immunoglobulin-like lectin) genes (Siglecs) have been implicated in the pathogenesis of SLE. Here, we performed in silico analysis of the function of three major protective alleles in the locus and found that these alleles were expression quantitative trait loci that enhanced expression of the adjacent SIGLEC12 gene. These data suggest that SIGLEC12 may protect against the development of SLE in Asian populations...
March 5, 2018: Cellular & Molecular Immunology
Marcel F Glaas, Constanze Wiek, Linda-Maria Wolter, Katharina Roellecke, Vera Balz, Vera Okpanyi, Martin Wagenmann, Thomas Karl Hoffmann, Rene Grässlin, Christian Plettenberg, Jörg Schipper, Helmut Hanenberg, Kathrin Scheckenbach
BACKGROUND/AIM: Head and neck squamous cell carcinomas (HNSCCs) form a heterogeneous tumor entity located throughout the oral cavity, pharynx and larynx that is caused predominantly by chemically or virally induced carcinogenesis. Heterozygous germline mutations in cancer susceptibility genes might also lead to increased incidence of HNSCCs. As DNA stability is typically impaired in HNSCC cells and genes of the Fanconi anemia/BRCA DNA repair pathway can be mutated or down-regulated in HNSCCs, we investigated here whether germline mutations occur in the X-chromosomal FANCB as candidate gene...
March 2018: Anticancer Research
Yuan-Yuan Qin, Ai-Qiu Wei, Qing-Wen Shan, Xiao-Ying Xian, Yang-Yang Wu, Lin Liao, Jie Yan, Zhan-Feng Lai, Fa-Quan Lin
BACKGROUND: Severe hypertriglyceridemia usually results from a combination of genetic and environmental factors and is most often attributable to mutations in the lipoprotein lipase (LPL) gene. OBJECTIVES: The aim of this study was to identify rare mutations in the LPL gene causing severe hypertriglyceridemia. METHODS: A Chinese infant who presented classical features of severe hypertriglyceridemia recruited for DNA sequencing of the LPL gene...
February 25, 2018: Journal of Clinical Laboratory Analysis
Nair Gopinathan Vidya, Sankaranarayanan Rajkumar, Abhay R Vasavada
BACKGROUND: Mutation in eye developmental genes has been reported to cause anophthalmia and microphthalmia. However, in India, especially in the Western Indian population, such reports are scarce. Hence, the present study aims to investigate mutations in 15 ocular developmental genes in patients with anophthalmia and microphthalmia in the western region of India. MATERIALS AND METHODS: Genomic DNA was isolated from the blood of 52 individuals affected with microphthalmia and anophthalmia, and 50 healthy normal controls...
February 20, 2018: Ophthalmic Genetics
D Thirumal Kumar, P Sneha, Jennifer Uppin, S Usha, C George Priya Doss
Protein-protein interaction (PPI) helps in maintaining the cellular homeostasis. In particular, the homodimeric proteins play a crucial role as cell regulators. Studying the critical functions of each PPI on the living system is very challenging. The mutations in the PPIs have given birth to various diseases including many types of cancers and it has soon become the target for drug discovery. The mutations in IDH1, an asymmetric homodimer in the cytoplasm, leads to various diseases including gliomas. In this study, we have used extensive computational approaches to identify the impact of missense mutations (R132C, R132G, R132H, R132L, R132S, and V178I) occurring in the interacting region of the IDH1 homodimer...
2018: Advances in Protein Chemistry and Structural Biology
S Spena, I Garagiola, A Cannavò, M Mortarino, P M Mannucci, F R Rosendaal, F Peyvandi
BACKGROUND: The type of F8 mutation is the main predictor of inhibitor development in patients with severe hemophilia A. Mutations expected to allow a residual synthesis of FVIII are likely to play a protective role towards alloantibody development by inducing immune tolerance. According to the expected full or partial impairment of FVIII synthesis, F8 variants are commonly classified as null and non-null. OBJECTIVES: To explore the mutation type-inhibitor risk association in a cohort of 231 patients with severe hemophilia A enrolled in the SIPPET (Survey of Inhibitors in Plasma-Product Exposed Toddlers) randomized trial...
February 5, 2018: Journal of Thrombosis and Haemostasis: JTH
Bianna Cao, Yuanfeng Zeng, Fei Wu, Jun Liu, Zeliang Shuang, Xiaoyun Xu, Jiubai Guo
Endometriosis is an estrogen-dependent precancerous lesion exhibiting frequently perturbed level of steroid hormones and transcriptional‑regulating factor 1 (TRERF1) has a crucial role in the production of steroid hormones including estrogen. Endometriosis has previously been revealed to be a precancerous lesion that harbors somatic mutations in cancer‑associated genes. Therefore, the authors of the present study hypothesize that TRERF1 aberrations may be involved in the development of endometriosis. In the present study, endometriotic lesions and paired blood samples from 92 individuals with ovarian endometriosis were analyzed for the potential presence of TRERF1 mutations by sequencing the entire coding region and the corresponding intron‑exon boundaries of the TRERF1 gene...
January 26, 2018: Molecular Medicine Reports
Katrina A Andrews, David B Ascher, Douglas Eduardo Valente Pires, Daniel R Barnes, Lindsey Vialard, Ruth T Casey, Nicola Bradshaw, Julian Adlard, Simon Aylwin, Paul Brennan, Carole Brewer, Trevor Cole, Jackie A Cook, Rosemarie Davidson, Alan Donaldson, Alan Fryer, Lynn Greenhalgh, Shirley V Hodgson, Richard Irving, Fiona Lalloo, Michelle McConachie, Vivienne P M McConnell, Patrick J Morrison, Victoria Murday, Soo-Mi Park, Helen L Simpson, Katie Snape, Susan Stewart, Susan E Tomkins, Yvonne Wallis, Louise Izatt, David Goudie, Robert S Lindsay, Colin G Perry, Emma R Woodward, Antonis C Antoniou, Eamonn R Maher
BACKGROUND: Germline pathogenic variants in SDHB/SDHC / SDHD are the most frequent causes of inherited phaeochromocytomas/paragangliomas. Insufficient information regarding penetrance and phenotypic variability hinders optimum management of mutation carriers. We estimate penetrance for symptomatic tumours and elucidate genotype-phenotype correlations in a large cohort of SDHB/SDHC / SDHD mutation carriers. METHODS: A retrospective survey of 1832 individuals referred for genetic testing due to a personal or family history of phaeochromocytoma/paraganglioma...
January 31, 2018: Journal of Medical Genetics
Xavier Pillois, Pierre Peters, Karin Segers, Alan T Nurden
BACKGROUND: Studies on the inherited bleeding disorder, Glanzmann thrombasthenia (GT), have helped define the role of the αIIbβ3 integrin in platelet aggregation. Stable bent αIIbβ3 undergoes conformation changes on activation allowing fibrinogen binding and its taking an extended form. The αIIb genu assures the fulcrum of the bent state. Our goal was to determine how structural changes induced by missense mutations in the αIIb genu define GT phenotype. METHODS: Sanger sequencing of ITGA2B and ITGB3 in the index case followed by in silico modeling of all known GT-causing missense mutations extending from the lower part of the β-propeller, and through the thigh and upper calf-1 domains...
January 31, 2018: Molecular Genetics & Genomic Medicine
Jibin John, Aditya Sharma, Prachi Kukshal, Triptish Bhatia, Vishwajit L Nimgaonkar, Smita N Deshpande, B K Thelma
Candidate gene and genome-wide association study based common risk variant identification is being complemented by whole exome sequencing (WES)/whole genome sequencing based rare variant discovery in elucidation of genetic landscape of schizophrenia (SZ), a common neuropsychiatric disorder. WES findings of de novo mutations in case-parent trios have further implied genetic etiology, but do not explain the high genetic risk in general populations. Conversely, WES in multiplex families may be an insightful strategy for the identification of highly penetrant rare variants in SZ and possibly enhance our understanding of disease biology...
January 29, 2018: Schizophrenia Bulletin
Charles Addo-Quaye, Mitch Tuinstra, Nicola Carraro, Clifford Weil, Brian P Dilkes
The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS) treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive induced variants in next-generation sequencing data permits higher throughput variant detection with greater accuracy...
January 29, 2018: G3: Genes—Genomes—Genetics
Katalin Koczok, Gabriella Merő, Gabriella P Szabó, László Madar, Éva Gombos, Éva Ajzner, János András Mótyán, Tibor Hortobágyi, István Balogh
Mutations in the DMD gene lead to Duchenne and Becker muscular dystrophy (DMD/BMD). Missense mutations are rare cause of DMD/BMD. A six-month-old male patient presented with mild generalized muscle weakness, hypotonia, and delayed motor development. Dystrophinopathy was suspected because of highly elevated serum creatine kinase level (1497 U/L) and tiered DMD gene analysis was performed. Multiplex ligation-dependent probe amplification (MLPA) assay showed deletion of exon 4, which could not be confirmed by another method...
December 7, 2017: Neuromuscular Disorders: NMD
Wen-Bin He, Chao-Feng Tu, Qiang Liu, Lan-Lan Meng, Shi-Min Yuan, Ai-Xiang Luo, Fu-Sheng He, Juan Shen, Wen Li, Juan Du, Chang-Gao Zhong, Guang-Xiu Lu, Ge Lin, Li-Qing Fan, Yue-Qiu Tan
BACKGROUND: The genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown. OBJECTIVE: To identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family. METHODS: We performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family...
January 13, 2018: Journal of Medical Genetics
Yanjie Yu, Yingni Lin, Yuto Takasaki, Chenyao Wang, Hiroki Kimura, Jingrui Xing, Kanako Ishizuka, Miho Toyama, Itaru Kushima, Daisuke Mori, Yuko Arioka, Yota Uno, Tomoko Shiino, Yukako Nakamura, Takashi Okada, Mako Morikawa, Masashi Ikeda, Nakao Iwata, Yuko Okahisa, Manabu Takaki, Shinji Sakamoto, Toshiyuki Someya, Jun Egawa, Masahide Usami, Masaki Kodaira, Akira Yoshimi, Tomoko Oya-Ito, Branko Aleksic, Kinji Ohno, Norio Ozaki
In schizophrenia (SCZ) and autism spectrum disorder (ASD), the dysregulation of glutamate transmission through N-methyl-D-aspartate receptors (NMDARs) has been implicated as a potential etiological mechanism. Previous studies have accumulated evidence supporting NMDAR-encoding genes' role in etiology of SCZ and ASD. We performed a screening study for exonic regions of GRIN1, GRIN2A, GRIN2C, GRIN2D, GRIN3A, and GRIN3B, which encode NMDAR subunits, in 562 participates (370 SCZ and 192 ASD). Forty rare variants were identified including 38 missense, 1 frameshift mutation in GRIN2C and 1 splice site mutation in GRIN2D...
January 10, 2018: Translational Psychiatry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"