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Prediction of missense mutation

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https://www.readbyqxmd.com/read/28920005/the-frequency-of-neoantigens-per-somatic-mutation-rather-than-overall-mutational-load-or-number-of-predicted-neoantigens-per-se-is-a-prognostic-factor-in-ovarian-clear-cell-carcinoma
#1
Hirokazu Matsushita, Kosei Hasegawa, Katsutoshi Oda, Shogo Yamamoto, Akira Nishijima, Yuichi Imai, Kayo Asada, Yuji Ikeda, Takahiro Karasaki, Keiichi Fujiwara, Hiroyuki Aburatani, Kazuhiro Kakimi
Neoantigens derived from tumor-specific somatic mutations are excellent targets for anti-tumor immune responses. In ovarian clear cell carcinoma (OCCC), checkpoint blockade yields durable responses in a subset of patients. To approach the question of why only some patients respond, we first investigated neoantigen loads and immune signatures using exome sequencing and expression array data for 74 OCCC patients treated conventionally. Neither the number of missense mutations nor total predicted neoantigens assessed in the tumor correlated with clinical outcomes...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28912669/identification-of-novel-mutations-in-congenital-afibrinogenemia-patients-and-molecular-modeling-of-missense-mutations-in-pakistani-population
#2
Arshi Naz, Arijit Biswas, Tehmina Nafees Khan, Anne Goodeve, Nisar Ahmed, Nazish Saqlain, Shariq Ahmed, Ikram Din Ujjan, Tahir S Shamsi, Johannes Oldenburg
BACKGROUND: Congenital afibrinogenemia (OMIM #202400) is a rare coagulation disorder that was first described in 1920. It is transmitted as an autosomal recessive trait that is characterized by absent levels of fibrinogen (factor I) in plasma. Consanguinity in Pakistan and its neighboring countries has resulted in a higher number of cases of congenital fibrinogen deficiency in their respective populations. This study focused on the detection of mutations in fibrinogen genes using DNA sequencing and molecular modeling of missense mutations in all three genes [Fibrinogen gene alpha (FGA), beta (FGB) and gamma (FGG)] in Pakistani patients...
2017: Thrombosis Journal
https://www.readbyqxmd.com/read/28912018/association-between-germline-mutations-in-brf1-a-subunit-of-the-rna-polymerase-iii-transcription-complex-and-hereditary-colorectal-cancer
#3
Fernando Bellido, Nadine Sowada, Pilar Mur, Conxi Lázaro, Tirso Pons, Rafael Valdés-Mas, Marta Pineda, Gemma Aiza, Silvia Iglesias, José Luís Soto, Miguel Urioste, Trinidad Caldés, Milagros Balbín, Pilar Blay, Daniel Rueda, Mercedes Durán, Alfonso Valencia, Victor Moreno, Joan Brunet, Ignacio Blanco, Matilde Navarro, George A Calin, Guntram Borck, Xose S Puente, Gabriel Capellá, Laura Valle
BACKGROUND & AIMS: Although there is a genetic predisposition to colorectal cancer (CRC), few of the genes that affect risk have been identified. We performed whole-exome sequence analysis of individuals in a high-risk family without mutations in genes previously associated with CRC risk to identify variants associated with inherited CRC. METHODS: We collected blood samples from 3 relatives with CRC in Spain (65, 62 and 40 years old at diagnosis) and perfomed whole-exome sequence analyses...
September 11, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28911202/pathogenicity-of-a-novel-missense-variant-associated-with-choroideremia-and-its-impact-on-gene-replacement-therapy
#4
Simona Torriano, Nejla Erkilic, Valérie Faugère, Krishna Damodar, Christian P Hamel, Anne-Francoise Roux, Vasiliki Kalatzis
Choroideremia (CHM) is an inherited retinal dystrophy characterised by progressive degeneration of photoreceptors, retinal pigment epithelium (RPE) and underlying choroid. It is caused by loss-of-function mutations in CHM, which has an X-linked inheritance, and is thus an ideal candidate for gene replacement strategies. CHM encodes REP1, which plays a key role in the prenylation of Rab GTPases. We recently showed that an induced pluripotent stem cell (iPSc)-derived RPE model for CHM is fully functional and reproduces the underlying prenylation defect...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28911001/whole-exome-analysis-of-a-li-fraumeni-family-trio-with-a-novel-tp53-prd-mutation-and-anticipation-profile
#5
Sara Franceschi, Laura Spugnesi, Paolo Aretini, Francesca Lessi, Rosa Scarpitta, Alvaro Galli, Caterina Congregati, Maria Adelaide Caligo, Chiara Maria Mazzanti
Li-Fraumeni syndrome is a clinically heterogeneous familial cancer predisposition syndrome with autosomal-dominant inheritance caused by heterozygous germline mutations in the TP53 gene. We here analyze the genetic background of a family with a 4-year-proband presented with a Li-Fraumeni tumor. The mother developed breast cancer at age 37 and the proband died at age 8. We performed Sanger sequencing and whole-exome sequencing on peripheral blood DNA from proband and relatives. Data analysis selected only high-quality score and depth reads, rare variants and protein impact involving missense, non-sense, frameshift and splice disrupt mutations...
September 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28910730/pathogenic-and-likely-pathogenic-genetic-alterations-and-polymorphisms-in-growth-hormone-gene-gh1-and-growth-hormone-releasing-hormone-receptor-gene-ghrhr-in-a-cohort-of-isolated-growth-hormone-deficient-ighd-children-in-sri-lanka
#6
Tharmini Sundralingam, Kamani Hemamala Tennekoon, Shamya de Silva, Sumadee De Silva, Asanka Sudeshini Hewage
OBJECTIVE: Genetic alterations in GH1 and GHRHR genes are known to cause isolated growth hormone deficiency (IGHD). Of these, GHRHR codon 72 mutation has been reported to be highly prevalent in the Indian subcontinent, but among Sri Lankans its prevalence was low compared to reports from neighboring countries. The present study was therefore carried out to identify genetic alterations in the GH1 gene and rest of the GHRHR gene in a cohort of Sri Lankan IGHD patients who tested negative for GHRHR codon 72 mutation...
September 5, 2017: Growth Hormone & IGF Research
https://www.readbyqxmd.com/read/28906061/opposite-effect-of-polymorphic-mutations-on-the-electrostatic-aggregation-of-human-alanine-glyoxylate-aminotransferase-implications-for-the-pathogenesis-of-primary-hyperoxaluria-type-i
#7
Mirco Dindo, Carolina Conter, Barbara Cellini
Protein aggregates formation is the basis of several misfolding diseases, including those displaying loss-of-function pathogenesis. Although aggregation is often attributed to the population of intermediates exposing hydrophobic surfaces, the contribution of electrostatic forces has recently gained attention. Here we combined computational and in vitro studies to investigate the aggregation process of human peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme involved in glyoxylate detoxification...
September 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28905428/cost-effective-screening-of-dnmt3a-coding-sequence-identifies-somatic-mutation-in-pediatric-t-cell-acute-lymphoblastic-leukemia
#8
Bronisława Szarzyńska-Zawadzka, Maria Kosmalska, Łukasz Sędek, Alicja Sonsala, Magdalena Twardoch, Jerzy R Kowalczyk, Tomasz Szczepański, Michał Witt, Małgorzata Dawidowska
BACKGROUND AND OBJECTIVES: In pediatric T-cell acute lymphoblastic leukemia (T-ALL) risk assignment schemes preclude reliable prediction of outcome and thus new prognostic factors are needed. Mutations in DNMT3A are candidate prognostic and classification markers in adults with acute myeloid leukemia (AML) and T-ALL and thus were considered as candidates prognostic markers in pediatric T-ALL. PATIENTS AND METHODS: DNMT3A mutational status was investigated in 74 pediatric T-ALL samples collected at diagnosis...
September 14, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/28900455/diverse-pattern-of-gap-junction-beta-2-and-gap-junction-beta-4-genes-mutations-and-lack-of-contribution-of-dfnb21-dfnb24-dfnb29-and-dfnb42-loci-in-autosomal-recessive-nonsyndromic-hearing-loss-patients-in-hormozgan-iran
#9
Masoud Akbarzadeh Laleh, Marzieh Naseri, Ali Akbar Poursadegh Zonouzi, Ahmad Poursadegh Zonouzi, Marjan Masoudi, Najmeh Ahangari, Leila Shams, Azim Nejatizadeh
BACKGROUND: We aimed to determine the contribution of four DFNB loci and mutation analysis of gap junction beta-2 (GJB2) and GJB4 genes in autosomal recessive nonsyndromic hearing loss (ARNSHL) in South of Iran. MATERIALS AND METHODS: A total of 36 large ARNSHL pedigrees with at least two affected subjects were enrolled in the current study. The GJB2 and GJB4 genes mutations were screened using direct sequencing method. The GJB2 and GJB4 negative families were analyzed for the linkage to DFNB21, DFNB24, DFNB29, and DFNB42 loci by genotyping the corresponding STR markers using polymerase chain reaction-PAGE method...
2017: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
https://www.readbyqxmd.com/read/28900022/binding-of-nad-glycohydrolase-to-streptolysin-o-stabilizes-both-toxins-and-promotes-virulence-of-group-a-streptococcus
#10
Jorge J Velarde, Maghnus O'Seaghdha, Buket Baddal, Benedicte Bastiat-Sempe, Michael R Wessels
The globally dominant, invasive M1T1 strain of group A Streptococcus (GAS) harbors polymorphisms in the promoter region of an operon that contains the genes encoding streptolysin O (SLO) and NAD(+)-glycohydrolase (NADase), resulting in high-level expression of these toxins. While both toxins have been shown experimentally to contribute to pathogenesis, many GAS isolates lack detectable NADase activity. DNA sequencing of such strains has revealed that reduced or absent enzymatic activity can be associated with a variety of point mutations in nga, the gene encoding NADase; a commonly observed polymorphism associated with near-complete abrogation of activity is a substitution of aspartic acid for glycine at position 330 (G330D)...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28898547/hlx-is-a-candidate-gene-for-a-pattern-of-anomalies-associated-with-congenital-diaphragmatic-hernia-short-bowel-and-asplenia
#11
Sandra A Farrell, Sandi Sodhi, Christian R Marshall, Andrea Guerin, Anne Slavotinek, Tara Paton, Karen Chong, Wilma L Sirkin, Stephen W Scherer, Félix-Antoine Bérubé-Simard, Nicolas Pilon
Isolated congenital diaphragmatic hernia is often a sporadic event with a low recurrence risk. However, underlying genetic etiologies, such as chromosome anomalies or single gene disorders, are identified in a small number of individuals. We describe two fetuses with a unique pattern of multiple congenital anomalies, including diaphragmatic hernia, short bowel and asplenia, born to first-cousin parents. Whole exome sequencing showed that both were homozygous for a missense variant, c.950A>C, predicting p...
September 12, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28895081/novel-de-novo-kcnd3-mutation-in-a-japanese-patient-with-intellectual-disability-cerebellar-ataxia-myoclonus-and-dystonia
#12
Masanori Kurihara, Hiroyuki Ishiura, Takuya Sasaki, Juuri Otsuka, Toshihiro Hayashi, Yasuo Terao, Takashi Matsukawa, Jun Mitsui, Juntaro Kaneko, Kazutoshi Nishiyama, Koichiro Doi, Jun Yoshimura, Shinichi Morishita, Jun Shimizu, Shoji Tsuji
Spinocerebellar ataxia 19/22 (SCA19/22) is a rare type of autosomal dominant SCA that was previously described in 11 families. We report the case of a 30-year-old Japanese man presenting with intellectual disability, early onset cerebellar ataxia, myoclonus, and dystonia without a family history. MRI showed cerebellar atrophy, and electroencephalograms showed paroxysmal sharp waves during hyperventilation and photic stimulation. Trio whole-exome sequencing analysis of DNA samples from the patient and his parents revealed a de novo novel missense mutation (c...
September 11, 2017: Cerebellum
https://www.readbyqxmd.com/read/28892125/novel-spondyloepimetaphyseal-dysplasia-due-to-ufsp2-gene-mutation
#13
M Di Rocco, M Rusmini, F Caroli, A Madeo, M Bertamino, G Marre-Brunenghi, I Ceccherini
Beukes Hip Dysplasia is an autosomal dominant disease which has to date been described only in a large South African family of Dutch origin. The patients presented with progressive epiphyseal dysplasia limited to femoral capital epiphysis and their height was not significantly reduced. A unique variant of the ubiquitin-fold modifier 1 (Ufm1)-specific peptidase 2 (UFSP2) gene (c.868T>C) has been reported in all individuals from Beukes family with clinical and radiological diagnosis of Beukes Hip Dysplasia...
September 11, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28887320/p53-gain-of-function-mutations-increase-cdc7-dependent-replication-initiation
#14
Arindam Datta, Dishari Ghatak, Sumit Das, Taraswi Banerjee, Anindita Paul, Ramesh Butti, Mahadeo Gorain, Sangeeta Ghuwalewala, Anirban Roychowdhury, Sk Kayum Alam, Pijush Das, Raghunath Chatterjee, Maitrayee Dasgupta, Chinmay Kumar Panda, Gopal C Kundu, Susanta Roychoudhury
Cancer-associated p53 missense mutants confer gain of function (GOF) and promote tumorigenesis by regulating crucial signaling pathways. However, the role of GOF mutant p53 in regulating DNA replication, a commonly altered pathway in cancer, is less explored. Here, we show that enhanced Cdc7-dependent replication initiation enables mutant p53 to confer oncogenic phenotypes. We demonstrate that mutant p53 cooperates with the oncogenic transcription factor Myb in vivo and transactivates Cdc7 in cancer cells...
September 8, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28886269/loss-of-function-grhl3-variants-detected-in-african-patients-with-isolated-cleft-palate
#15
M A Eshete, H Liu, M Li, W L Adeyemo, L J J Gowans, P A Mossey, T Busch, W Deressa, P Donkor, P B Olaitan, B S Aregbesola, R O Braimah, G O Oseni, F Oginni, R Audu, C Onwuamah, O James, E Augustine-Akpan, L A Rahman, M O Ogunlewe, F K N Arthur, S A Bello, P Agbenorku, P Twumasi, F Abate, T Hailu, Y Demissie, A Hailu, G Plange-Rhule, S Obiri-Yeboah, M M Dunnwald, P E Gravem, M L Marazita, A A Adeyemo, J C Murray, R A Cornell, A Butali
In contrast to the progress that has been made toward understanding the genetic etiology of cleft lip with or without cleft palate, relatively little is known about the genetic etiology for cleft palate only (CPO). A common coding variant of grainyhead like transcription factor 3 ( GRHL3) was recently shown to be associated with risk for CPO in Europeans. Mutations in this gene were also reported in families with Van der Woude syndrome. To identify rare mutations in GRHL3 that might explain the missing heritability for CPO, we sequenced GRHL3 in cases of CPO from Africa...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28884921/survival-beyond-the-perinatal-period-expands-the-phenotypes-caused-by-mutations-in-gle1
#16
Edith Said, Jessica X Chong, Maja Hempel, Jonas Denecke, Paul Soler, Tim Strom, Deborah A Nickerson, Christian Kubisch, Michael J Bamshad, Davor Lessel
Mutations in GLE1 underlie Lethal Congenital Contracture syndrome (LCCS) and Lethal Arthrogryposis with Anterior Horn Cell Disease (LAAHD). Both LCCS and LAAHD are characterized by reduced fetal movements, congenital contractures, and a severe form of motor neuron disease that results in fetal death or death in the perinatal period, respectively. We identified bi-allelic mutations in GLE1 in two unrelated individuals with motor delays, feeding difficulties, and respiratory insufficiency who survived beyond the perinatal period...
September 8, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28879565/comparative-computational-assessment-of-the-pathogenicity-of-mutations-in-the-aspartoacylase-enzyme
#17
C George Priya Doss, Hatem Zayed
Aspartoacylase (ASPA) is a zinc-dependent abundant enzyme in the brain, which catalyzes the conversion of N-acetyl aspartate (NAA) into acetate and aspartate. Mutations in the ASPA gene are associated with the development of Canavan disease (CD), leading to the deficiency of ASPA activity. Patients with CD were characterized by degeneration of the white matter of the brain. We reported earlier on two patients with severe form of CD that both had two novel missense mutations in the ASPA: c.427 A > G; p. I143V and c...
September 6, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28875386/novel-spg20-mutation-in-an-extended-family-with-troyer-syndrome
#18
S Bizzari, A R Hamzeh, P Nair, M Mohamed, F Saif, G Aithala, M T Al-Ali, F Bastaki
Troyer Syndrome (TRS) is a rare autosomal recessive complicated spastic paraplegia disorder characterized by various neurological and musculoskeletal manifestations. Pathogenicity stems from mutations in SPG20 which encodes Spartin, a multifunctional protein that is thought to be essential for neuron viability. Here we report on the clinical and molecular characterization of TRS in five patients from an extended consanguineous family in the United Arab Emirates. Molecular analysis involved Whole Exome Sequencing and Sanger sequencing for identification and confirmation of the causative variant respectively...
September 5, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28870703/a-novel-mutation-at-antxr1-in-an-indian-patient-with-growth-retardation-alopecia-pseudoanodontia-optic-atrophy-syndrome
#19
Esita Chattopadhyay, Sandip Ghose, Anindita Ray, Nishat Anjum, Anjana Mazumdar, Bidyut Roy
OBJECTIVE: Growth retardation-alopecia-pseudoanodontia-optic atrophy (GAPO) syndrome (Online Mendelian Inheritance in Man [OMIM] ID 230740) is one of the rarest autosomal recessive syndromes. It is characterized by many phenotypes, including wide anterior fontanel, frontal bossing of the face, depressed nasal bridge, along with the 4 classic phenotypes contained in the name of the syndrome. Recent reports identified nonsense, missense, and splicing mutations at different exons of ANTXR1 responsible for GAPO syndrome in patients from different ethnic populations...
August 4, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/28867931/targeted-next-generation-sequencing-analysis-identifies-novel-mutations-in-families-with-severe-familial-exudative-vitreoretinopathy
#20
Xiao-Yan Huang, Hong Zhuang, Ji-Hong Wu, Jian-Kang Li, Fang-Yuan Hu, Yu Zheng, Laurent Christian Asker M Tellier, Sheng-Hai Zhang, Feng-Juan Gao, Jian-Guo Zhang, Ge-Zhi Xu
PURPOSE: Familial exudative vitreoretinopathy (FEVR) is a genetically and clinically heterogeneous disease, characterized by failure of vascular development of the peripheral retina. The symptoms of FEVR vary widely among patients in the same family, and even between the two eyes of a given patient. This study was designed to identify the genetic defect in a patient cohort of ten Chinese families with a definitive diagnosis of FEVR. METHODS: To identify the causative gene, next-generation sequencing (NGS)-based target capture sequencing was performed...
2017: Molecular Vision
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