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Human Mutation

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https://www.readbyqxmd.com/read/28220625/predicting-gene-expression-in-massively-parallel-reporter-assays-a-comparative-study
#1
Anat Kreimer, Haoyang Zeng, Matthew D Edwards, Yuchun Guo, Kevin Tian, Sunyoung Shin, Rene Welch, Michael Wainberg, Rahul Mohan, Nicholas A Sinnott-Armstrong, Yue Li, Gökcen Eraslan, Talal Bin Amin, Jonathan Goke, Nikola S Mueller, Manolis Kellis, Anshul Kundaje, Michael A Beer, Sunduz Keles, David K Gifford, Nir Yosef
In many human diseases, associated genetic changes tend to occur within non-coding regions, whose effect might be related to transcriptional control. A central goal in human genetics is to understand the function of such non-coding regions: Given a region that is statistically associated with changes in gene expression (expression Quantitative Trait Locus; eQTL), does it in fact play a regulatory role? And if so, how is this role "coded" in its sequence? These questions were the subject of the Critical Assessment of Genome Interpretation eQTL challenge...
February 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28185376/matchmaking-facilitates-the-diagnosis-of-an-autosomal-recessive-mitochondrial-disease-caused-by-biallelic-mutation-of-the-trna-isopentenyltransferase-trit1-gene
#2
Kristin D Kernohan, David A Dyment, Mihaela Pupavac, Zvi Cramer, Arran McBride, Genevieve Bernard, Isabella Straub, Martine Tetreault, Taila Hartley, Lijia Huang, Erick Sell, Jacek Majewski, David S Rosenblatt, Eric Shoubridge, Aziz Mhanni, Tara Myers, Virginia Proud, Samanta Vergano, Brooke Spangler, Emily Farrow, Jennifer Kussman, Nicole Safina, Carol Saunders, Kym M Boycott, Isabelle Thiffault
Deleterious variants in the same gene present in 2 or more families with overlapping clinical features provides convincing evidence of a disease-gene association; this can be a challenge in the study of ultra-rare diseases. To facilitate the identification of additional families, several groups have created "matching" platforms. We describe four individuals from three unrelated families "matched" by GeneMatcher and MatchMakerExchange. Individuals had microcephaly, developmental delay, epilepsy and recessive mutations in TRIT1...
February 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28181337/deficiency-of-the-sphingosine-1-phosphate-lyase-sgpl1-is-associated-with-congenital-nephrotic-syndrome-and-congenital-adrenal-calcifications
#3
Andreas R Janecke, Ruijuan Xu, Elisabeth Steichen-Gersdorf, Siegfried Waldegger, Andreas Entenmann, Thomas Giner, Iris Krainer, Lukas A Huber, Michael W Hess, Yaacov Frishberg, Hila Barash, Shay Tzur, Nira Schreyer-Shafir, Rivka Sukenik-Halevy, Tania Zehavi, Annick Raas-Rothschild, Cungui Mao, Thomas Müller
We identified two unrelated consanguineous families with three children affected by the rare association of congenital nephrotic syndrome diagnosed in the first days of life, of hypogonadism, and of prenatally detected adrenal calcifications, associated with congenital adrenal insufficiency in one case. Using exome sequencing and targeted Sanger sequencing two homozygous truncating mutations, c.1513C>T (p.Arg505*) and c.934delC (p.Leu312Phefs*30), were identified in SGPL1 encoding sphingosine-1-phosphate lyase 1...
February 8, 2017: Human Mutation
https://www.readbyqxmd.com/read/28168870/annotation-of-functional-impact-of-voltage-gated-sodium-channel-mutations
#4
Valérie Hinard, Aurore Britan, Mathieu Schaeffer, Monique Zahn-Zabal, Urs Thomet, Jean-Sébastien Rougier, Amos Bairoch, Hugues Abriel, Pascale Gaudet
Voltage-gated sodium channels are pore-forming transmembrane proteins that selectively allow sodium ions to flow across the plasma membrane according to the electro-chemical gradient thus mediating the rising phase of action potentials in excitable cells and playing key roles in physiological processes such as neurotransmission, skeletal muscle contraction, heart rhythm and pain sensation. Genetic variations in the nine human genes encoding these channels are known to cause a large range of diseases affecting the nervous and cardiac systems...
February 7, 2017: Human Mutation
https://www.readbyqxmd.com/read/28150392/loss-of-function-mutations-in-kif15-underlying-a-braddock-carey-genocopy
#5
Patrick M A Sleiman, Michael March, Kenny Nguyen, Lifeng Tian, Renata Pellegrino, Cuiping Hou, Walid Dridi, Mohamed Sager, Yousef H Housawi, Hakon Hakonarson
Braddock-Carey Syndrome (BCS) is characterized by microcephaly, congenital thrombocytopenia the Pierre-Robin sequence (PRS) and agenesis of the corpus callosum. BCS has been shown to be caused by a 21q22.11 microdeletion that encompasses multiple genes. Here we report a BCS genocopy characterized by congenital thrombocytopenia and PRS that is caused by a loss of function mutation in KIF15 in a consanguineous Saudi Arabian family. Mutations of mitotic kinesins are a well established cause of microcephaly. To our knowledge KIF15 is the first kinesin to be associated with congenital thrombocytopenia...
February 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28150386/an-emerging-female-phenotype-with-loss-of-function-mutations-in-the-aristaless-related-homeodomain-transcription-factor-arx
#6
Tessa Mattiske, Ching Moey, Lisenka E Vissers, Natalie Thorne, Peter Georgeson, Madhura Bakshi, Cheryl Shoubridge
The devastating clinical presentation of X-linked lissencephaly with abnormal genitalia (XLAG) is invariably caused by loss of function mutations in the Aristaless-related homeobox (ARX) gene. Mutations in this X-chromosome gene contribute to intellectual disability (ID) with co-morbidities including seizures and movement disorders such as dystonia in affected males. The detection of affected females with mutations in ARX is increasing. We present a family with multiple affected individuals, including two females...
February 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28145000/filamin-b-loss-of-function-mutation-in-dimerization-domain-causes-autosomal-recessive-spondylocarpotarsal-synostosis-syndrome-with-rib-anomalies
#7
Chi-Fan Yang, Chung-Hsing Wang, Weng Siong H'ng, Chun-Ping Chang, Wei- De Lin, Yuan-Tsong Chen, Jer-Yuarn Wu, Fuu-Jen Tsai
Spondylocarpotarsal synostosis syndrome (SCT) is a distinct group of disorders characterized by short stature, disrupted vertebral segmentation with vertebral fusion, scoliosis, lordosis, carpal/tarsal synostosis, and lack of rib anomalies. Mutations in FLNB and MYH3 have been reported for autosomal recessive and autosomal dominant SCT, respectively. We present a family with two patients suffering from autosomal recessive SCT with rib anomalies, including malalignment, crowding, and uneven size and shape of ribs...
February 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28144995/axonal-neuropathies-due-to-mutations-in-small-heat-shock-proteins-clinical-genetic-and-functional-insights-into-novel-mutations
#8
Andoni Echaniz-Laguna, Thomas Geuens, Philippe Petiot, Yann Péréon, Elias Adriaenssens, Mansour Haidar, Simona Capponi, Thierry Maisonobe, Emmanuel Fournier, Odile Dubourg, Bertrand Degos, François Salachas, Timothée Lenglet, Bruno Eymard, Emilien Delmont, Jean Pouget, Raoul Morales, Cyril Goizet, Philippe Latour, Vincent Timmerman, Tanya Stojkovic
In this study, we describe the phenotypic spectrum of distal hereditary motor neuropathy caused by mutations in the small heat shock proteins HSPB1 and HSPB8 and investigate the functional consequences of newly discovered variants. Among 510 unrelated patients with distal motor neuropathy, we identified mutations in HSPB1 (28 index patients/510; 5.5%) and HSPB8 (4 index patients/510; 0.8%) genes. Patients have slowly progressive distal (100%) and proximal (13%) weakness in lower limbs (100%), mild lower limbs sensory involvement (31%), foot deformities (73%), progressive distal upper limb weakness (29%), mildly raised serum creatine kinase levels (100%) and central nervous system involvement (9%)...
February 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28120510/predicting%C3%A2-enhancer-activity-and-variant-impact-using-gkm-svm
#9
Michael A Beer
We participated in the Critical Assessment of Genome Interpretation eQTL challenge to further test computational models of regulatory variant impact and their association with human disease. Our prediction model is based on a discriminative gapped-kmer SVM (gkm-SVM) trained on genome-wide chromatin accessibility data in the cell type of interest. The comparisons with Massively Parallel Reporter Assays (MPRA) in lymphoblasts show that gkm-SVM is among the most accurate prediction models even though all other models used the MPRA data for model training, while gkm-SVM did not...
January 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28111830/mutations-in-the-human-argininosuccinate-synthetase-ass1-gene-impact-on-patients-common-changes-and-structural-considerations
#10
Carmen Diez-Fernandez, Véronique Rüfenacht, Johannes Häberle
Citrullinemia type 1 is an autosomal recessive urea cycle disorder caused by defects in the argininosuccinate synthetase (ASS) enzyme due to mutations in ASS1 gene. An impairment of ASS function can lead to a wide spectrum of phenotypes, from life-threatening neonatal hyperammonemia to a later onset with mild symptoms, and even some asymptomatic patients exhibiting an only biochemical phenotype. The disease is panethnic. In this update, we report 137 mutations (64 of which are novel), consisting of 89 missense mutations, 19 nonsense mutations, 17 mutations that affect splicing and 12 deletions...
January 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28106320/classification-of-genes-standardized-clinical-validity-assessment-of-gene-disease-associations-aids-diagnostic-exome-analysis-and-reclassifications
#11
Erica D Smith, Kelly Radtke, Mari Rossi, Deepali N Shinde, Sourat Darabi, Dima El-Khechen, Zöe Powis, Katherine Helbig, Kendra Waller, Dorothy K Grange, Sha Tang, Kelly D Farwell Hagman
Ascertaining a diagnosis through exome sequencing can provide potential benefits to patients, insurance companies, and the healthcare system. Yet as diagnostic sequencing is increasingly employed, vast amounts of human genetic data are produced that need careful curation. We discuss methods for accurately assessing the clinical validity of gene-disease relationships to interpret new research findings in a clinical context and increase the diagnostic rate. The specifics of a gene-disease scoring system adapted for use in a clinical laboratory are described...
January 20, 2017: Human Mutation
https://www.readbyqxmd.com/read/28102005/blind-prediction-of-deleterious-amino-acid-variations-with-snps-go
#12
Emidio Capriotti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
: SNPs&GO is a machine learning method for predicting the association of single amino acid variations (SAVs) to disease, considering protein functional annotation. The method is a binary classifier that implements a Support Vector Machine algorithm to discriminate between disease-related and neutral SAVs. SNPs&GO combines information from protein sequence with functional annotation encoded by Gene Ontology terms. Tested in sequence mode on more than 38,000 SAVs from the SwissVar dataset, our method reached 81% overall accuracy and an area under the receiving operating characteristic curve (AUC) of 0...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101991/clinically-distinct-phenotypes-of-canavan-disease-correlate-with-residual-aspartoacylase-enzyme-activity
#13
Marisa I Mendes, Desirée Ec Smith, Ana Pop, Pascal Lennertz, Matilde R Fernandez Ojeda, Warsha A Kanhai, Silvy J M van Dooren, Yair Anikster, Ivo Barić, Carolien Boelen, Jaime Campistol, Lonneke de Boer, Ariana Kariminejad, Hulya Kayserili, Agathe Roubertie, Krijn T Verbruggen, Christine Vianey-Saban, Monique Williams, Gajja S Salomons
We describe 14 patients with 12 novel missense mutations in ASPA, the gene causing Canavan disease (CD). We developed a method to study the effect of these 12 variants on the function of aspartoacylase - the hydrolysis of N-acetyl-L-aspartic acid (NAA) to aspartate and acetate. The wild-type ASPA open reading frame (ORF) and the ORFs containing each of the variants were transfected into HEK293 cells. Enzyme activity was determined by incubating cell lysates with NAA and measuring the released aspartic acid by LC-MS/MS...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101908/recurrent-rearrangements-of-human-amylase-genes-create-multiple-independent-cnv-series
#14
Nzar A A Shwan, Sandra Louzada, Fengtang Yang, John A L Armour
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of copy number variation (CNV) has only been defined in detail very recently. In this work we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A and AMY2B...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28087897/fgfr1-analyses-in-four-patients-with-hypogonadotropic-hypogonadism-with-split-hand-foot-malformation-implications-for-the-promoter-region
#15
Kohnosuke Ohtaka, Yasuko Fujisawa, Fumio Takada, Yukihiro Hasegawa, Tatsuya Miyoshi, Tomonobu Hasegawa, Hideaki Miyoshi, Hiraku Kameda, Misuzu Kurokawa Seo, Maki Fukami, Tsutomu Ogata
Heterozygous loss-of-function mutations of FGFR1 cause various disorders including hypogonadotropic hypogonadism with split-hand/foot malformation (HH-SHFM). We examined FGFR1 in four Japanese patients with HH-SHFM (cases 1-4) and the mother of case 4 with HH only. Cases 1 and 2 had heterozygous loss-of-function mutations with no dominant negative effect [c.289G>A, p.(G97S); and c.2231G>C, p.(R744T)], and case 3 had a splice donor site mutation [c.1663+1G>T]. Notably, case 4 had a maternally inherited 8,312 bp microdeletion that involved non-coding exon 1U and impaired FGFR1 expression...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28087895/crohn-disease-risk-prediction-best-practices-and-pitfalls-with-exome-data
#16
Manuel Giollo, David T Jones, Marco Carraro, Emanuela Leonardi, Carlo Ferrari, Silvio C E Tosatto
The Critical Assessment of Genome Interpretation (CAGI) experiment is the first attempt to evaluate the state-of-the-art in genetic data interpretation. Among the proposed challenges, Crohn disease (CD) risk prediction has become the most classic problem spanning three editions. The scientific question is very hard: can anybody assess the risk to develop CD given the exome data alone? This is one of the ultimate goals of genetic analysis, which motivated most CAGI participants to look for powerful new methods...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28074631/transdifferentiation-of-human-dermal-fibroblasts-to-smooth-muscle-like-cells-to-study-the-effect-of-myh11-and-acta2-mutations-in-aortic-aneurysms
#17
Kak K Yeung, Natalija Bogunovic, Niels Keekstra, Adriaan A M Beunders, Jorrit Pals, Kim van der Kuij, Eline Overwater, Willem Wisselink, Jan D Blankensteijn, Victor W M van Hinsbergh, Rene J P Musters, Gerard Pals, Dimitra Micha, Behrouz Zandieh-Doulabi
Mutations in genes encoding proteins of the smooth muscle cell (SMC) contractile apparatus contribute to familial aortic aneurysms. To investigate the pathogenicity of these mutations, SMC are required. We demonstrate a novel method to generate SMC-like cells from human dermal fibroblasts by transdifferentiation to study the effect of variants in genes encoding proteins of the SMC contractile apparatus (ACTA2 and MYH11) in patients with aortic aneurysms. Dermal fibroblasts from seven healthy donors and cells from seven patients with MYH11 or ACTA2 variants were transdifferentiated into SMC-like cells within a 2-week duration using 5 ng/ml TGFβ1 on a scaffold containing collagen and elastin...
January 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28074630/quantification-of-phenotype-information-aids-the-identification-of-novel-disease-genes
#18
Anneke T Vulto-van Silfhout, Christian Gilissen, Jelle J Goeman, Sandra Jansen, Claudia J M van Amen-Hellebrekers, Bregje W M van Bon, David A Koolen, Erik A Sistermans, Han G Brunner, Arjan P M de Brouwer, Bert B A de Vries
Next generation sequencing led to the identification of many potential novel disease genes. The presence of mutations in the same gene in multiple unrelated patients is, however, a priori insufficient to establish that these genes are truly involved in the respective disease. Here, we show how phenotype information can be incorporated within statistical approaches to provide additional evidence for the causality of mutations. We developed a broadly applicable statistical model that integrates gene-specific mutation rates, cohort size, mutation type and phenotype frequency information to assess the chance of identifying de novo mutations affecting the same gene in multiple patients with shared phenotype features...
January 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28074573/structural-functional-and-clinical-characterization-of-a-novel-ptpn11-mutation-cluster-underlying-noonan-syndrome
#19
Luca Pannone, Gianfranco Bocchinfuso, Elisabetta Flex, Cesare Rossi, Giuseppina Baldassarre, Christina Lissewski, Francesca Pantaleoni, Federica Consoli, Francesca Lepri, Monia Magliozzi, Massimiliano Anselmi, Giovanni Sorge, Kadri Karaer, Goran Cuturilo, Alessandro Sartorio, Sigrid Tinschert, Maria Accadia, Maria C Digilio, Giuseppe Zampino, Alessandro De Luca, Hélène Cavé, Martin Zenker, Bruce D Gelb, Bruno Dallapiccola, Lorenzo Stella, Giovanni B Ferrero, Simone Martinelli, Marco Tartaglia
Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu(261) , Leu(262) and Arg(265) in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling...
January 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28070986/predicting-severity-of-disease-causing-variants
#20
Abhishek Niroula, Mauno Vihinen
Most diseases, including those of genetic origin, express a continuum of severity. Clinical interventions for numerous diseases are based on the severity of the phenotype. Predicting severity due to genetic variants could facilitate diagnosis and choice of therapy. Although computational predictions have been used as evidence for classifying the disease-relevance of genetic variants, special tools for predicting disease severity in large scale are missing. Here, we manually curated a dataset containing variants leading to severe and less severe phenotypes and studied the abilities of variation impact predictors to distinguish between them...
January 9, 2017: Human Mutation
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