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Human Mutation

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https://www.readbyqxmd.com/read/28106320/classification-of-genes-standardized-clinical-validity-assessment-of-gene-disease-associations-aids-diagnostic-exome-analysis-and-reclassifications
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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 7 healthy donors and cells from 7 patients with MYH11 or ACTA2 variants were transdifferentiated into SMC-like cells within a 2 week duration using 5ng/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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28058752/orai1-mutations-with-distinct-channel-gating-defects-in-tubular-aggregate-myopathy
#11
Johann Böhm, Monica Bulla, Jill E Urquhart, Edoardo Malfatti, Simon G Williams, James O'Sullivan, Anastazja Szlauer, Catherine Koch, Giovanni Baranello, Marina Mora, Michela Ripolone, Raffaella Violano, Maurizio Moggio, Helen Kingston, Timothy Dawson, Christian G DeGoede, John Nixon, Anne Boland, Jean-François Deleuze, Norma Romero, William G Newman, Nicolas Demaurex, Jocelyn Laporte
Calcium (Ca(2+) ) is a physiological key factor, and the precise modulation of free cytosolic Ca(2+) levels regulates multiple cellular functions. Store-operated Ca(2+) entry (SOCE) is a major mechanism controlling Ca(2+) homeostasis, and is mediated by the concerted activity of the Ca(2+) sensor STIM1 and the Ca(2+) channel ORAI1. Dominant gain-of-function mutations in STIM1 or ORAI1 cause tubular aggregate myopathy (TAM) or Stormorken syndrome, while recessive loss-of-function mutations are associated with immunodeficiency...
January 6, 2017: Human Mutation
https://www.readbyqxmd.com/read/28055140/eif2s3-mutations-associated-with-severe-x-linked-intellectual-disability-syndrome-mehmo
#12
Martina Skopkova, Friederike Hennig, Byung-Sik Shin, Clesson E Turner, Daniela Stanikova, Katarina Brennerova, Juraj Stanik, Ute Fischer, Lyndal Henden, Ulrich Müller, Daniela Steinberger, Esther Leshinsky-Silver, Armand Bottani, Timea Kurdiova, Jozef Ukropec, Olga Nyitrayova, Miriam Kolnikova, Iwar Klimes, Guntram Borck, Melanie Bahlo, Stefan A Haas, Joo-Ran Kim, Leda E Lotspeich-Cole, Daniela Gasperikova, Thomas E Dever, Vera M Kalscheuer
Impairment of translation initiation and its regulation within the integrated stress response (ISR) and related unfolded-protein response has been identified as a cause of several multi-systemic syndromes. Here we link MEHMO syndrome, whose genetic etiology was unknown, to this group of disorders. MEHMO is a rare X-linked syndrome characterized by profound intellectual disability, epilepsy, hypogonadism, and hypogenitalism, microcephaly, and obesity. We have identified a C-terminal frameshift mutation (Ile465Serfs) in the EIF2S3 gene in three families with MEHMO syndrome and a novel maternally inherited missense EIF2S3 variant (c...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28054750/somatic-med12-nonsense-mutation-escapes-mrna-decay-and-reveals-a-motif-required-for-nuclear-entry
#13
Tuomas Heikkinen, Kati Kämpjärvi, Salla Keskitalo, Pernilla von Nandelstadh, Xiaonan Liu, Ville Rantanen, Esa Pitkänen, Matias Kinnunen, Heikki Kuusanmäki, Mika Kontro, Mikko Turunen, Netta Mäkinen, Jussi Taipale, Caroline Heckman, Kaisa Lehti, Satu Mustjoki, Markku Varjosalo, Pia Vahteristo
MED12 is a key component of the transcription-regulating Mediator complex. Specific missense and in-frame insertion/deletion mutations in exons 1 and 2 have been identified in uterine leiomyomas, breast tumors, and chronic lymphocytic leukemia. Here, we characterize the first MED12 5' end nonsense mutation (c.97G>T, p.E33X) identified in acute lymphoblastic leukemia and show that it escapes nonsense-mediated mRNA decay (NMD) by using an alternative translation initiation site. The resulting N-terminally truncated protein is unable to enter the nucleus due to the lack of identified nuclear localization signal (NLS)...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28054739/compound-heterozygosity-for-null-mutations-and-a-common-hypomorphic-risk-haplotype-in-tbx6-causes-congenital-scoliosis
#14
Kazuki Takeda, Ikuyo Kou, Noriaki Kawakami, Aritoshi Iida, Masahiro Nakajima, Yoji Ogura, Eri Imagawa, Noriko Miyake, Naomichi Matsumoto, Yukuto Yasuhiko, Hideki Sudo, Toshiaki Kotani, Masaya Nakamura, Morio Matsumoto, Kota Watanabe, Shiro Ikegawa
Congenital scoliosis (CS) occurs as a result of vertebral malformations and has an incidence of 0.5-1/1,000 births. Recently, TBX6 on chromosome 16p11.2 was reported as a disease gene for CS; about 10% of Chinese CS patients were compound heterozygotes for rare null mutations and a common haplotype defined by three SNPs in TBX6. All patients had hemivertebrae. We recruited 94 Japanese CS patients, investigated the TBX6 locus for both mutations and the risk haplotype, examined transcriptional activities of mutant TBX6 in vitro, and evaluated clinical and radiographic features...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28054444/heterozygous-pathogenic-variant-in-dact1-causes-an-autosomal-dominant-syndrome-with-features-overlapping-townes-brocks-syndrome
#15
Bryn D Webb, Sanjeeva Metikala, Patricia G Wheeler, Mingma D Sherpa, Sander M Houten, Marko E Horb, Eric E Schadt
A heterozygous nonsense variant was identified in dapper, antagonist of beta-catenin, 1 (DACT1) via whole exome sequencing in family members with imperforate anus, structural renal abnormalities, genitourinary anomalies, and/or ear anomalies. The DACT1 c.1256G>A;p.Trp419* variant segregated appropriately in the family consistent with an autosomal dominant mode of inheritance. DACT1 is a member of the Wnt signaling pathway, and mice homozygous for null alleles display multiple congenital anomalies including absent anus with blind-ending colon and genitourinary malformations...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28054414/non-coding-variation-the-2016-annual-scientific-meeting-of-the-human-genome-variation-society
#16
William S Oetting, Christophe Béroud, Steven E Brenner, Marc Greenblatt, Rachel Karchin, Sean D Mooney, Shamir Sunyaev
Significant advances have been made in recent years in the assessment and interpretation of the non-coding DNA that comprises 98% of our genome. Studying non-coding variants helps us better understand gene regulation and expression, non-coding RNA, and other non-coding genome functions. The 2016 annual scientific meeting of the Human Genome Variation Society (HGVS; http://www.hgvs.org) was held on the 18(th) of October in Vancouver, British Colombia, Canada, on the topic of "Non-Coding Variation". By using multiple data sets and wide-ranging methods including in vitro assays, high-throughput functional assays, statistical, machine learning, and other computational analyses, important sequence motifs, and the effect of variants in these regions, are being better understood...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28044414/flexible-and-scalable-full-length-cyp2d6-long-amplicon-pacbio-sequencing
#17
Henk P J Buermans, Rolf H A M Vossen, Seyed Yahya Anvar, William G Allard, Henk-Jan Guchelaar, Stefan J White, Johan T den Dunnen, Jesse J Swen, Tahar van der Straaten
Cytochrome P450 2D6 (CYP2D6) is among the most important genes involved in drug metabolism. Specific variants are associated with changes in the enzyme's amount and activity. Multiple technologies exist to determine these variants, like the AmpliChip CYP450 test, Taqman qPCR, or Second-Generation Sequencing, however, sequence homology between cytochrome P450 genes and pseudogene CYP2D7 impairs reliable CYP2D6 genotyping, and variant phasing cannot accurately be determined using these assays. To circumvent this, we sequenced CYP2D6 using the Pacific Biosciences RSII and obtained high-quality, full-length, phased CYP2D6 sequences, enabling accurate variant calling and haplotyping of the entire gene-locus including exonic, intronic, and upstream and downstream regions...
January 3, 2017: Human Mutation
https://www.readbyqxmd.com/read/28044389/in-silico-functional-meta-analysis-of-5-962-abca4-variants-in-3-928-retinal-dystrophy-cases
#18
Stéphanie S Cornelis, Nathalie M Bax, Jana Zernant, Rando Allikmets, Lars G Fritsche, Johan T den Dunnen, Muhammad Ajmal, Carel B Hoyng, Frans P M Cremers
Variants in the ABCA4 gene are associated with a spectrum of inherited retinal diseases (IRDs), most prominently with autosomal recessive Stargardt disease (STGD1) and cone-rod dystrophy (arCRD). The clinical outcome to a large degree depends on the severity of the variants. To provide an accurate prognosis and to select patients for novel treatments, functional significance assessment of non-truncating ABCA4 variants is important. We collected all published ABCA4 variants from 3,931 retinal dystrophy cases in a Leiden Open Variation Database, and compared their frequency in 3,270 Caucasian IRD cases with 33,370 non-Finnish European control individuals...
January 3, 2017: Human Mutation
https://www.readbyqxmd.com/read/28035777/mendelian-disorders-of-cornification-caused-by-defects-in-intracellular-calcium-pumps-mutation-update-and-database-for-variants-in-atp2a2-and-atp2c1-associated-with-darier-disease-and-hailey-hailey-disease
#19
Ruud G L Nellen, Peter M Steijlen, Maurice A M van Steensel, Maaike Vreeburg, Jorge Frank, Michel van Geel
The two disorders of cornification associated with mutations in genes coding for intracellular calcium pumps are Darier Disease (DD) and Hailey-Hailey Disease (HHD). DD is caused by mutations in the ATP2A2 gene, while the ATP2C1 gene is associated with HHD. Both are inherited as autosomal dominant traits. DD is mainly defined by warty papules in seborrheic and flexural areas, whereas the major symptoms of HHD are vesicles and erosions in flexural skin. Both phenotypes are highly variable. In 12- 40% of DD patients and 12-55% of HHD patients, no mutations in ATP2A2 or ATP2C1 are found...
December 30, 2016: Human Mutation
https://www.readbyqxmd.com/read/28026089/synonymous-somatic-variants-in-human-cancer-are-not-infamous-a-plea-for-full-disclosure-in-databases-and-publications
#20
Thierry Soussi, Peter E M Taschner, Yardena Samuels
Single Nucleotide Variants (SNVs) are the most frequent genetic changes found in human cancer. Most driver alterations are missense and nonsense variants localized in the coding region of cancer genes. Unbiased cancer genome sequencing shows that synonymous SNVs (sSNVs) can be found clustered in the coding regions of several cancer oncogenes or tumor suppressor genes suggesting purifying selection. sSNVs are currently underestimated, as they are usually discarded during analysis. Furthermore, several public databases do not display sSNVs, which can lead to analytical bias and the false assumption that this mutational event is uncommon...
December 27, 2016: Human Mutation
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