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https://www.readbyqxmd.com/read/28742792/evidence-for-genetic-association-between-chromosome-1q-loci-and-predisposition-to-colorectal-neoplasia
#1
Stephanie A Schubert, Dina Ruano, Fadwa A Elsayed, Arnoud Boot, Stijn Crobach, Arantza Farina Sarasqueta, Bruce Wolffenbuttel, Melanie M van der Klauw, Jan Oosting, Carli M Tops, Ronald van Eijk, Hans Fa Vasen, Rolf Ham Vossen, Maartje Nielsen, Sergi Castellví-Bel, Clara Ruiz-Ponte, Ian Tomlinson, Malcolm G Dunlop, Pavel Vodicka, Juul T Wijnen, Frederik J Hes, Hans Morreau, Noel Fcc de Miranda, Rolf H Sijmons, Tom van Wezel
BACKGROUND: A substantial fraction of familial colorectal cancer (CRC) and polyposis heritability remains unexplained. This study aimed to identify predisposing loci in patients with these disorders. METHODS: Homozygosity mapping was performed using 222 563 SNPs in 302 index patients with various colorectal neoplasms and 3367 controls. Linkage analysis, exome and whole-genome sequencing were performed in a family affected by microsatellite stable CRCs. Candidate variants were genotyped in 10 554 cases and 21 480 controls...
July 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28742285/variable-expressivity-and-incomplete-penetrance-in-a-large-family-with-non-classical-diamond-blackfan-anemia-associated-with-ribosomal-protein-l11-splicing-variant
#2
Colleen M Carlston, Zeinab A Afify, Janice C Palumbos, Heidi Bagley, Carlos Barbagelata, Whitney L Wooderchak-Donahue, Rong Mao, John C Carey
Diamond-Blackfan anemia (DBA) is a group of clinically and genetically heterogeneous bone marrow failure disorders with or without congenital anomalies. Variable expressivity and incomplete penetrance have been observed within affected families. Diamond-Blackfan anemia-7 (DBA7), caused by heterozygous mutations in ribosomal protein L11 (RPL11), accounts for approximately 5% of DBA. DBA7 is usually characterized by early-onset bone marrow failure often accompanied by congenital malformations, especially thumb defects...
July 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28742282/med-resulting-from-recessively-inherited-mutations-in-the-gene-encoding-calcium-activated-nucleotidase-cant1
#3
Karthika Balasubramanian, Bing Li, Deborah Krakow, Lisette Nevarez, Patric J Ho, Julia A Ainsworth, Deborah A Nickerson, Michael J Bamshad, LaDonna Immken, Ralph S Lachman, Daniel H Cohn
Multiple Epiphyseal Dysplasia (MED) is a relatively mild skeletal dysplasia characterized by mild short stature, joint pain, and early-onset osteoarthropathy. Dominantly inherited mutations in COMP, MATN3, COL9A1, COL9A2, and COL9A3, and recessively inherited mutations in SLC26A2, account for the molecular basis of disease in about 80-85% of the cases. In two families with recurrent MED of an unknown molecular basis, we used exome sequencing and candidate gene analysis to identify homozygosity for recessively inherited missense mutations in CANT1, which encodes calcium-activated nucleotidase 1...
July 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28742274/whole-exome-sequencing-identified-genetic-variations-in-chinese-hemangioblastoma-patients
#4
Dexuan Ma, Jingyun Yang, Ying Wang, Xiang Huang, Guhong Du, Liangfu Zhou
Hemangioblastomas (HBs) are uncommon tumors characterized by the presence of inactivating alterations in the von Hippel-Lindau (VHL) gene in inherited cases and by infrequent somatic mutation in sporadic entities. We performed whole exome sequencing on 11 HB patients to further elucidate the genetics of HBs. A total of 270 somatic variations in 219 genes, of which there were 86 mutations in 67 genes, were found in sporadic HBs, and 184 mutations were found in 154 genes in familial HBs. C: G>T: A and T: A>C: G mutations are relatively common in most HB patients...
July 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28742119/doestrare-a-statistical-test-to-identify-local-enrichments-in-rare-genomic-variants-associated-with-disease
#5
Elodie Persyn, Matilde Karakachoff, Solena Le Scouarnec, Camille Le Clézio, Dominique Campion, French Exome Consortium, Jean-Jacques Schott, Richard Redon, Lise Bellanger, Christian Dina
Next-generation sequencing technologies made it possible to assay the effect of rare variants on complex diseases. As an extension of the "common disease-common variant" paradigm, rare variant studies are necessary to get a more complete insight into the genetic architecture of human traits. Association studies of these rare variations show new challenges in terms of statistical analysis. Due to their low frequency, rare variants must be tested by groups. This approach is then hindered by the fact that an unknown proportion of the variants could be neutral...
2017: PloS One
https://www.readbyqxmd.com/read/28742110/evaluation-of-exome-variants-using-the-ion-proton-platform-to-sequence-error-prone-regions
#6
Heewon Seo, Yoomi Park, Byung Joo Min, Myung Eui Seo, Ju Han Kim
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58...
2017: PloS One
https://www.readbyqxmd.com/read/28742085/clinically-severe-cacna1a-alleles-affect-synaptic-function-and-neurodegeneration-differentially
#7
Xi Luo, Jill A Rosenfeld, Shinya Yamamoto, Tamar Harel, Zhongyuan Zuo, Melissa Hall, Klaas Wierenga, Matthew T Pastore, Dennis Bartholomew, Mauricio R Delgado, Joshua Rotenberg, Richard Alan Lewis, Lisa Emrick, Carlos A Bacino, Mohammad K Eldomery, Zeynep Coban Akdemir, Fan Xia, Yaping Yang, Seema R Lalani, Timothy Lotze, James R Lupski, Brendan Lee, Hugo J Bellen, Michael F Wangler
Dominant mutations in CACNA1A, encoding the α-1A subunit of the neuronal P/Q type voltage-dependent Ca2+ channel, can cause diverse neurological phenotypes. Rare cases of markedly severe early onset developmental delay and congenital ataxia can be due to de novo CACNA1A missense alleles, with variants affecting the S4 transmembrane segments of the channel, some of which are reported to be loss-of-function. Exome sequencing in five individuals with severe early onset ataxia identified one novel variant (p.R1673P), in a girl with global developmental delay and progressive cerebellar atrophy, and a recurrent, de novo p...
July 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28741757/equivalent-missense-variant-in-the-foxp2-and-foxp1-transcription-factors-causes-distinct-neurodevelopmental-disorders
#8
Elliot Sollis, Pelagia Deriziotis, Hirotomo Saitsu, Noriko Miyake, Naomichi Matsumoto, Mariette J V Hoffer, Claudia A L Ruivenkamp, Mariëlle Alders, Nobuhiko Okamoto, Emilia K Bijlsma, Astrid S Plomp, Simon E Fisher
The closely related paralogues FOXP2 and FOXP1 encode transcription factors with shared functions in the development of many tissues, including the brain. However, while mutations in FOXP2 lead to a speech/language disorder characterized by childhood apraxia of speech (CAS), the clinical profile of FOXP1 variants includes a broader neurodevelopmental phenotype with global developmental delay, intellectual disability and speech/language impairment. Using clinical whole-exome sequencing, we report an identical de novo missense FOXP1 variant identified in three unrelated patients...
July 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28741255/genetics-of-schizophrenia-ready-to-translate
#9
REVIEW
Claire Foley, Aiden Corvin, Shigeki Nakagome
PURPOSE OF REVIEW: This is an era where we have significantly advanced the understanding of the genetic architecture of schizophrenia. In this review, we consider how this knowledge may translate into advances that will improve patient care. RECENT FINDINGS: Large-scale genome-wide association studies (GWAS) have identified more than a hundred loci each making a small contribution to illness risk. Meta-analysis of copy number variants (CNVs) in the Psychiatric Genomics Consortium (PGC) dataset has confirmed that some variants have a moderate or large impact on risk, although these are rare in the population...
September 2017: Current Psychiatry Reports
https://www.readbyqxmd.com/read/28739660/a-gene-implicated-in-activation-of-retinoic-acid-receptor-targets-is-a-novel-renal-agenesis-gene-in-humans
#10
Patrick D Brophy, Maria Rasmussen, Mrutyunjaya Parida, Greg Bonde, Benjamin W Darbro, Xiaojing Hong, Jason C Clarke, Kevin A Peterson, James Denegre, Michael Schneider, Caroline R Sussman, Lone Sunde, Dorte L Lildballe, Jens Michael Hertz, Robert A Cornell, Stephen A Murray, John R Manak
Renal agenesis (RA) is one of the more extreme examples of congenital anomalies of the kidney and urinary tract (CAKUT). Bilateral renal agenesis is almost invariably fatal at birth, and unilateral renal agenesis can lead to future health issues including end stage renal disease. Genetic investigations have identified several gene variants which cause RA, including EYA1, LHX1, and WT1 However, whereas compound null mutations of genes encoding α and γ retinoic acid receptors (RARs) cause RA in mice, to date there have been no reports of variants in RAR genes causing RA in humans...
July 24, 2017: Genetics
https://www.readbyqxmd.com/read/28739549/mutations-in-the-abcg8-gene-are-associated-with-sitosterolaemia-in-the-homozygous-form-and-xanthelasmas-in-the-heterozygous-form
#11
Tara Bardawil, Abdallah Rebeiz, Myriam Chaabouni, Jessica El Halabi, Zakaria Kambris, Ossama Abbas, Ossama Abou Hassan, Lamiaa Hamie, Fadi Bitar, Abdul Ghani Kibbi, Georges Nemer, Mazen Kurban
Sitosterol is the most abundant plant sterol found in our diet. Sitosterolemia (OMIM 210250), also known as phytosterolaemia, is a rare autosomal recessive disease caused by the inability to efficiently excrete plant sterol, and is characterized by cutaneous xanthomas and accelerated atherosclerosis. Sitosterolaemia is caused by homozygous or compound heterozygous mutations in either ABCG5 or ABCG8 (both on chromosome 2p21), which encode the sterol efflux transporter ABCG5 (sterolin-1) and ABCG8 (sterolin-2), respectively...
July 25, 2017: European Journal of Dermatology: EJD
https://www.readbyqxmd.com/read/28738844/analysis-of-sdhaf3-in-familial-and-sporadic-pheochromocytoma-and-paraganglioma
#12
Trisha Dwight, Un Na, Edward Kim, Ying Zhu, Anne Louise Richardson, Bruce G Robinson, Katherine M Tucker, Anthony J Gill, Diana E Benn, Roderick J Clifton-Bligh, Dennis R Winge
BACKGROUND: Germline mutations in genes encoding subunits of succinate dehydrogenase (SDH) are associated with the development of pheochromocytoma (PC) and/or paraganglioma (PGL). As assembly factors have been identified as playing a role in maturation of individual SDH subunits and assembly of the functioning SDH complex, we hypothesized that SDHAF3 variants may be associated with PC/PGL and functionality of SDH. METHODS: DNA was extracted from the blood of 37 individuals (from 23 families) with germline SDH mutations and 18 PC/PGL (15 sporadic, 3 familial) and screened for mutations using a custom gene panel, containing SDHAF3 (SDH assembly factor 3) as well as eight known PC/PGL susceptibility genes...
July 24, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28738127/early-onset-alzheimer-disease-and-candidate-risk-genes-involved-in-endolysosomal-transport
#13
Brian W Kunkle, Badri N Vardarajan, Adam C Naj, Patrice L Whitehead, Sophie Rolati, Susan Slifer, Regina M Carney, Michael L Cuccaro, Jeffery M Vance, John R Gilbert, Li-San Wang, Lindsay A Farrer, Christiane Reitz, Jonathan L Haines, Gary W Beecham, Eden R Martin, Gerard D Schellenberg, Richard P Mayeux, Margaret A Pericak-Vance
Importance: Mutations in APP, PSEN1, and PSEN2 lead to early-onset Alzheimer disease (EOAD) but account for only approximately 11% of EOAD overall, leaving most of the genetic risk for the most severe form of Alzheimer disease unexplained. This extreme phenotype likely harbors highly penetrant risk variants, making it primed for discovery of novel risk genes and pathways for AD. Objective: To search for rare variants contributing to the risk for EOAD. Design, Setting, and Participants: In this case-control study, whole-exome sequencing (WES) was performed in 51 non-Hispanic white (NHW) patients with EOAD (age at onset <65 years) and 19 Caribbean Hispanic families previously screened as negative for established APP, PSEN1, and PSEN2 causal variants...
July 24, 2017: JAMA Neurology
https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#14
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28735903/genetics-of-non-syndromic-childhood-obesity-and-the-use-of-high-throughput-dna-sequencing-technologies
#15
REVIEW
Ana Carolina Proença da Fonseca, Claudio Mastronardi, Angad Johar, Mauricio Arcos-Burgos, Gilberto Paz-Filho
BACKGROUND: Childhood obesity is a serious public health problem associated with the development of several chronic diseases, such as type 2 diabetes mellitus, dyslipidemia, and hypertension. The elevated prevalence of obesity is mostly due to inadequate diet and lifestyle, but it is also influenced by genetic factors. OBJECTIVES: To review recent advances in the field of the genetics of obesity. We summarize the list of genes associated with the rare non-syndromic forms of obesity, and explain their function...
June 16, 2017: Journal of Diabetes and its Complications
https://www.readbyqxmd.com/read/28735798/the-etiology-of-essential-tremor-genes-versus-environment
#16
Franziska Hopfner, Rick C Helmich
INTRODUCTION: Essential tremor (ET) is characterized by bilateral upper limb action tremor. Here we review the pathophysiology (cerebral mechanisms) and etiology (genetic and environmental risk factors) of ET. METHODS: We reviewed the literature (until June 2017) by searching PubMed for relevant papers. RESULTS: The pathophysiology of ET involves oscillatory activity in the cortico-olivo-cerebello-thalamic circuit, evidenced by electrophysiological and metabolic imaging...
July 17, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28735482/design-and-application-of-multiplex-pcr-seq-for-the-detection-of-somatic-mutations-associated-with-myeloid-malignancies
#17
Naomi Park, George Vassiliou
Targeted sequencing, in which only a selected set of genomic loci are sequenced, enables a much higher coverage of each target than what is obtained using whole genome or exome sequencing. Multiplex PCR offers a simple and affordable technique for specific capture of target regions and can be easily adapted to generate next-generation sequencing (NGS)-ready amplicons. Here we describe a multiplex PCR (MxPCR) approach for capturing 13 leukemia-associated mutation hotspots followed by MiSeq sequencing that enables robust detection of mutations with a variant allele fraction (VAF) as low as 0...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734953/estimating-relative-mitochondrial-dna-copy-number-using-high-throughput-sequencing-data
#18
Pan Zhang, Brian D Lehmann, David C Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo
We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data...
July 19, 2017: Genomics
https://www.readbyqxmd.com/read/28734699/an-update-on-the-genetics-of-dementia-with-lewy-bodies
#19
REVIEW
Leonie J M Vergouw, Inger van Steenoven, Wilma D J van de Berg, Charlotte E Teunissen, John C van Swieten, Vincenzo Bonifati, Afina W Lemstra, Frank Jan de Jong
The genetic architecture of dementia with Lewy bodies (DLB) is increasingly taking shape. Initially, genetic research focused mainly on linkage and candidate gene studies in small series of DLB patients. More recently, association and exome sequencing studies in larger groups have been conducted, and have shown that several variants in GBA and the APOE ε4 allele are important genetic risk factors for DLB. However, genetic research in DLB is still in its infancy. So far, many genetic studies have been biased and performed in clinically and pathologically heterogeneous populations...
July 13, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28733840/identification-of-a%C3%A2-rare-coch-mutation-by-whole-exome-sequencing-implications-for-personalized-therapeutic-rehabilitation-in-an-austrian-family-with-non-syndromic-autosomal-dominant-late-onset-hearing-loss
#20
Thomas Parzefall, Alexandra Frohne, Martin Koenighofer, Andreas Kirchnawy, Berthold Streubel, Christian Schoefer, Wolfgang Gstoettner, Klemens Frei, Trevor Lucas
BACKGROUND: Non-syndromic autosomal dominant hearing impairment is characteristically postlingual in onset. Genetic diagnostics are essential for genetic counselling, disease prognosis and understanding of the molecular mechanisms of disease. To date, 36 causative genes have been identified, many in only individual families. Gene selection for genetic screening by traditional methods and genetic diagnosis in autosomal dominant patients has therefore been fraught with difficulty. Whole-exome sequencing provides a powerful tool to analyze all protein-coding genomic regions in parallel, thus allowing the comprehensive screening of all known genes and associated alterations...
July 21, 2017: Wiener Klinische Wochenschrift
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