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https://www.readbyqxmd.com/read/28645073/analysis-of-ldlr-variants-from-homozygous-fh-patients-carrying-multiple-mutations-in-the-ldlr-gene
#1
Long Jiang, Asier Benito-Vicente, Ling Tang, Aitor Etxebarria, Wei Cui, Kepa B Uribe, Xiao-Dong Pan, Helena Ostolaza, Shi-Wei Yang, Yu-Jie Zhou, Cesar Martin, Lu-Ya Wang
BACKGROUND AND AIMS: Familial hypercholesterolemia (FH) is an autosomal dominant disease with widespread global prevalence that partially accounts for the high prevalence of premature coronary heart disease. Although the majority of research on FH has focused on single heterozygous LDLR mutations, there have been limited reports of double LDLR mutations on the same chromosome. The aim of this study was to gain insight into the clinical consequences of the presence of multiple mutations in the LDLR gene...
June 8, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#2
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643950/atypical-dyskeratosis-congenita-diagnosed-using-whole-exome-sequencing
#3
Ayaka Monoi, Masahiro Sugawa, Motohiro Kato, Masafumi Seki, Kenichi Yoshida, Yuichi Shiraishi, Hirotoshi Sakaguchi, Seishi Ogawa, Junko Takita
No abstract text is available yet for this article.
June 23, 2017: Pediatrics International: Official Journal of the Japan Pediatric Society
https://www.readbyqxmd.com/read/28643921/whole-exome-sequencing-identified-a-variant-in-eftud2-gene-in-establishing-a-genetic-diagnosis
#4
S Rengasamy Venugopalan, E G Farrow, M Lypka
OBJECTIVES: Craniofacial anomalies are complex and have an overlapping phenotype. Mandibulofacial Dysostosis and Oculo-Auriculo-Vertebral Spectrum are conditions that share common craniofacial phenotype and present a challenge in arriving at a diagnosis. In this report, we present a case of female proband who was given a differential diagnosis of Treacher Collins syndrome or Hemifacial Microsomia without certainty. Prior genetic testing reported negative for 22q deletion and FGFR screenings...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643274/an-unexplained-congenital-disorder-of-glycosylation-ii-in-a-child-with-neurohepatic-involvement-hypercholesterolemia-and-hypoceruloplasminemia
#5
Pier Luigi Calvo, Marco Spada, Ivana Rabbone, Michele Pinon, Francesco Porta, Fabio Cisarò, Stefania Reggiani, Angelo B Cefalù, Luisella Sturiale, Domenico Garozzo, Dirk J Lefeber, Jaak Jaeken
We report on a 12-year-old adopted boy with psychomotor disability, absence seizures, and normal brain MRI. He showed increased (but initially, at 5 months, normal) serum cholesterol, increased alkaline phosphatases, transiently increased transaminases and hypoceruloplasminemia with normal serum and urinary copper. Blood levels of immunoglobulins, haptoglobin, antithrombin, and factor XI were normal. A type 2 serum transferrin isoelectrofocusing and hypoglycosylation of apoCIII pointed to a combined N- and O-glycosylation defect...
June 23, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28642824/identification-of-quantitative-trait-loci-that-determine-plasma-total-cholesterol-and-triglyceride-concentrations-in-ddd-sgn-and-c57bl-6j-inbred-mice
#6
Jun-Ichi Suto, Misaki Kojima
DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG...
2017: Cholesterol
https://www.readbyqxmd.com/read/28642787/mutational-signatures-are-critical-for-proper-estimation-of-purifying-selection-pressures-in-cancer-somatic-mutation-data-when-using-the-dn-ds-metric
#7
Jimmy Van den Eynden, Erik Larsson
Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28642624/whole-exome-sequencing-to-identify-genetic-variants-associated-with-raised-atherosclerotic-lesions-in-young-persons
#8
James E Hixson, Goo Jun, Lawrence C Shimmin, Yizhi Wang, Guoqiang Yu, Chunhong Mao, Andrew S Warren, Timothy D Howard, Richard S Vander Heide, Jennifer Van Eyk, Yue Wang, David M Herrington
We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified a PDAY case group with the highest total amounts of raised lesions (n = 359) for comparisons with a control group with no detectable raised lesions (n = 626). In addition to the standard exome capture, we included genome-wide proximal promoter regions that contain sequences that regulate gene expression...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642336/the-evolving-genetic-risk-for-sporadic-als
#9
Summer B Gibson, Jonathan M Downie, Spyridoula Tsetsou, Julie E Feusier, Karla P Figueroa, Mark B Bromberg, Lynn B Jorde, Stefan M Pulst
OBJECTIVE: To estimate the genetic risk conferred by known amyotrophic lateral sclerosis (ALS)-associated genes to the pathogenesis of sporadic ALS (SALS) using variant allele frequencies combined with predicted variant pathogenicity. METHODS: Whole exome sequencing and repeat expansion PCR of C9orf72 and ATXN2 were performed on 87 patients of European ancestry with SALS seen at the University of Utah. DNA variants that change the protein coding sequence of 31 ALS-associated genes were annotated to determine which were rare and deleterious as predicted by MetaSVM...
June 22, 2017: Neurology
https://www.readbyqxmd.com/read/28642161/digenic-inheritance-of-mutations-in-the-cardiac-troponin-tnnt2-and-cardiac-beta-myosin-heavy-chain-myh7-as-the-cause-of-severe-dilated-cardiomyopathy
#10
Evmorfia Petropoulou, Mohammadhossein Soltani, Ali Dehghani Firoozabadi, Seyedeh Mahdieh Namayandeh, Jade Crockford, Reza Maroofian, Yalda Jamshidi
Familial dilated cardiomyopathy (DCM) is characterized by ventricular dilation and depressed myocardial performance. It is a genetically heterogeneous disorder associated with mutations in over 60 genes. We carried out whole exome sequencing in combination with cardiomyopathy-related gene-filtering on two affected family members to identify the possible causative mutation in a consanguineous Iranian family with DCM. Two novel variants in cardiomyopathy-related genes were identified: c.247 A > C; p.N83H in the Troponin T Type 2 gene (TNNT2) and c...
June 19, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28642160/a-novel-missense-variant-gln220arg-of-gnb4-encoding-guanine-nucleotide-binding-protein-subunit-beta-4-in-a-japanese-family-with-autosomal-dominant-motor-and-sensory-neuropathy
#11
Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata
Dominant intermediate Charcot-Marie-Tooth disease F (CMTDIF) is an autosomal dominant hereditary form of Charcot-Marie-Tooth disease (CMT) caused by variations in the guanine nucleotide-binding protein, subunit beta-4 gene (GNB4). We examined two Japanese familial cases with CMT. Case 1 was a 49-year-old male whose chief complaint was slowly progressive gait disturbance and limb dysesthesia that appeared at the age of 47. On neurological examination, he showed hyporeflexia or areflexia, distal limb muscle weakness, and distal sensory impairment with lower dominancy...
June 19, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28640830/optimal-sequencing-strategies-for-identifying-disease-associated-singletons
#12
Sara Rashkin, Goo Jun, Sai Chen, Goncalo R Abecasis
With the increasing focus of genetic association on the identification of trait-associated rare variants through sequencing, it is important to identify the most cost-effective sequencing strategies for these studies. Deep sequencing will accurately detect and genotype the most rare variants per individual, but may limit sample size. Low pass sequencing will miss some variants in each individual but has been shown to provide a cost-effective alternative for studies of common variants. Here, we investigate the impact of sequencing depth on studies of rare variants, focusing on singletons-the variants that are sampled in a single individual and are hardest to detect at low sequencing depths...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28640655/usual-interstitial-pneumonia-can-be-detected-in-transbronchial-biopsies-using-machine-learning
#13
Daniel G Pankratz, Yoonha Choi, Urooj Imtiaz, Grażyna M Fedorowicz, Jessica D Anderson, Thomas V Colby, Jeffrey L Myers, David A Lynch, Kevin K Brown, Kevin R Flaherty, Mark P Steele, Steve D Groshong, Ganesh Raghu, Neil M Barth, P Sean Walsh, Jing Huang, Giulia C Kennedy, Fernando J Martinez
RATIONALE: Usual interstitial pneumonia (UIP) is the histopathologic hallmark of idiopathic pulmonary fibrosis. While UIP can be detected by high-resolution computed tomography (HRCT) of the chest, HRCT results are frequently inconclusive, and pathology from transbronchial biopsy (TBB) has poor sensitivity. Surgical lung biopsy (SLB) may be necessary for a definitive diagnosis. OBJECTIVES: To develop a genomic classifier in tissue obtained by TBB that distinguishes UIP from non-UIP, trained against central pathology as the reference standard...
June 22, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28640243/in-depth-investigations-of-adolescents-and-adults-with-holoprosencephaly-identify-unique-characteristics
#14
Karin Weiss, Paul Kruszka, Maria J Guillen Sacoto, Yonit A Addissie, Donald W Hadley, Casey K Hadsall, Bethany Stokes, Ping Hu, Erich Roessler, Beth Solomon, Edythe Wiggs, Audrey Thurm, Robert B Hufnagel, Wadih M Zein, Jin S Hahn, Elaine Stashinko, Eric Levey, Debbie Baldwin, Nancy J Clegg, Mauricio R Delgado, Maximilian Muenke
PurposeWith improved medical care, some individuals with holoprosencephaly (HPE) are surviving into adulthood. We investigated the clinical manifestations of adolescents and adults with HPE and explored the underlying molecular causes.MethodsParticipants included 20 subjects 15 years of age and older. Clinical assessments included dysmorphology exams, cognitive testing, swallowing studies, ophthalmic examination, and brain magnetic resonance imaging. Genetic testing included chromosomal microarray, Sanger sequencing for SHH, ZIC2, SIX3, and TGIF, and whole-exome sequencing (WES) of 10 trios...
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28640240/pitfalls-of-trio-based-exome-sequencing-imprinted-genes-and-parental-mosaicism-magel2-as-an-example
#15
María Palomares-Bralo, Elena Vallespín, Ángela Del Pozo, Kristina Ibañez, Juan Carlos Silla, Enrique Galán, Gema Gordo, Víctor Martínez-Glez, Lázaro I Alba-Valdivia, Karen E Heath, Sixto García-Miñaúr, Pablo Lapunzina, Fernando Santos-Simarro
No abstract text is available yet for this article.
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28638727/identification-of-an-immunogenic-neo-epitope-encoded-by-mouse-sarcoma-using-cxcr3-ligand-mrnas-as-sensors
#16
Keisuke Fujii, Yoshihiro Miyahara, Naozumi Harada, Daisuke Muraoka, Mitsuhiro Komura, Rui Yamaguchi, Hideo Yagita, Junko Nakamura, Sahoko Sugino, Satoshi Okumura, Seiya Imoto, Satoru Miyano, Hiroshi Shiku
The CXCR3 ligands CXCL9, 10, and 11 play critical roles in the amplification of immune responses by recruiting CXCR3(+) immune effector cells to the tumor site. Taking advantage of this property of CXCR3 ligands, we aimed to establish a novel approach to identify immunogenic mutated-antigens. We examined the feasibility of using CXCR3 ligand mRNAs as sensors for detection of specific immune responses in human and murine systems. We further investigated whether this approach is applicable for the identification of immunogenic mutated-antigens by using murine sarcoma lines...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28638141/al-mena-a-comprehensive-resource-of-human-genetic-variants-integrating-genomes-and-exomes-from-arab-middle-eastern-and-north-african-populations
#17
Remya Koshy, Anop Ranawat, Vinod Scaria
Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations...
June 22, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28637487/the-nf1-somatic-mutational-landscape-in-sporadic-human-cancers
#18
REVIEW
Charlotte Philpott, Hannah Tovell, Ian M Frayling, David N Cooper, Meena Upadhyaya
BACKGROUND: Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia...
June 21, 2017: Human Genomics
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#19
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT...
June 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28636844/clonal-hematopoiesis-and-risk-of-atherosclerotic-cardiovascular-disease
#20
Siddhartha Jaiswal, Pradeep Natarajan, Alexander J Silver, Christopher J Gibson, Alexander G Bick, Eugenia Shvartz, Marie McConkey, Namrata Gupta, Stacey Gabriel, Diego Ardissino, Usman Baber, Roxana Mehran, Valentin Fuster, John Danesh, Philippe Frossard, Danish Saleheen, Olle Melander, Galina K Sukhova, Donna Neuberg, Peter Libby, Sekar Kathiresan, Benjamin L Ebert
Background Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of an expanded somatic blood-cell clone in persons without other hematologic abnormalities, is common among older persons and is associated with an increased risk of hematologic cancer. We previously found preliminary evidence for an association between CHIP and atherosclerotic cardiovascular disease, but the nature of this association was unclear. Methods We used whole-exome sequencing to detect the presence of CHIP in peripheral-blood cells and associated such presence with coronary heart disease using samples from four case-control studies that together enrolled 4726 participants with coronary heart disease and 3529 controls...
June 21, 2017: New England Journal of Medicine
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