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https://www.readbyqxmd.com/read/28530713/bach2-immunodeficiency-illustrates-an-association-between-super-enhancers-and-haploinsufficiency
#1
Behdad Afzali, Juha Grönholm, Jana Vandrovcova, Charlotte O'Brien, Hong-Wei Sun, Ine Vanderleyden, Fred P Davis, Ahmad Khoder, Yu Zhang, Ahmed N Hegazy, Alejandro V Villarino, Ira W Palmer, Joshua Kaufman, Norman R Watts, Majid Kazemian, Olena Kamenyeva, Julia Keith, Anwar Sayed, Dalia Kasperaviciute, Michael Mueller, Jason D Hughes, Ivan J Fuss, Mohammed F Sadiyah, Kim Montgomery-Recht, Joshua McElwee, Nicholas P Restifo, Warren Strober, Michelle A Linterman, Paul T Wingfield, Holm H Uhlig, Rahul Roychoudhuri, Timothy J Aitman, Peter Kelleher, Michael J Lenardo, John J O'Shea, Nichola Cooper, Arian D J Laurence
The transcriptional programs that guide lymphocyte differentiation depend on the precise expression and timing of transcription factors (TFs). The TF BACH2 is essential for T and B lymphocytes and is associated with an archetypal super-enhancer (SE). Single-nucleotide variants in the BACH2 locus are associated with several autoimmune diseases, but BACH2 mutations that cause Mendelian monogenic primary immunodeficiency have not previously been identified. Here we describe a syndrome of BACH2-related immunodeficiency and autoimmunity (BRIDA) that results from BACH2 haploinsufficiency...
May 22, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#2
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28526010/next-generation-sequencing-for-d47n-mutation-in-cx50-analysis-associated-with-autosomal-dominant-congenital-cataract-in-a-six-generation-chinese-family
#3
Chao Shen, Jingbing Wang, Xiaotang Wu, Fuchao Wang, Yang Liu, Xiaoying Guo, Lina Zhang, Yanfei Cao, Xiuhua Cao, Hongxing Ma
BACKGROUND: Congenital cataract is the most frequent cause of blindness during infancy or early childhood. To date, more than 40 loci associated with congenital cataract have been identified, including at least 26 genes on different chromosomes associated with inherited cataract. This present study aimed to identify the genetic mutation in a six-generation Chinese family affected with congenital cataract. METHODS: A detailed six-generation Chinese cataract family history and clinical data of the family members were recorded...
May 19, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28524179/a-fkbp5-mutation-is-associated-with-paget-s-disease-of-bone-and-enhances-osteoclastogenesis
#4
Bingru Lu, Yulian Jiao, Yinchang Wang, Jing Dong, Muyun Wei, Bin Cui, Yafang Sun, Laicheng Wang, Bingchang Zhang, Zijiang Chen, Yueran Zhao
Paget's disease of bone (PDB) is a common metabolic bone disease that is characterized by aberrant focal bone remodeling, which is caused by excessive osteoclastic bone resorption followed by disorganized osteoblastic bone formation. Genetic factors are a critical determinant of PDB pathogenesis, and several susceptibility genes and loci have been reported, including SQSTM1, TNFSF11A, TNFRSF11B, VCP, OPTN, CSF1 and DCSTAMP. Herein, we report a case of Chinese familial PDB without mutations in known genes and identify a novel c...
May 19, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28524162/targeted-sequencing-based-analyses-of-candidate-gene-variants-in-ulcerative-colitis-associated-colorectal-neoplasia
#5
Sanjiban Chakrabarty, Vinay Koshy Varghese, Pranoy Sahu, Pradyumna Jayaram, Bhadravathi M Shivakumar, Cannanore Ganesh Pai, Kapaettu Satyamoorthy
BACKGROUND: Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma. METHODS: Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia...
May 18, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28522871/mug-mel2-a-novel-highly-pigmented-and-well-characterized-nras-mutated-human-melanoma-cell-line
#6
Beate Rinner, Greta Gandolfi, Katharina Meditz, Marie-Therese Frisch, Karin Wagner, Alessia Ciarrocchi, Federica Torricelli, Raili Koivuniemi, Johanna Niklander, Bernadette Liegl-Atzwanger, Birgit Lohberger, Ellen Heitzer, Nassim Ghaffari-Tabrizi-Wizsy, Dagmar Zweytick, Iris Zalaudek
NRAS mutation in melanoma has been associated with aggressive tumor biology and poor prognosis. Although targeted therapy has been tested for NRAS mutated melanoma, response rates still appear much weaker, than in BRAF mutated melanoma. While plenty of cell lines exist, however, only few melanogenic cell lines retain their in vivo characteristics. In this work we present an intensively pigmented and well-characterized cell line derived from a highly aggressive NRAS mutated cutaneous melanoma, named MUG-Mel2...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522810/integrative-analysis-of-genomic-sequencing-data-reveals-higher-prevalence-of-lrp1b-mutations-in-lung-adenocarcinoma-patients-with-copd
#7
Dakai Xiao, Fuqiang Li, Hui Pan, Han Liang, Kui Wu, Jianxing He
Both chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#8
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#9
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28521875/exome-sequencing-reveals-a-de-novo-pold1-mutation-causing-phenotypic-variability-in-mandibular-hypoplasia-deafness-progeroid-features-and-lipodystrophy-syndrome-mdpl
#10
Sahar Elouej, Ana Beleza-Meireles, Richard Caswell, Kevin Colclough, Sian Ellard, Jean Pierre Desvignes, Christophe Béroud, Nicolas Lévy, Shehla Mohammed, Annachiara De Sandre-Giovannoli
BACKGROUND: Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) is an autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, a characteristic facial appearance and metabolic abnormalities. This syndrome is caused by heterozygous de novo mutations in the POLD1 gene. To date, 19 patients with MDPL have been reported in the literature and among them 14 patients have been characterized at the molecular level. Twelve unrelated patients carried a recurrent in-frame deletion of a single codon (p...
June 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28521526/the-impact-of-genetics-on-future-drug-discovery-in-schizophrenia
#11
Mitsuyuki Matsumoto, Noah M Walton, Hiroshi Yamada, Yuji Kondo, Gerard J Marek, Katsunori Tajinda
Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies...
May 18, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28521042/induced-pluripotent-stem-cell-modelling-of-hlhs-underlines-the-contribution-of-dysfunctional-notch-signalling-to-impaired-cardiogenesis
#12
Chunbo Yang, Yaobo Xu, Min Yu, David Lee, Sameer Alharti, Nicola Hellen, Noor Ahmad Shaik, Babajan Banaganapalli, Hussein Ali Mohamoud Sheikh, Elango Ramu, Stefan Przyborski, Gennadiy Tenin, Simon Williams, John O'Sullivan, Osman O Al-Radi, Jameel Atta, Sian E Harding, Bernard Keavney, Majlinda Lako, Lyle Armstrong
Hypoplastic left heart syndrome (HLHS) is among the most severe forms of congenital heart disease. Although the consensus view is that reduced flow through the left heart during development is a key factor in the development of the condition, the molecular mechanisms leading to hypoplasia of left heart structures are unknown. We have generated induced pluripotent stem cells (iPSC) from five HLHS patients and two unaffected controls, differentiated these to cardiomyocytes and identified reproducible in vitro cellular and functional correlates of the HLHS phenotype...
May 17, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28521008/gemstone-orchestrated-prioritization-of-human-germline-mutations-in-the-cloud
#13
Siwei Chen, Juan F Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu
Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#14
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520167/kmt2b-rare-missense-variants-in-generalized-dystonia
#15
Michael Zech, Robert Jech, Petra Havránková, Anna Fečíková, Riccardo Berutti, Dušan Urgošík, David Kemlink, Tim M Strom, Jan Roth, Evžen Růžička, Juliane Winkelmann
BACKGROUND: Recently a novel syndrome of childhood-onset generalized dystonia originating from mutations in lysine-specific methyltransferase 2B (KMT2B) has been reported. METHODS: We sequenced the exomes of 4 generalized dystonia-affected probands recruited from a Prague movement disorders center (Czech Republic). Bioinformatics analyses were conducted to select candidate causal variants in described dystonia-mutated genes. After cosegregation testing, checklists from the American College of Medical Genetics and Genomics were adopted to judge variant pathogenicity...
May 18, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28518170/prenatal-exome-sequencing-in-anomalous-fetuses-new-opportunities-and-challenges
#16
Neeta L Vora, Bradford Powell, Alicia Brandt, Natasha Strande, Emily Hardisty, Kelly Gilmore, Ann Katherine M Foreman, Kirk Wilhelmsen, Chris Bizon, Jason Reilly, Phil Owen, Cynthia M Powell, Debra Skinner, Christine Rini, Anne D Lyerly, Kim A Boggess, Karen Weck, Jonathan S Berg, James P Evans
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28518168/using-high-resolution-variant-frequencies-to-empower-clinical-genome-interpretation
#17
Nicola Whiffin, Eric Minikel, Roddy Walsh, Anne H O'Donnell-Luria, Konrad Karczewski, Alexander Y Ing, Paul J R Barton, Birgit Funke, Stuart A Cook, Daniel MacArthur, James S Ware
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28516087/dna-sequence-analysis-in-clinical-medicine-proceeding-cautiously
#18
REVIEW
Moyra Smith
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28515472/carrier-frequency-of-wilson-s-disease-in-the-korean-population-a-dna-based-approach
#19
Ja-Hyun Jang, Taeheon Lee, Sunghee Bang, Young-Eun Kim, Eun-Hae Cho
Wilson's disease (WD) is an autosomal recessive disorder caused by ATP7B gene mutation. The frequency of WD is about 1 in 30 000 worldwide. In the present study, we screened 14 835 dried blood spots (DBSs) from asymptomatic Korean neonates and retrospectively reviewed massively parallel sequencing of 1090 control individuals to estimate carrier frequency. TaqMan real-time PCR assays were conducted to detect six mutations that account for 58.3% of mutations in Korean WD patients: c.2333G>T (p.Arg778Leu), c...
May 18, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28515470/a-novel-missense-mutation-in-the-hect-domain-of-nedd4l-identified-in-a-girl-with-periventricular-nodular-heterotopia-polymicrogyria-and-cleft-palate
#20
Koji Kato, Fuyuki Miya, Ikumi Hori, Daisuke Ieda, Kei Ohashi, Yutaka Negishi, Ayako Hattori, Nobuhiko Okamoto, Mitsuhiro Kato, Tatsuhiko Tsunoda, Mami Yamasaki, Yonehiro Kanemura, Kenjiro Kosaki, Shinji Saitoh
We identified a novel de novo heterozygous missense mutation in the NEDD4L gene (NM_015277: c.2617G>A; p.Glu873Lys) through whole-exome sequencing in a 3-year-old girl showing severe global developmental delay, infantile spasms, cleft palate, periventricular nodular heterotopia and polymicrogyria. Mutations in the HECT domain of NEDD4L have been reported in patients with a neurodevelopmental disorder along with similar brain malformations. All patients reported with NEDD4L HECT domain mutations showed periventricular nodular heterotopia, and most had seizures, cortex anomalies, cleft palate and syndactyly...
May 18, 2017: Journal of Human Genetics
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