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Danielle Aberdein, John S Munday, Barbara Gandolfi, Keren E Dittmer, Richard Malik, Dorian J Garrick, Leslie A Lyons
British shorthair (BSH) kittens in multiple litters died as a result of a severe non-neoplastic lymphoproliferative disease that showed many similarities with human autoimmune lymphoproliferative syndrome (ALPS). Human ALPS is caused by inherited defects in FAS-mediated lymphocyte apoptosis and the possibility of similar defects was investigated in BSH cats. The whole genomes of two affected kittens were sequenced and compared to 82 existing cat genomes. Both BSH kittens had homozygous insertions of an adenine within exon 3 of the FAS-ligand gene...
October 21, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
Lily Marsden, Lawrence J Jennings, Samantha Gadd, Min Yu, Elizabeth J Perlman, Mariana M Cajaiba
Metanephric stromal tumors are rare renal stromal tumors that predominantly affect children. They belong to the metanephric family of tumors along with metanephric adenofibroma and metanephric adenoma. The previous documentation of BRAF exon 15 mutations in 88% of metanephric adenomas and in isolated cases of metanephric adenofibroma prompted us to investigate the prevalence of these mutations in metanephric stromal tumors and in other pediatric renal stromal tumors. In this study, 17 metanephric stromal tumors, 22 congenital mesoblastic nephromas and 6 ossifying renal tumors of infancy were selected for BRAF exon 15 testing...
October 18, 2016: Human Pathology
Ron Bochner, Liat Samuelov, Ofer Sarig, Qiaoli Li, Christopher A Adase, Ofer Isakov, Natalia Malchin, Dan Vodo, Ronna Shayevitch, Alon Peled, Benjamin D Yu, Gilad Fainberg, Emily Warshauer, Noam Adir, Noam Erez, Andrea Gat, Yehonatan Gottlieb, Tova Rogers, Mor Pavlovsky, Ilan Goldberg, Noam Shomron, Aileen Sandilands, Linda E Campbell, Stephanie MacCallum, W H Irwin McLean, Gil Ast, Richard L Gallo, Jouni Uitto, Eli Sprecher
Congenital erythroderma is a rare and often life-threatening condition, which has been shown to result from mutations in several genes encoding important components of the epidermal differentiation program. Using whole exome sequencing, we identified in a child with congenital exfoliative erythroderma, hypotrichosis, severe nail dystrophy and failure to thrive, two heterozygous mutations in ABCA12 (c.2956C>T, p.R986W; c.5778+2T>C, p. G1900Mfs*16), a gene known to be associated with 2 forms of ichthyosis, autosomal recessive congenital ichthyosis and harlequin ichthyosis...
October 18, 2016: Journal of Investigative Dermatology
Hassol Lim, Young-Mi Park, Jong-Keuk Lee, Hyun Taek Lim
OBJECTIVE: To present an efficient and successful application of a single-exome sequencing study in a family clinically diagnosed with X-linked retinitis pigmentosa. DESIGN: Exome sequencing study based on clinical examination data. PARTICIPANTS: An 8-year-old proband and his family. METHODS: The proband and his family members underwent comprehensive ophthalmologic examinations. Exome sequencing was undertaken in the proband using Agilent SureSelect Human All Exon Kit and Illumina HiSeq 2000 platform...
October 2016: Canadian Journal of Ophthalmology. Journal Canadien D'ophtalmologie
Tânia Nobre, Manuela Oliveira, Birgit Arnholdt-Schmitt
By definition, the domestication process leads to an overall reduction of crop genetic diversity. This lead to the current search of genomic regions in wild crop relatives (CWR), an important task for modern carrot breeding. Nowadays massive sequencing possibilities can allow for discovery of novel genetic resources in wild populations, but this quest could be aided by the use of a surrogate gene (to first identify and prioritize novel wild populations for increased sequencing effort). Alternative oxidase (AOX) gene family seems to be linked to all kinds of abiotic and biotic stress reactions in various organisms and thus have the potential to be used in the identification of CWR hotspots of environment-adapted diversity...
2016: PloS One
Mala Ganesan, Sheikh Nizamuddin, Shiva Krishna Katkam, Konda Kumaraswami, Uday Kumar Hosad, Limmy Loret Lobo, Vijay Kumar Kutala, Kumarasamy Thangaraj
BACKGROUND: Coronary artery disease (CAD) is one of the leading causes of mortality worldwide. It is a multi-factorial disease and several studies have demonstrated that the genetic factors play a major role in CAD. Although variations in cholesteryl ester transfer protein (CETP) gene are reported to be associated with CAD, this gene has not been studied in South Indian populations. Hence we evaluated the CETP gene variations in CAD patients of South Indian origin. METHODS: We sequenced all the exons, exon-intron boundaries and UTRs of CETP in 323 CAD patients along with 300 ethnically and age matched controls...
2016: PloS One
Francesco Parmeggiani, Vanessa Barbaro, Angelo Migliorati, Paolo Raffa, Patrizia Nespeca, Katia De Nadai, Claudia Del Vecchio, Giorgio Palù, Cristina Parolin, Enzo Di Iorio
PURPOSE: To identify novel mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene and retinitis pigmentosa 2 (RP2) gene underlying X-linked retinitis pigmentosa (XLRP) and assess genotype-phenotype correlations. METHODS: The patient cohort, consisting of 13 individuals from 3 unrelated XLRP families, underwent comprehensive ophthalmologic examination. The open reading frames of RPGR and RP2 were analyzed with Sanger sequencing in each patient. The identified genetic variants were defined as mutations or polymorphisms on the basis of their pathological effect...
October 21, 2016: European Journal of Ophthalmology
Glenn Yiu, Eric Tieu, Anthony T Nguyen, Brittany Wong, Zeljka Smit-McBride
Purpose: To employ type II clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 endonuclease to suppress ocular angiogenesis by genomic disruption of VEGF-A in human RPE cells. Methods: CRISPR sequences targeting exon 1 of human VEGF-A were computationally identified based on predicted Cas9 on- and off-target probabilities. Single guide RNA (gRNA) cassettes with these target sequences were cloned into lentiviral vectors encoding the Streptococcuspyogenes Cas9 endonuclease (SpCas9) gene...
October 1, 2016: Investigative Ophthalmology & Visual Science
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single molecule molecular inversion probe (smMIP)-based targeted next generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
Aimi Huang, Rong Li, Jikai Zhao, Xiaofei Wang, Bo Jin, Yanjie Niu, Jie Zhang, Liyan Jiang, Baohui Han
This article demonstrates a case of a lung adenocarcinoma patient in stage IV harboring an epidermal growth factor receptor (EGFR) 19 exon deletion mutation treated with 500 mg/m(2) pemetrexed and 75 mg/m(2) cisplatin on day 1, sequenced with 250 mg gefitinib on prescription on days 4-28 for six cycles as first-line, then by gefitinib combined with pemetrexed as maintenance therapy. The patient achieved a partial response. Performance status increased from grade 2 to 1. The progression-free survival period was 17 months...
September 2016: Thoracic Cancer
Brendan D Crawford, Christopher E Gillies, Catherine C Robertson, Matthias Kretzler, Edgar Otto, Virginia Vega-Wagner, Matthew G Sampson
BACKGROUND: More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation...
October 20, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
Rosa Calvello, Maria A Panaro, Rosaria Salvatore, Vincenzo Mitolo, Antonia Cianciulli
The "canonical" introns begin by the dinucleotide GT and end by the dinucleotide AG. GT, together with a few downstream nucleotides, and AG, with a few of the immediately preceding nucleotides, are thought to be the strongest splicing signals (5'ss and 3'ss, respectively). We examined the composition of the intronic initial and terminal hexanucleotides of the mitochondrial solute carrier genes (SLC25A's) of zebrafish, chicken, mouse, and human. These genes are orthologous and we selected the transcripts in which the arrangement of exons and introns was superimposable in the species considered...
October 20, 2016: Journal of Molecular Evolution
Catherine Breen, Jean Mercer, Simon A Jones, Amir Jahic, Lesley Heptinstall, Karen Tylee, William G Newman, Christian Beetz
Mucopolysaccharidosis I (MPS I) is a rare autosomal recessive multisystem lysosomal storage disorder. It is caused by biallelic loss-of-function variants in IDUA, encoding alpha-l iduronidase. Here, we describe an individual affected by MPS I due to a paternally inherited deletion of IDUA exons 1 and 2, c.(?_-88)_(299+1_300-1)del and a whole-gene deletion of IDUA (?_-88?)_(*136?)del secondary to maternal somatic mosaicism. We define a previously unreported mutational mechanism for this disorder.
2016: Human Genome Variation
Ming Chen, Shun-Ping Chang, Gwo-Chin Ma, Wen-Hsian Lin, Hsin-Fu Chen, Shee-Uan Chen, Horng-Der Tsai, Feng-Po Tsai, Ming-Ching Shen
Preimplantation genetic diagnosis (PGD) is a powerful tool to tackle the transmission of monogenic inherited disorders in families carrying the diseases from generation to generation. It currently remains a challenging task, despite PGD having been developed over 25 years ago. The major difficulty is it does not have an easy and general formula for all mutations. Different gene locus needs individualized, customized design to make the diagnosis accurate enough to be applied on PGD, in which the quantity of DNA is scanty, whereas timely laboratory diagnosis is mandatory if fresh embryo transfer is desired occasionally...
2016: Thrombosis Journal
Vivek Subbiah, Oliver Holmes, Kyle Gowen, Daniel Spritz, Behrang Amini, Wei-Lien Wang, Alexa B Schrock, Funda Meric-Bernstam, Ralph Zinner, Sarina Piha-Paul, Maria Zarzour, Julia A Elvin, Rachel L Erlich, David L Stockman, Jo-Anne Vergilio, James H Suh, Philip J Stephens, Vincent Miller, Jeffrey S Ross, Siraj M Ali
Malignant gastrointestinal neuroectodermal tumor (GNET) is an aggressive rare tumor, primarily occurring in young adults with frequent local-regional metastases and recurrence after local control. The tumor is characterized by the presence of EWSR1-ATF1 or EWSR1-CREB1 and immunohistochemical positivity for S-100 protein without melanocytic marker positivity. Due to poor responses to standard sarcoma regimens, GNET has a poor prognosis, and development of effective systemic therapy is desperately needed to treat these patients...
October 21, 2016: Oncology
Thomas J Hoffmann, Bronya J Keats, Noriko Yoshikawa, Catherine Schaefer, Neil Risch, Lawrence R Lustig
Age-related hearing impairment (ARHI), one of the most common sensory disorders, can be mitigated, but not cured or eliminated. To identify genetic influences underlying ARHI, we conducted a genome-wide association study of ARHI in 6,527 cases and 45,882 controls among the non-Hispanic whites from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We identified two novel genome-wide significant SNPs: rs4932196 (odds ratio = 1.185, p = 4.0x10-11), 52Kb 3' of ISG20, which replicated in a meta-analysis of the other GERA race/ethnicity groups (1,025 cases, 12,388 controls, p = 0...
October 2016: PLoS Genetics
Satsuki Nishigaki, Takashi Hamazaki, Keinosuke Fujita, Shuntaro Morikawa, Toshihiro Tajima, Haruo Shintaku
BACKGROUND: Hemizygous mutations in the<i> immunoglobulin superfamily member 1 (IGSF1) </i>gene have been demonstrated to cause congenital central hypothyroidism in males. We report one family with a novel mutation of the<i> IGSF1 </i>gene located on the long arm of the X chromosome. PATIENT FINDINGS: A two-month-old boy was diagnosed with central hypothyroidism because of prolonged jaundice. A thyrotropin releasing hormone (TRH) stimulation test indicated dysfunction in both the hypothalamus and the pituitary gland and prompted us to analyze the<i> IGSF1 </i>gene...
October 20, 2016: Thyroid: Official Journal of the American Thyroid Association
Xiao-Jie Xu, Fang Lv, Yi Liu, Jian-Yi Wang, Dou-Dou Ma, Asan, Jia-Wei Wang, Li-Jie Song, Yan Jiang, Ou Wang, Wei-Bo Xia, Xiao-Ping Xing, Mei Li
Osteogenesis imperfecta (OI) is a group of hereditary disorders characterized by decreased bone mass and increased fracture risk. The majority of OI cases have an autosomal dominant pattern of inheritance and are usually caused by mutations in genes encoding type I collagen. OI cases of autosomal recessive inheritance are rare, and OI type XI is attributable to mutation of the FKBP10 gene. Here, we used next-generation sequencing and Sanger sequencing to detect mutations in FKBP10 and to analyze their relation to the phenotypes of OI type XI in three Chinese patients...
August 25, 2016: Journal of Human Genetics
Aleksandra Biedrzycka, Alvaro Sebastian, Magdalena Migalska, Helena Westerdahl, Jacek Radwan
Characterisation of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated dataset, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches...
October 19, 2016: Molecular Ecology Resources
Tara M Newcomb, Kevin M Flanigan
The cloning of the DMD gene, and the identifications of mutations in it as the cause of Duchenne muscular dystrophy (DMD), makes a compelling story that is aptly told elsewhere.(1) The locus-the largest in the human genome-consists of 79 exons, distributed over 2.5 million nucleotides on the X chromosome, which are assembled into a complementary DNA (cDNA) of around 14 kb encoding the predominant muscle isoform of the dystrophin protein.(2) The size of the gene, and the number of exons, had historically made mutation analysis challenging...
October 2016: Neurology. Genetics
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