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Whole exome sequencing

Dong Li, Tara L Wenger, Christoph Seiler, Michael E March, Alvaro Gutierrez-Uzquiza, Charlly Kao, Elizabeth Bhoj, Lifeng Tian, Misha Rosenbach, Yichuan Liu, Nora Robinson, Mechenzie Behr, Rosetta Chiavacci, Cuiping Hou, Tiancheng Wang, Marina Bakay, Renata Pellegrino da Silva, Jonathan A Perkins, Patrick Sleiman, Michael A Levine, Patricia J Hicks, Maxim Itkin, Yoav Dori, Hakon Hakonarson
Central conducting lymphatic anomaly (CCLA) is one of the complex lymphatic anomalies characterized by dilated lymphatic channels, lymphatic channel dysmotility, and distal obstruction affecting lymphatic drainage. We performed whole exome sequencing (WES) of DNA from a four-generation pedigree and examined the consequences of the variant by transfection of mammalian cells and morpholino and rescue studies in zebrafish. WES revealed a heterozygous mutation in EPHB4 (RefSeq NM_004444.4; c.2334 + 1G>C) and RNA-Seq demonstrated that the EPHB4 mutation destroys the normal donor site, which leads to the use of a cryptic splice donor that results in retention of the intervening 12-bp intron sequence...
June 14, 2018: Human Molecular Genetics
John K L Wong, Hongsheng Gui, Maxwell Kwok, Ping Wing Ng, Colin H T Lui, Larry Baum, Pak Chung Sham, Patrick Kwan, Stacey S Cherny
Objective: We investigated the role of rare genetic variants and of de novo variants in the pathogenesis of mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS). Methods: Whole-exome sequencing (WES) was performed in patients with MTLE-HS and their unaffected parents (trios). Genes or gene sets that were enriched with predicted damaging rare variants in the patients as compared to population controls were identified. Patients and their parents were compared to identify whether the variants were de novo or inherited...
June 2018: Neurology. Genetics
Pasquale Striano, Carlo Nobile
No abstract text is available yet for this article.
June 2018: Neurology. Genetics
Andrew J Aguirre, Jonathan A Nowak, Nicholas D Camarda, Richard A Moffitt, Arezou A Ghazani, Mehlika Hazar-Rethinam, Srivatsan Raghavan, Jaegil Kim, Lauren K Brais, Dorisanne Ragon, Marisa W Welch, Emma Reilly, Devin McCabe, Lori Marini, Kristin Anderka, Karla Helvie, Nelly Oliver, Ana Babic, Annacarolina Da Silva, Brandon Nadres, Emily E Van Seventer, Heather A Shahzade, Joseph P St Pierre, Kelly P Burke, Thomas E Clancy, James M Cleary, Leona A Doyle, Kunal Jajoo, Nadine J McCleary, Jeffrey A Meyerhardt, Janet E Murphy, Kimmie Ng, Anuj K Patel, Kimberly Perez, Michael H Rosenthal, Douglas A Rubinson, Marvin Ryou, Geoffrey I Shapiro, Ewa Sicinska, Stuart G Silverman, Rebecca J Nagy, Richard B Lanman, Deborah Knoerzer, Dean J Welsch, Matthew B Yurgelun, Charles S Fuchs, Levi A Garraway, Gad Getz, Jason L Hornick, Bruce E Johnson, Matthew H Kulke, Robert J Mayer, Jeffrey W Miller, Paul B Shyn, David A Tuveson, Nikhil Wagle, Jen Jen Yeh, William C Hahn, Ryan B Corcoran, Scott L Carter, Brian M Wolpin
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole exome sequencing and RNA-sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data...
June 14, 2018: Cancer Discovery
Jehan Suleiman, Nadia Hamwi, Ayman W El-Hattab
Parkinson disease is a common neurodegenerative disease that typically starts around the age of 60 years; however, juvenile-onset disease can occur rarely. Although Parkinson disease is typically sporadic; in rare occasions, it can be caused by a single gene defect that is inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Herein, we describe a 10-year-old child who had juvenile-onset parkinsonism with rigidity, bradykinesia, dystonia, gait disturbance, and cognitive impairment. Whole exome sequencing showed compound heterozygosity for two previously unreported novel mutations in ATP13A2 (PARK9): a paternally inherited c...
June 11, 2018: Brain & Development
Mingsheng Guo, Wei Yue, David C Samuels, Hui Yu, Jing He, Ying-Yong Zhao, Yan Guo
Genotyping arrays characterize genome-wide SNPs for a study cohort and were the primary technology behind genome wide association studies over the last decade. The Cancer Genome Atlas (TCGA) is one of the largest cancer consortium studies, and it collected genotyping data for all of its participants. Using TCGA SNP data genotyped using the Affymetrix 6.0 SNP array from 12,064 samples, we conducted a comprehensive comparisons across DNA sources (tumor tissue, normal tissue, and blood) and sample storage protocols (formalin-fixed paraffin-embedded (FFPE) vs...
June 11, 2018: Genomics
Xiaoqi Liu, Yaqi Wu, Zequn Miao, Houbin Zhang, Bo Gong, Xianjun Zhu, Lulin Huang, Yi Shi, Fang Hao, Shi Ma, He Lin, Lejin Wang, Zhenglin Yang
PURPOSE: Congenital aniridia, a severe bilateral panocular visual disorder, is an autosomal dominantly inherited eye anomaly. Mutations in the paired box 6 gene (PAX6) have been shown to be responsible for congenital aniridia in most patients. The purpose of the present study was to report clinical features of a Chinese family with congenital aniridia and to screen novel genetic mutations for congenital aniridia. METHODS: All members of a three-generation family underwent comprehensive ophthalmic examination, and 8 of its 25 members were diagnosed with congenital aniridia...
June 14, 2018: Ophthalmic Genetics
Chiara Colombo, Milena Urbini, Annalisa Astolfi, Paola Collini, Valentina Indio, Antonino Belfiore, Nicholas Paielli, Federica Perrone, Giuseppe Tarantino, Elena Palassini, Marco Fiore, Andrea Pession, Silvia Stacchiotti, Maria Abbondanza Pantaleo, Alessandro Gronchi
A wait and see approach for desmoid tumors (DT) has become part of the routine treatment strategy. However, predictive factors to select the risk of progressive disease are still lacking. A translational project was run in order to identify genomic signatures in patients enrolled within an Italian prospective observational study. Among 12 DT patients (ten CTNNB1-mutated and two WT) enrolled from our Institution only two patients (17%) showed a progressive disease. Tumor biopsies were collected for whole exome sequencing...
June 14, 2018: Genes, Chromosomes & Cancer
Wenjin Yan, Jin Dai, Dongquan Shi, Xingquan Xu, Xiao Han, Zhihong Xu, Dongyang Chen, Huajiang Teng, Qing Jiang
Schwartz-Jampel syndrome type 1 (SJS1) is a rare autosomal recessive disease caused by mutations in the gene heparan sulfate proteoglycan 2 (HSPG2; also known as basement membrane‑specific heparin sulfate). In the present study, a 10‑year‑old female SJS1 proband from a Chinese family, who was diagnosed by X‑ray and physical examination, was recruited. The key clinical features of the patient with SJS1 included short stature, joint contractures, pigeon breast, and myotonia that led to progressive stiffness of the face and limbs; barely discernible kyphosis was also noted...
June 6, 2018: Molecular Medicine Reports
Robert Smigiel, Gerd Landsberg, Maximilian Schilling, Małgorzata Rydzanicz, Agnieszka Pollak, Anna Walczak, Anna Stodolak, Piotr Stawinski, Hanna Mierzewska, Maria M Sasiadek, Oliver J Gruss, Rafal Ploski
PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies...
June 13, 2018: European Journal of Human Genetics: EJHG
Keiichi Hatakeyama, Takeshi Nagashima, Kenichi Urakami, Keiichi Ohshima, Masakuni Serizawa, Sumiko Ohnami, Yuji Shimoda, Shumpei Ohnami, Koji Maruyama, Akane Naruoka, Yasuto Akiyama, Masatoshi Kusuhara, Tohru Mochizuki, Ken Yamaguchi
Tumor mutational burden (TMB) is an emerging characteristic in cancer and has been associated with microsatellite instability, defective DNA replication/repair, and response to PD-1 and PD-L1 blockade immunotherapy. When estimating TMB, targeted panel sequencing is performed using a few hundred genes; however, a comparison of TMB results obtained with this platform and with whole exome sequencing (WES) has not been performed for various cancer types. In the present study, we compared TMB results using the above two platforms in 2,908 solid tumors that were obtained from Japanese patients...
2018: Biomedical Research
Shaohua Tang, Manli Jia, Chong Chen, Huanzheng Li, Lin Hu, Zhaotang Luan, Xueqin Xu, Jianxin Lyu
OBJECTIVE: To explore the clinical features and genetic mutation in a family affected with non-syndrome X-linked intellectual disability (NS-XLID) using whole exome sequencing (WES). METHODS: Multiplex ligation-dependent probe amplification (MLPA) was applied to screen potential mutations of Fragile X syndrome (FXS). Whole exome sequencing (WES) and Sanger sequencing were screen for pathological mutations. RESULTS: FXS was excluded by MLPA analysis...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Matthew J Huentelman, Ignazio S Piras, Ashley L Siniard, Matthew D De Both, Ryan F Richholt, Chris D Balak, Pouya Jamshidi, Eileen H Bigio, Sandra Weintraub, Emmaleigh T Loyer, M-Marsel Mesulam, Changiz Geula, Emily J Rogalski
Introduction : SuperAgers are adults age 80+ with episodic memory performance that is at least as good as that of average middle-aged adults. Understanding the biological determinants of SuperAging may have relevance to preventing age-related cognitive decline and dementia. This study aimed to identify associations between genetic variations and the SuperAging phenotype using Whole Exome Sequencing (WES). Methods : Sequence Kernel Association Combined (SKAT-C) test was conducted at the gene level including both rare and common variants in 56 SuperAgers and 22 cognitively-average controls from the Alzheimer's disease Neuroimaging Initiative (ADNI)...
2018: Frontiers in Aging Neuroscience
Boris Chaumette, Vladimir Ferrafiat, Amirthagowri Ambalavanan, Alice Goldenberg, Alexandre Dionne-Laporte, Dan Spiegelman, Patrick A Dion, Priscille Gerardin, Claudine Laurent, David Cohen, Judith Rapoport, Guy A Rouleau
Childhood-onset schizophrenia (COS) is a rare and severe form of schizophrenia defined as onset before age of 13. Here we report on two unrelated cases diagnosed with both COS and alternating hemiplegia of childhood (AHC), and for whom two distinct pathogenic de novo variants were identified in the ATP1A3 gene. ATP1A3 encodes the α-subunit of a neuron-specific ATP-dependent transmembrane sodium-potassium pump. Using whole exome sequencing data derived from a cohort of 17 unrelated COS cases, we also examined ATP1A3 and all of its interactors known to be expressed in the brain to establish if variants could be identified...
June 12, 2018: Molecular Psychiatry
Andrey V Marakhonov, Vyacheslav Yu Tabakov, Nikolay V Zernov, Elena L Dadali, Inna V Sharkova, Mikhail Yu Skoblov
Here we present a case report of collagen VI related myopathy in a patient, 8 y.o. boy, with intermediate phenotype between severe Ullrich congenital muscular dystrophy and milder Bethlem myopathy. Whole exome sequencing revealed two novel single nucleotide variants in COL6A3 gene: paternal p.Glu2402Ter, resulting in premature translation termination codon and degradation of mRNA from this allele probably due to nonsense-mediated decay, and maternal p.Arg1660Cys leading to amino-acid substitution in N2-terminal domain...
June 9, 2018: Gene
Marc Ferrer, Sara J C Gosline, Marigo Stathis, Xiaohu Zhang, Xindi Guo, Rajarshi Guha, Dannielle A Ryman, Margaret R Wallace, Laura Kasch-Semenza, Haiping Hao, Roxann Ingersoll, David Mohr, Craig Thomas, Sharad Verma, Justin Guinney, Jaishri O Blakeley
Neurofibromatosis type I (NF1) is an autosomal dominant genetic condition characterized by peripheral nervous system tumors (PNSTs), including plexiform neurofibromas (pNFs) that cause nerve dysfunction, deformity, pain damage to adjacent structures, and can undergo malignant transformation. There are no effective therapies to prevent or treat pNFs. Drug discovery efforts are slowed by the 'benign' nature of the Schwann cells that are the progenitor cells of pNF. In this work we characterize a set of pNF-derived cell lines at the genomic level (via SNP Arrays, RNAseq, and Whole Exome- Sequencing), and carry out dose response-based quantitative high-throughput screening (qHTS) with a collection of 1,912 oncology-focused compounds in a 1536-well microplate cell proliferation assays...
June 12, 2018: Scientific Data
Da Eun Nam, Da Hye Yoo, Sun Seong Choi, Byung-Ok Choi, Ki Wha Chung
The kinesin heavy chain isoform 5A (KIF5A) gene, which encodes a microtubule-based motor protein, plays an important role in the transport of organelles in the nerve cells. Mutations in the KIF5A showed a wide phenotypic spectrum from hereditary spastic paraplegia (HSP) to axonal Charcot-Marie-Tooth peripheral neuropathy type 2 (CMT2). This study identified three pathogenic KIF5A mutations in Korean CMT2 patients by whole exome sequencing. Two mutations (p.Arg204Trp and p.Arg280His) were previously reported, but p...
January 2018: Genes & Genomics
Yong Ju Ahn, Kesavan Markkandan, In-Pyo Baek, Seyoung Mun, Wooseok Lee, Heui-Soo Kim, Kyudong Han
Next generation sequencing (NGS) has traditionally been performed in various fields including agricultural to clinical and there are so many sequencing platforms available in order to obtain accurate and consistent results. However, these platforms showed amplification bias when facilitating variant calls in personal genomes. Here, we sequenced whole genomes and whole exomes from ten Korean individuals using Illumina and Ion Proton, respectively to find the vulnerability and accuracy of NGS platform in the GC rich/poor area...
January 2018: Genes & Genomics
Eric J Norris, Wendell D Jones, Marius D Surleac, Andrei J Petrescu, Darla Destephanis, Qing Zhang, Issam Hamadeh, Jeffrey S Kneisl, Chad A Livasy, Ram N Ganapathi, David L Tait, Mahrukh K Ganapathi
Neurofibromatosis type 1 (NF1) is caused by mutations in the NF1 gene encoding neurofibromin, which negatively regulates Ras signaling. NF1 patients have an increased risk of developing early onset breast cancer, however, the association between NF1 and high grade serous ovarian cancer (HGSOC) is unclear. Since most NF1-related tumors exhibit early biallelic inactivation of NF1 , we evaluated the evolution of genetic alterations in HGSOC in an NF1 patient. Somatic variation analysis of whole exome sequencing of tumor samples from both ovaries and a peritoneal metastasis showed a clonal lineage originating from an ancestral clone within the left adnexa, which exhibited copy number (CN) loss of heterozygosity (LOH) in the region of chromosome 17 containing TP53, NF1 , and BRC A1 and mutation of the other TP53 allele...
February 2018: Gynecologic Oncology Reports
Núria Camats, Mónica Fernández-Cancio, Laura Audí, André Schaller, Christa E Flück
SF-1/NR5A1 is a transcriptional regulator of adrenal and gonadal development. NR5A1 disease-causing variants cause disorders of sex development (DSD) and adrenal failure, but most affected individuals show a broad DSD/reproductive phenotype only. Most NR5A1 variants show in vitro pathogenic effects, but not when tested in heterozygote state together with wild-type NR5A1 as usually seen in patients. Thus, the genotype-phenotype correlation for NR5A1 variants remains an unsolved question. We analyzed heterozygous 46,XY SF-1/NR5A1 patients by whole exome sequencing and used an algorithm for data analysis based on selected project-specific DSD- and SF-1-related genes...
June 11, 2018: European Journal of Human Genetics: EJHG
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