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Exome sequencing

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https://www.readbyqxmd.com/read/28343239/improved-full-length-killer-cell-immunoglobulin-like-receptor-transcript-discovery-in-mauritian-cynomolgus-macaques
#1
Trent M Prall, Michael E Graham, Julie A Karl, Roger W Wiseman, Adam J Ericsen, Muthuswamy Raveendran, R Alan Harris, Donna M Muzny, Richard A Gibbs, Jeffrey Rogers, David H O'Connor
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS)...
March 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28343148/de-novo-mutations-in-cbl-causing-early-onset-paediatric-moyamoya-angiopathy
#2
Stéphanie Guey, Lou Grangeon, Francis Brunelle, Françoise Bergametti, Jeanne Amiel, Stanislas Lyonnet, Audrey Delaforge, Minh Arnould, Béatrice Desnous, Céline Bellesme, Dominique Hervé, Jan C Schwitalla, Markus Kraemer, Elisabeth Tournier-Lasserve, Manoelle Kossorotoff
BACKGROUND: Moyamoya angiopathy (MMA) is characterised by a progressive stenosis of the terminal part of the internal carotid arteries and the development of abnormal collateral deep vessels. Its pathophysiology is unknown. MMA can be the sole manifestation of the disease (moyamoya disease) or be associated with various conditions (moyamoya syndrome) including some Mendelian diseases. We aimed to investigate the genetic basis of moyamoya using a whole exome sequencing (WES) approach conducted in sporadic cases without any overt symptom suggestive of a known Mendelian moyamoya syndrome...
March 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28342698/targeted-exome-sequencing-and-chromosomal-microarray-for-the-molecular-diagnosis-of-nevoid-basal-cell-carcinoma-syndrome
#3
Yoshihiro Matsudate, Takuya Naruto, Yumiko Hayashi, Mitsuyoshi Minami, Mikiko Tohyama, Kenji Yokota, Daisuke Yamada, Issei Imoto, Yoshiaki Kubo
BACKGROUND: Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder mainly caused by heterozygous mutations of PTCH1. In addition to characteristic clinical features, detection of a mutation in causative genes is reliable for the diagnosis of NBCCS; however, no mutations have been identified in some patients using conventional methods. OBJECTIVE: To improve the method for the molecular diagnosis of NBCCS. METHODS: We performed targeted exome sequencing (TES) analysis using a multi-gene panel, including PTCH1, PTCH2, SUFU, and other sonic hedgehog signaling pathway-related genes, based on next-generation sequencing (NGS) technology in 8 cases in whom possible causative mutations were not detected by previously performed conventional analysis and 2 recent cases of NBCCS...
March 11, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28339689/genomic-decision-support-needs-in-pediatric-primary-care
#4
Jeffrey W Pennington, Dean J Karavite, Edward M Krause, Jeffrey Miller, Barbara A Bernhardt, Robert W Grundmeier
Clinical genome and exome sequencing can diagnose pediatric patients with complex conditions that often require follow-up care with multiple specialties. The American Academy of Pediatrics emphasizes the role of the medical home and the primary care pediatrician in coordinating care for patients who need multidisciplinary support. In addition, the electronic health record (EHR) with embedded clinical decision support is recognized as an important component in providing care in this setting. We interviewed 6 clinicians to assess their experience caring for patients with complex and rare genetic findings and hear their opinions about how the EHR currently supports this role...
February 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339163/next-generation-sequencing-of-urine-specimens-a-novel-platform-for-genomic-analysis-in-patients-with-non-muscle-invasive-urothelial-carcinoma-treated-with-bacille-calmette-gu%C3%A3-rin
#5
Sasinya N Scott, Irina Ostrovnaya, Caroline M Lin, Nancy Bouvier, Bernard H Bochner, Gopakumar Iyer, David Solit, Michael F Berger, Oscar Lin
BACKGROUND: Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment...
March 24, 2017: Cancer
https://www.readbyqxmd.com/read/28339086/identification-of-novel-mutations-in-endometrial-cancer-patients-by-whole-exome-sequencing
#6
Ya-Sian Chang, Hsien-Da Huang, Kun-Tu Yeh, Jan-Gowth Chang
The aim of the present study was to identify genomic alterations in Taiwanese endometrial cancer patients. This information is vitally important in Taiwan, where endometrial cancer is the second most common gynecological cancer. We performed whole-exome sequencing on DNA from 14 tumor tissue samples from Taiwanese endometrial cancer patients. We used the Genome Analysis Tool kit software package for data analysis, and the dbSNP, Catalogue of Somatic Mutations in Cancer (COSMIC) and The Cancer Genome Atlas (TCGA) databases for comparisons...
March 20, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28338821/phylogenomic-insights-into-mouse-evolution-using-a-pseudoreference-approach
#7
Brice A J Sarver, Sara Keeble, Ted Cosart, Priscilla K Tucker, Matthew D Dean, Jeffrey M Good
Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338218/evaluation-of-targeted-exome-sequencing-for-28-protein-based-blood-group-systems-including-the-homologous-gene-systems-for-blood-group-genotyping
#8
Elizna M Schoeman, Genghis H Lopez, Eunike C McGowan, Glenda M Millard, Helen O'Brien, Eileen V Roulis, Yew-Wah Liew, Jacqueline R Martin, Kelli A McGrath, Tanya Powley, Robert L Flower, Catherine A Hyland
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform...
March 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28335750/novel-compound-heterozygous-mutations-in-the-otof-gene-identified-by-whole-exome-sequencing-in-auditory-neuropathy-spectrum-disorder
#9
Fengzhu Tang, Dengke Ma, Yulan Wang, Yuecai Qiu, Fei Liu, Qingqing Wang, Qiutian Lu, Min Shi, Liang Xu, Min Liu, Jianping Liang
BACKGROUND: Many hearing-loss diseases are demonstrated to have Mendelian inheritance caused by mutations in single gene. However, many deaf individuals have diseases that remain genetically unexplained. Auditory neuropathy is a sensorineural deafness in which sounds are able to be transferred into the inner ear normally but the transmission of the signals from inner ear to auditory nerve and brain is injured, also known as auditory neuropathy spectrum disorder (ANSD). The pathogenic mutations of the genes responsible for the Chinese ANSD population remain poorly understood...
March 23, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28335073/clinical-characteristics-and-whole-exome-transcriptome-sequencing-of-coexisting-chronic-myeloid-leukemia-and-myelofibrosis
#10
Malathi Kandarpa, Yi-Mi Wu, Dan Robinson, Patrick William Burke, Arul M Chinnaiyan, Moshe Talpaz
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell (HSC) disorders that can be classified on the basis of genetic, clinical, phenotypic features. Genetic lesions such as JAK2 mutations and BCR-ABL translocation are often mutually exclusive in MPN patients and lead to essential thrombocythemia, polycythemia vera or myelofibrosis (ET/PV/MF) or chronic myeloid leukemia, respectively. Nevertheless, coexistence of these genetic aberrations in the same patient has been reported. Whether these aberrations occur in the same stem cell or a different cell is unclear, but an unstable genome in the HSCs seems to be the common antecedent...
March 23, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28335020/znhit3-is-defective-in-peho-syndrome-a-severe-encephalopathy-with-cerebellar-granule-neuron-loss
#11
Anna-Kaisa Anttonen, Anni Laari, Maria Kousi, Yawei J Yang, Tiina Jääskeläinen, Mirja Somer, Eija Siintola, Eveliina Jakkula, Mikko Muona, Saara Tegelberg, Tuula Lönnqvist, Helena Pihko, Leena Valanne, Anders Paetau, Melody P Lun, Johanna Hästbacka, Outi Kopra, Tarja Joensuu, Nicholas Katsanis, Maria K Lehtinen, Jorma J Palvimo, Anna-Elina Lehesjoki
Progressive encephalopathy with oedema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is an early childhood onset, severe autosomal recessive encephalopathy characterized by extreme cerebellar atrophy due to almost total granule neuron loss. By combining homozygosity mapping in Finnish families with Sanger sequencing of positional candidate genes and with exome sequencing a homozygous missense substitution of leucine for serine at codon 31 in ZNHIT3 was identified as the primary cause of PEHO syndrome. ZNHIT3 encodes a nuclear zinc finger protein previously implicated in transcriptional regulation and in small nucleolar ribonucleoprotein particle assembly and thus possibly to pre-ribosomal RNA processing...
March 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334964/mutations-in-the-leukemia-inhibitory-factor-receptor-lifr-gene-and-lifr-deficiency-cause-urinary-tract-malformations
#12
Anne Kosfeld, Frank Brand, Anna-Carina Weiss, Martin Kreuzer, Michaela Goerk, Helge Martens, Stephanie Schubert, Anne-Kathrin Schäfer, Vera Riehmer, Imke Hennies, Jan Hinrich Bräsen, Lars Pape, Kerstin Amann, Lars Krogvold, Anna Bjerre, Christoph Daniel, Andreas Kispert, Dieter Haffner, Ruthild G Weber
Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease in children. As CAKUT is a genetically heterogeneous disorder and most cases are genetically unexplained, we aimed to identify new CAKUT causing genes. Using whole-exome sequencing and trio-based de novo analysis, we identified a novel heterozygous de novo frameshift variant in the leukemia inhibitory factor receptor (LIFR) gene causing instability of the mRNA in a patient presenting with bilateral CAKUT and requiring kidney transplantation at one year of age...
March 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334938/clinical-and-genetic-characterization-of-leukoencephalopathies-in-adults
#13
David S Lynch, Anderson Rodrigues Brandão de Paiva, Wei Jia Zhang, Enrico Bugiardini, Fernando Freua, Leandro Tavares Lucato, Lucia Inês Macedo-Souza, Rahul Lakshmanan, Justin A Kinsella, Aine Merwick, Alexander M Rossor, Nin Bajaj, Brian Herron, Paul McMonagle, Patrick J Morrison, Deborah Hughes, Alan Pittman, Matilde Laurà, Mary M Reilly, Jason D Warren, Catherine J Mummery, Jonathan M Schott, Matthew Adams, Nick C Fox, Elaine Murphy, Indran Davagnanam, Fernando Kok, Jeremy Chataway, Henry Houlden
Leukodystrophies and genetic leukoencephalopathies are a rare group of disorders leading to progressive degeneration of cerebral white matter. They are associated with a spectrum of clinical phenotypes dominated by dementia, psychiatric changes, movement disorders and upper motor neuron signs. Mutations in at least 60 genes can lead to leukoencephalopathy with often overlapping clinical and radiological presentations. For these reasons, patients with genetic leukoencephalopathies often endure a long diagnostic odyssey before receiving a definitive diagnosis or may receive no diagnosis at all...
March 2, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334855/slc30a9-mutation-affecting-intracellular-zinc-homeostasis-causes-a-novel-cerebro-renal-syndrome
#14
Yonatan Perez, Zamir Shorer, Keren Liani-Leibson, Pauline Chabosseau, Rotem Kadir, Michael Volodarsky, Daniel Halperin, Shiran Barber-Zucker, Hanna Shalev, Ruth Schreiber, Libe Gradstein, Evgenia Gurevich, Raz Zarivach, Guy A Rutter, Daniel Landau, Ohad S Birk
A novel autosomal recessive cerebro-renal syndrome was identified in consanguineous Bedouin kindred: neurological deterioration was evident as of early age, progressing into severe intellectual disability, profound ataxia, camptocormia and oculomotor apraxia. Brain MRI was normal. Four of the six affected individuals also had early-onset nephropathy with features of tubulo-interstitial nephritis, hypertension and tendency for hyperkalemia, though none had rapid deterioration of renal function. Genome wide linkage analysis identified an ∼18 Mb disease-associated locus on chromosome 4 (maximal logarithm of odds score 4...
February 9, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334355/a-zoom-focus-algorithm-zfa-to-locate-the-optimal-testing-region-for-rare-variant-association-tests
#15
Maggie Haitian Wang, Haoyi Weng, Rui Sun, Jack Lee, William Ka Kei Wu, Ka Chun Chong, Benny Chung-Ying Zee
Motivation: Increasing amounts of whole exome or genome sequencing data present the challenge of analysing rare variants with extremely small minor allele frequencies. Various statistical tests have been proposed, which are specifically configured to increase power for rare variants by conducting the test within a certain bin, such as a gene or a pathway. However, a gene may contain from several to thousands of markers, and not all of them are related to the phenotype. Combining functional and non-functional variants in an arbitrary genomic region could impair the testing power...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333919/exome-sequencing-based-molecular-autopsy-of-formalin-fixed-paraffin-embedded-tissue-after-sudden-death
#16
Richard D Bagnall, Jodie Ingles, Laura Yeates, Samuel F Berkovic, Christopher Semsarian
PURPOSE: Sudden death in the young is a devastating complication of inherited heart disorders. Finding the precise cause of death is important, but it is often unresolved after postmortem investigation. The addition of postmortem genetic testing, i.e., the molecular autopsy, can identify additional causes of death. We evaluated DNA extracted from formalin-fixed paraffin-embedded postmortem tissue for exome sequencing-based molecular autopsy after sudden death in the young. METHODS: We collected clinical and postmortem information from patients with sudden death...
March 23, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28333917/a-clinical-utility-study-of-exome-sequencing-versus-conventional-genetic-testing-in-pediatric-neurology
#17
Lisenka E L M Vissers, Kirsten J M van Nimwegen, Jolanda H Schieving, Erik-Jan Kamsteeg, Tjitske Kleefstra, Helger G Yntema, Rolph Pfundt, Gert Jan van der Wilt, Lotte Krabbenborg, Han G Brunner, Simone van der Burg, Janneke Grutters, Joris A Veltman, Michèl A A P Willemsen
PURPOSE: Implementation of novel genetic diagnostic tests is generally driven by technological advances because they promise shorter turnaround times and/or higher diagnostic yields. Other aspects, including impact on clinical management or cost-effectiveness, are often not assessed in detail prior to implementation. METHODS: We studied the clinical utility of whole-exome sequencing (WES) in complex pediatric neurology in terms of diagnostic yield and costs. We analyzed 150 patients (and their parents) presenting with complex neurological disorders of suspected genetic origin...
March 23, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28333167/a-complex-intragenic-rearrangement-of-ercc8-in-chinese-siblings-with-cockayne-syndrome
#18
Hua Xie, Xiaoyan Li, Jiping Peng, Qian Chen, ZhiJie Gao, Xiaozhen Song, WeiYu Li, Jianqiu Xiao, Caihua Li, Ting Zhang, James F Gusella, Jianmin Zhong, Xiaoli Chen
Cockayne syndrome is an autosomal recessive disorder principally characterized by postnatal growth failure and progressive neurological dysfunction, due primarily to mutations in ERCC6 and ERCC8. Here, we report our diagnostic experience for two patients in a Chinese family suspected on clinical grounds to have Cockayne syndrome. Using multiple molecular techniques, including whole exome sequencing, array comparative genomic hybridization and quantitative polymerase chain reaction, we identified compound heterozygosity for a maternal splicing variant (chr5:60195556, NM_000082:c...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28332767/bcap31-associated-encephalopathy-and-complex-movement-disorder-mimicking-mitochondrial-encephalopathy
#19
Saleh Albanyan, Amal Al Teneiji, Nasim Monfared, Saadet Mercimek-Mahmutoglu
BCAP31, encoded by BCAP31, is involved in the export of transmembrane proteins from the endoplasmic reticulum. Pathogenic variants in BCAP31 results in global developmental delay, dystonia, deafness and dysmorphic features in males, called deafness, dystonia, and cerebral hypomyelination (DDCH) syndrome. We report a new patient with BCAP3-associated encephalopathy, DDCH syndrome, sensorineural hearing loss, generalized dystonia, and choreoathetosis. This 3.5-year-old boy had microcephaly and failure to thrive within the first 3 months of life...
March 23, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28332297/hereditary-spastic-paraplegia-caused-by-compound-heterozygous-mutations-outside-the-motor-domain-of-the-kif1a-gene
#20
M Krenn, G Zulehner, C Hotzy, J Rath, E Stogmann, M Wagner, T B Haack, T M Strom, A Zimprich, F Zimprich
BACKGROUND AND PURPOSE: Hereditary spastic paraplegia is a clinically and genetically heterogeneous group of rare, inherited disorders causing an upper motor neuron syndrome with (complex) or without (pure) additional neurological symptoms. Mutations in the KIF1A gene have already been associated with recessive and dominant forms of hereditary spastic paraplegia (SPG30) in a few cases. METHODS: All family members included in the study were examined neurologically...
March 22, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
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