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https://www.readbyqxmd.com/read/29334593/reanalysis-of-clinical-whole-exome-sequence-data-yields-multiple-new-diagnoses-a-time-intensive-but-successful-strategy-highlights-the-benefits-of-data-sharing-and-international-collaborations
#1
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February 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29332568/fgf-21-as-a-potential-biomarker-for-mitochondrial-diseases
#2
Leila Motlagh Scholle, Diana Lehmann, Marcus Deschauer, Torsten Kraya, Stephan Zierz
The diagnosis of mitochondrial diseases is still challenging due to clinical and genetical heterogeneity. The development of advanced technologies including Whole-Exome-Sequencing (WES) and Whole-Genome-Sequencing (WGS) have led to improvements in genetic diagnosis. However, a reliable biomarker in serum could enhance and ease the diagnosis and indeed reduce the need for muscle biopsy. Several studies suggest Fibroblast growth factor 21 (FGF-21) as a biomarker for diagnosis in mitochondrial disorders. It is known, that in patients with mitochondrial disorders, the expression of FGF-21 gets elevated in an effort to counteract the underlying metabolic deficiency...
January 10, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29331980/dmc1-mutation-that-causes-human-non-obstructive-azoospermia-and-premature-ovarian-insufficiency-identified-by-whole-exome-sequencing
#3
Wen-Bin He, Chao-Feng Tu, Qiang Liu, Lan-Lan Meng, Shi-Min Yuan, Ai-Xiang Luo, Fu-Sheng He, Juan Shen, Wen Li, Juan Du, Chang-Gao Zhong, Guang-Xiu Lu, Ge Lin, Li-Qing Fan, Yue-Qiu Tan
BACKGROUND: The genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown. OBJECTIVE: To identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family. METHODS: We performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family...
January 13, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29331839/functional-characterization-of-a-novel-herg-variant-in-a-family-with-recurrent-sudden-infant-death-syndrome-retracting-a-genetic-diagnosis
#4
Valentine Sergeev, Frances Perry, Thomas M Roston, Shubhayan Sanatani, Glen F Tibbits, Thomas W Claydon
Long QT syndrome (LQTS) is the most common cardiac ion channelopathy and has been found to be responsible for approximately 10% of sudden infant death syndrome (SIDS) cases. Despite increasing use of broad panels and now whole exome sequencing (WES) in the investigation of SIDS, the probability of identifying a pathogenic mutation in a SIDS victim is low. We report a family-based study who are afflicted by recurrent SIDS in which several members harbor a variant, p.Pro963Thr, in the C-terminal region of the human-ether-a-go-go (hERG) gene, published to be responsible for cases of LQTS type 2...
December 20, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29331481/genetic-contribution-of-sun5-mutations-to-acephalic-spermatozoa-in-fujian-china
#5
Yan-Wei Sha, Xiaohui Xu, Zhi-Yong Ji, Shao-Bin Lin, Xu Wang, Ping-Ping Qiu, Yulin Zhou, Li-Bin Mei, Zhi-Ying Su, Lin Li, Ping Li
Acephalic spermatozoa is an extremely rare disease associated with primary infertility. A recent study showed that genetic alterations in the SUN5 gene lead to this disease, and SUN5 mutations could explain the disease in about half of the patients. Therefore, in the present study, to re-visit the genetic contribution of SUN5 mutations to acephalic spermatozoa, we recruited 15 unrelated affected individuals and screened the SUN5 gene for mutations by whole-exome sequencing (WES) and Sanger sequencing. Five of the 15 (33...
January 10, 2018: Gene
https://www.readbyqxmd.com/read/29331079/lmod3-associated-nemaline-myopathy-prenatal-ultrasonographic-pathologic-and-molecular-findings
#6
Michal Berkenstadt, Ben Pode-Shakked, Ortal Barel, Hila Barash, Reuven Achiron, Yinon Gilboa, Dvora Kidron, Annick Raas-Rothschild
To describe the prenatal presentation, including ultrasonographic, histologic, and molecular findings, in 2 fetuses affected with LMOD3-related nemaline myopathy. Prenatal ultrasonographic examinations and histopathologic studies were performed on 2 fetuses with evidence of nemaline myopathy. To establish a molecular diagnosis, whole-exome sequencing was pursued for the affected fetuses. Nemaline myopathy is a common form of congenital myopathy manifesting with nonprogressive generalized muscle weakness, hypotonia, and electron-dense protein inclusions in skeletal myofibers...
January 13, 2018: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/29330474/a-de-novo-foxp1-truncating-mutation-in-a-patient-originally-diagnosed-as-c-syndrome
#7
Roser Urreizti, Sarah Damanti, Carla Esteve, Héctor Franco-Valls, Laura Castilla-Vallmanya, Raul Tonda, Bru Cormand, Lluïsa Vilageliu, John M Opitz, Giovanni Neri, Daniel Grinberg, Susana Balcells
De novo FOXP1 mutations have been associated with intellectual disability (ID), motor delay, autistic features and a wide spectrum of speech difficulties. C syndrome (Opitz C trigonocephaly syndrome) is a rare and genetically heterogeneous condition, characterized by trigonocephaly, craniofacial anomalies and ID. Several different chromosome deletions and and point mutations in distinct genes have been associated with the disease in patients originally diagnosed as Opitz C. By whole exome sequencing we identified a de novo splicing mutation in FOXP1 in a patient, initially diagnosed as C syndrome, who suffers from syndromic intellectual disability with trigonocephaly...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330011/mutations-in-pi3k110%C3%AE-cause-impaired-nk-cell-function-partially-rescued-by-rapamycin-treatment
#8
Raquel Ruiz-García, Alexander Vargas-Hernandez, Ivan K Chinn, Laura S Angelo, Tram N Cao, Zeynep Coban-Akdemir, Shalini N Jhangiani, Qingchang Meng, Lisa R Forbes, Donna M Muzny, Luis M Allende, Mohammed S Ehlayel, Richard A Gibbs, James R Lupski, Gulbu Uzel, Jordan S Orange, Emily M Mace
BACKGROUND: Heterozygous gain-of-function mutations in PI3K110 lead to lymphadenopathy, lymphoid hyperplasia, Epstein-Barr virus (EBV) and cytomegalovirus (CMV) viremia, and sinopulmonary infections. OBJECTIVE: The known role of NK cell function in the control of EBV and CMV prompted us to investigate the functional and phenotypic effect of PI3K110δ mutations on NK cell subsets and cytotoxic function. METHODS: Patient mutations were identified by whole exome or targeted sequencing...
January 9, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29329938/pipeline-to-gene-discovery-analysing-familial-parkinsonism-in-the-queensland-parkinson-s-project
#9
Steven R Bentley, Stephanie Bortnick, Ilaria Guella, Javed Y Fowdar, Peter A Silburn, Stephen A Wood, Matthew J Farrer, George D Mellick
INTRODUCTION: Family based study designs provide an informative resource to identify disease-causing mutations. The Queensland Parkinson's Project (QPP) has been involved in numerous genetic screening studies; however, details of the families enrolled into the register have not been comprehensively reported. This article characterises the families enrolled in the QPP and summarises monogenic forms of hereditary Parkinsonism found in the register. METHOD: The presence of pathogenic point mutations and copy number variations (CNVs) were, generally, screened in a sample of over 1000 PD patients from the total of 1725...
January 3, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29329714/mutation-burden-profile-in-familial-alzheimer-s-disease-cases-from-india
#10
Adhikarla Syama, Somdatta Sen, Lakshmi Narayanan Kota, Biju Viswanath, Meera Purushottam, Mathew Varghese, Sanjeev Jain, Mitradas M Panicker, Odity Mukherjee
This study attempts to identify coding risk variants in genes previously implicated in Alzheimer's disease (AD) pathways, through whole-exome sequencing of subjects (N = 17) with AD, with a positive family history of dementia (familial AD). We attempted to evaluate the mutation burden in genes encoding amyloid precursor protein metabolism and previously linked to risk of dementias. Novel variants were identified in genes involved in amyloid precursor protein metabolism such as PSEN1 (chr 14:73653575, W161C, tgg > tgT), PLAT (chr 8:42039530,G272R), and SORL1 (chr11:121414373,G601D)...
December 12, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29325629/bioinformatics-and-genomic-databases
#11
Jason Chen, Giovanni Coppola
High-throughput, low-cost sequencing technologies have begun to yield new insights into biology and medicine. New data enable the interrogation of the molecular biology of disease from DNA to RNA to protein, charting the central dogma. This chapter reviews some of the key advances and resources in the application of bioinformatics to understanding, and ultimately diagnosing and treating, diseases of the nervous system. Array genotyping, exome sequencing, and whole-genome sequencing, in both disease and healthy populations, have enabled the interpretation of new genetic data...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325618/neurodegeneration-with-brain-iron-accumulation
#12
Susan J Hayflick, Manju A Kurian, Penelope Hogarth
Neurodegeneration with brain iron accumulation (NBIA) comprises a clinically and genetically heterogeneous group of disorders affecting children and adults. These rare disorders are often first suspected when increased basal ganglia iron is observed on brain magnetic resonance imaging. For the majority of NBIA disorders the genetic basis has been delineated, and clinical testing is available. The four most common NBIA disorders include pantothenate kinase-associated neurodegeneration (PKAN) due to mutations in PANK2, phospholipase A2-associated neurodegeneration caused by mutation in PLA2G6, mitochondrial membrane protein-associated neurodegeneration from mutations in C19orf12, and beta-propeller protein-associated neurodegeneration due to mutations in WDR45...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325523/fanconi-anemia-with-sun-sensitivity-caused-by-a-xeroderma-pigmentosum-associated-missense-mutation-in-xpf
#13
Isabell Popp, Maqsood Punekar, Nick Telford, Stavros Stivaros, Kate Chandler, Meenakshi Minnis, Anna Castleton, Claire Higham, Louise Hopewell, D Gareth Evans, Anja Raams, Arjan F Theil, Stefan Meyer, Detlev Schindler
BACKGROUND: Fanconi anemia (FA) is an inherited genomic instability disorder with congenital and developmental abnormalities, bone marrow failure and predisposition to cancer early in life, and cellular sensitivity to DNA interstrand crosslinks. CASE PRESENTATION: A fifty-one-year old female patient, initially diagnosed with FA in childhood on the basis of classic features and increased chromosomal breakage, and remarkable sun-sensitivity is described. She only ever had mild haematological abnormalities and no history of malignancy...
January 11, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29325224/hereditary-kidney-cancer-syndromes-genetic-disorders-driven-by-alterations-in-metabolism-and-epigenome-regulation
#14
Hisashi Hasumi, Masahiro Yao
Although hereditary kidney cancer syndrome accounts for around five percent of all kidney cancers, the mechanistic insight into tumor development in these rare conditions has provided the foundation for the development of molecular targeting agents currently used for sporadic kidney cancer. In the late 1980s, the comprehensive study for hereditary kidney cancer syndrome was launched in the National Cancer Institute, U.S.A. and the first kidney cancer associated gene, VHL was identified through kindred analysis of von Hippel-Lindau syndrome in 1993...
January 11, 2018: Cancer Science
https://www.readbyqxmd.com/read/29324843/beta-hpv38-oncoproteins-act-with-a-hit-and-run-mechanism-in-ultraviolet-radiation-induced-skin-carcinogenesis-in-mice
#15
Daniele Viarisio, Karin Müller-Decker, Rosita Accardi, Alexis Robitaille, Matthias Dürst, Katrin Beer, Lars Jansen, Christa Flechtenmacher, Matthias Bozza, Richard Harbottle, Catherine Voegele, Maude Ardin, Jiri Zavadil, Sandra Caldeira, Lutz Gissmann, Massimo Tommasino
Cutaneous beta human papillomavirus (HPV) types are suspected to be involved, together with ultraviolet (UV) radiation, in the development of non-melanoma skin cancer (NMSC). Studies in in vitro and in vivo experimental models have highlighted the transforming properties of beta HPV E6 and E7 oncoproteins. However, epidemiological findings indicate that beta HPV types may be required only at an initial stage of carcinogenesis, and may become dispensable after full establishment of NMSC. Here, we further investigate the potential role of beta HPVs in NMSC using a Cre-loxP-based transgenic (Tg) mouse model that expresses beta HPV38 E6 and E7 oncogenes in the basal layer of the skin epidermis and is highly susceptible to UV-induced carcinogenesis...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29323771/association-of-igfn1-variant-with-polypoidal-choroidal-vasculopathy
#16
Xiaofeng Wen, Yu Liu, Qi Yan, Minling Liang, Miao Tang, Ran Liu, Jianying Pan, Qiuhui Liu, Tingting Chen, Shixin Guo, Juanran Liang, Lin Lu, Xiaoyan Ding, Wei Chen, Lai Wei
BACKGROUND: Polypoidal choroidal vasculopathy (PCV) and neovascular age-related macular degeneration (nAMD) share similar phenotype but are different in clinical manifestations, responses to treatment, and prognosis. Whether PCV is a subtype of AMD or a distinct entity from nAMD remains elusive. Therefore, we performed a whole-exome sequencing (WES) based association analysis to compare the genetic architecture of PCV and nAMD in Han Chinese. METHODS: Whole-exome sequencing analysis was performed on 21 nAMD cases, 20 PCV cases and 20 healthy controls...
January 11, 2018: Journal of Gene Medicine
https://www.readbyqxmd.com/read/29323667/making-new-genetic-diagnoses-with-old-data-iterative-reanalysis-and-reporting-from-genome-wide-data-in-1-133-families-with-developmental-disorders
#17
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord, Alejandro Sifrim, Rosemary Kelsell, Michael J Parker, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
PurposeGiven the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.MethodsWe tested this hypothesis in the United Kingdom-wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29322350/monogenic-disorders-that-mimic-the-phenotype-of-rett-syndrome
#18
Siddharth Srivastava, Sonal Desai, Julie Cohen, Constance Smith-Hicks, Kristin Barañano, Ali Fatemi, SakkuBai Naidu
Rett syndrome (RTT) is caused by mutations in methyl-CpG-binding protein 2 (MECP2), but defects in a handful of other genes (e.g., CDKL5, FOXG1, MEF2C) can lead to presentations that resemble, but do not completely mirror, classical RTT. In this study, we attempted to identify other monogenic disorders that share features with RTT. We performed a retrospective chart review on n = 319 patients who had undergone clinical whole exome sequencing (WES) for further etiological evaluation of neurodevelopmental diagnoses that remained unexplained despite extensive prior workup...
January 10, 2018: Neurogenetics
https://www.readbyqxmd.com/read/29322253/identification-of-a-mutation-in-cnnm4-by-whole-exome-sequencing-in-an-amish-family-and-functional-link-between-cnnm4-and-iqcb1
#19
Sisi Li, Quansheng Xi, Xiaoyu Zhang, Dong Yu, Lin Li, Zhenyang Jiang, Qiuyun Chen, Qing K Wang, Elias I Traboulsi
We investigated an Amish family in which three siblings presented with an early-onset childhood retinal dystrophy inherited in an autosomal recessive fashion. Genome-wide linkage analysis identified significant linkage to marker D2S2216 on 2q11 with a two-point LOD score of 1.95 and a multi-point LOD score of 3.76. Whole exome sequencing was then performed for the three affected individuals and identified a homozygous nonsense mutation (c.C1813T, p.R605X) in the cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene located within the 2p14-2q14 Jalili syndrome locus...
January 10, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29322246/de-novo-variants-in-setd1b-are-associated-with-intellectual-disability-epilepsy-and-autism
#20
Takuya Hiraide, Mitsuko Nakashima, Kaori Yamoto, Tokiko Fukuda, Mitsuhiro Kato, Hiroko Ikeda, Yoko Sugie, Kazushi Aoto, Tadashi Kaname, Kazuhiko Nakabayashi, Tsutomu Ogata, Naomichi Matsumoto, Hirotomo Saitsu
SETD1B (SET domain containing 1B) is a component of SET1 histone methyltransferase complex, which mediates the methylation of histone H3 on lysine 4 (H3K4). Here, we describe two unrelated individuals with de novo variants in SETD1B identified by trio-based whole exome sequencing: c.5524C>T, p.(Arg1842Trp) and c.5575C>T, p.(Arg1859Cy). The two missense variants occurred at evolutionarily conserved amino acids and are located within the SET domain, which plays a pivotal role in catalyzing histone methylation...
January 10, 2018: Human Genetics
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