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Human Genomics

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https://www.readbyqxmd.com/read/29020978/precision-medicine-at-the-crossroads
#1
Maynard V Olson
There are bioethical, institutional, economic, legal, and cultural obstacles to creating the robust-precompetitive-data resource that will be required to advance the vision of "precision medicine," the ability to use molecular data to target therapies to patients for whom they offer the most benefit at the least risk. Creation of such an "information commons" was the central recommendation of the 2011 report Toward Precision Medicine issued by a committee of the National Research Council of the USA (Committee on a Framework for Development of a New Taxonomy of Disease; National Research Council...
October 11, 2017: Human Genomics
https://www.readbyqxmd.com/read/28870239/evaluating-somatic-tumor-mutation-detection-without-matched-normal-samples
#2
Jamie K Teer, Yonghong Zhang, Lu Chen, Eric A Welsh, W Douglas Cress, Steven A Eschrich, Anders E Berglund
BACKGROUND: Observations of recurrent somatic mutations in tumors have led to identification and definition of signaling and other pathways that are important for cancer progression and therapeutic targeting. As tumor cells contain both an individual's inherited genetic variants and somatic mutations, challenges arise in distinguishing these events in massively parallel sequencing datasets. Typically, both a tumor sample and a "normal" sample from the same individual are sequenced and compared; variants observed only in the tumor are considered to be somatic mutations...
September 4, 2017: Human Genomics
https://www.readbyqxmd.com/read/28865488/distinct-transcriptional-and-metabolic-profiles-associated-with-empathy-in-buddhist-priests-a-pilot-study
#3
Junji Ohnishi, Satoshi Ayuzawa, Seiji Nakamura, Shigeko Sakamoto, Miyo Hori, Tomoko Sasaoka, Eriko Takimoto-Ohnishi, Masakazu Tanatsugu, Kazuo Murakami
BACKGROUND: Growing evidence suggests that spiritual/religious involvement may have beneficial effects on both psychological and physical functions. However, the biological basis for this relationship remains unclear. This study explored the role of spiritual/religious involvement across a wide range of biological markers, including transcripts and metabolites, associated with the psychological aspects of empathy in Buddhist priests. METHODS: Ten professional Buddhist priests and 10 age-matched non-priest controls were recruited...
September 2, 2017: Human Genomics
https://www.readbyqxmd.com/read/28851444/falling-giants-and-the-rise-of-gene-editing-ethics-private-interests-and-the-public-good
#4
Benjamin Capps, Ruth Chadwick, Yann Joly, John J Mulvihill, Tamra Lysaght, Hub Zwart
This paper considers the tensions created in genomic research by public and private for-profit ideals. Our intent is to strengthen the public good at a time when doing science is strongly motivated by market possibilities and opportunities. Focusing on the emergence of gene editing, and in particular CRISPR, we consider how commercialisation encourages hype and hope-a sense that only promise and idealism can achieve progress. At this rate, genomic research reinforces structures that promote, above all else, private interests, but that may attenuate conditions for the public good of science...
August 29, 2017: Human Genomics
https://www.readbyqxmd.com/read/28810924/mutational-analysis-of-col1a1-and-col1a2-genes-among-estonian-osteogenesis-imperfecta-patients
#5
Lidiia Zhytnik, Katre Maasalu, Ene Reimann, Ele Prans, Sulev Kõks, Aare Märtson
BACKGROUND: Osteogenesis imperfecta (OI) is a rare bone disorder. In 90% of cases, OI is caused by mutations in the COL1A1/2 genes, which code procollagen α1 and α2 chains. The main aim of the current research was to identify the mutational spectrum of COL1A1/2 genes in Estonian patients. The small population size of Estonia provides a unique chance to explore the collagen I mutational profile of 100% of OI families in the country. METHODS: We performed mutational analysis of peripheral blood gDNA of 30 unrelated Estonian OI patients using Sanger sequencing of COL1A1 and COL1A2 genes, including all intron-exon junctions and 5'UTR and 3'UTR regions, to identify causative OI mutations...
August 15, 2017: Human Genomics
https://www.readbyqxmd.com/read/28764803/a-novel-rlbp1-gene-geographical-area-related-mutation-present-in-a-young-patient-with-retinitis-punctata-albescens
#6
Concetta Scimone, Luigi Donato, Teresa Esposito, Carmela Rinaldi, Rosalia D'Angelo, Antonina Sidoti
BACKGROUND: Autosomal recessive forms of retinitis punctata albescens (RPA) have been described. RPA is characterized by progressive retinal degeneration due to alteration in visual cycle and consequent deposit of photopigments in retinal pigment epithelium. Five loci have been linked to RPA onset. Among these, the retinaldehyde-binding protein 1 gene, RLBP1, is the most frequently involved and several founder mutations were reported. We report results of a genetic molecular investigation performed on a large Sicilian family in which appears a young woman with RPA...
August 1, 2017: Human Genomics
https://www.readbyqxmd.com/read/28738846/long-non-coding-rnas-as-novel-players-in-%C3%AE-cell-function-and-type-1-diabetes
#7
REVIEW
Aashiq H Mirza, Simranjeet Kaur, Flemming Pociot
BACKGROUND: Long non-coding RNAs (lncRNAs) are a sub-class within non-coding RNA repertoire that have emerged as crucial regulators of the gene expression in various pathophysiological conditions. lncRNAs display remarkable versatility and wield their functions through interactions with RNA, DNA, or proteins. Accumulating body of evidence based on multitude studies has highlighted the role of lncRNAs in many autoimmune and inflammatory diseases, including type 1 diabetes (T1D). This review highlights emerging roles of lncRNAs in immune and islet β cell function as well as some of the challenges and opportunities in understanding the pathogenesis of T1D and its complications...
July 24, 2017: Human Genomics
https://www.readbyqxmd.com/read/28724397/partial-uniparental-isodisomy-of-chromosome-16-unmasks-a-deleterious-biallelic-mutation-in-ift140-that-causes-mainzer-saldino-syndrome
#8
Benjamin M Helm, Jason R Willer, Azita Sadeghpour, Christelle Golzio, Eric Crouch, Samantha Schrier Vergano, Nicholas Katsanis, Erica E Davis
BACKGROUND: The ciliopathies represent an umbrella group of >50 clinical entities that share both clinical features and molecular etiology underscored by structural and functional defects of the primary cilium. Despite the advances in gene discovery, this group of entities continues to pose a diagnostic challenge, in part due to significant genetic and phenotypic heterogeneity and variability. We consulted a pediatric case from asymptomatic, non-consanguineous parents who presented as a suspected ciliopathy due to a constellation of retinal, renal, and skeletal findings...
July 19, 2017: Human Genomics
https://www.readbyqxmd.com/read/28697807/inferring-clonal-structure-in-htlv-1-infected-individuals-towards-bridging-the-gap-between-analysis-and-visualization
#9
Amir Farmanbar, Sanaz Firouzi, Wojciech Makałowski, Masako Iwanaga, Kaoru Uchimaru, Atae Utsunomiya, Toshiki Watanabe, Kenta Nakai
BACKGROUND: Human T cell leukemia virus type 1 (HTLV-1) causes adult T cell leukemia (ATL) in a proportion of infected individuals after a long latency period. Development of ATL is a multistep clonal process that can be investigated by monitoring the clonal expansion of HTLV-1-infected cells by isolation of provirus integration sites. The clonal composition (size, number, and combinations of clones) during the latency period in a given infected individual has not been clearly elucidated...
July 11, 2017: Human Genomics
https://www.readbyqxmd.com/read/28651617/development-and-validation-of-a-variant-detection-workflow-for-brca1-and-brca2-genes-and-its-clinical-application-based-on-the-ion-torrent-technology
#10
Ana Lígia Buzolin, Caroline Mônaco Moreira, Patricia Rossi Sacramento, Andre Yuji Oku, Alexandre Ricardo Dos Santos Fornari, David Santos Marco Antonio, Caio Robledo D Angioli Costa Quaio, Wagner Rosa Baratela, Miguel Mitne-Neto
BACKGROUND: Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. RESULTS: Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes...
June 26, 2017: Human Genomics
https://www.readbyqxmd.com/read/28637487/the-nf1-somatic-mutational-landscape-in-sporadic-human-cancers
#11
REVIEW
Charlotte Philpott, Hannah Tovell, Ian M Frayling, David N Cooper, Meena Upadhyaya
BACKGROUND: Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia...
June 21, 2017: Human Genomics
https://www.readbyqxmd.com/read/28545550/genetic-variation-in-neurodegenerative-diseases-and-its-accessibility-in-the-model-organism-caenorhabditis-elegans
#12
REVIEW
Yiru Anning Wang, Jan Edward Kammenga, Simon Crawford Harvey
BACKGROUND: Neurodegenerative diseases (NGDs) such as Alzheimer's and Parkinson's are debilitating and largely untreatable conditions strongly linked to age. The clinical, neuropathological, and genetic components of NGDs indicate that neurodegeneration is a complex trait determined by multiple genes and by the environment. MAIN BODY: The symptoms of NGDs differ among individuals due to their genetic background, and this variation affects the onset and progression of NGD and NGD-like states...
May 25, 2017: Human Genomics
https://www.readbyqxmd.com/read/28532469/a-pipeline-combining-multiple-strategies-for-prioritizing-heterozygous-variants-for-the-identification-of-candidate-genes-in-exome-datasets
#13
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
BACKGROUND: The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets...
May 22, 2017: Human Genomics
https://www.readbyqxmd.com/read/28511696/variant-effect-prediction-tools-assessed-using-independent-functional-assay-based-datasets-implications-for-discovery-and-diagnostics
#14
Khalid Mahmood, Chol-Hee Jung, Gayle Philip, Peter Georgeson, Jessica Chung, Bernard J Pope, Daniel J Park
BACKGROUND: Genetic variant effect prediction algorithms are used extensively in clinical genomics and research to determine the likely consequences of amino acid substitutions on protein function. It is vital that we better understand their accuracies and limitations because published performance metrics are confounded by serious problems of circularity and error propagation. Here, we derive three independent, functionally determined human mutation datasets, UniFun, BRCA1-DMS and TP53-TA, and employ them, alongside previously described datasets, to assess the pre-eminent variant effect prediction tools...
May 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28499422/identification-of-novel-genes-associated-with-hiv-1-latency-by-analysis-of-histone-modifications
#15
LETTER
Kyung-Chang Kim, Sunyoung Lee, Junseock Son, Younghyun Shin, Cheol-Hee Yoon, Chun Kang, Byeong-Sun Choi
BACKGROUND: A reservoir of HIV-1 is a major obstacle in eliminating HIV-1 in patients because it can reactivate in stopping antiretroviral therapy (ART). Histone modifications, such as acetylation and methylation, play a critical role in the organization of chromatin domains and the up- or downregulation of gene expression. Although many studies have reported that an epigenetic mechanism is strongly involved in the maintenance of HIV-1 transcriptional latency, neither the epigenetic control of viral replication nor how HIV-1 latency is maintained is not fully understood...
May 12, 2017: Human Genomics
https://www.readbyqxmd.com/read/28499412/genome-wide-dna-methylation-analysis-reveals-hypomethylation-in-the-low-cpg-promoter-regions-in-lymphoblastoid-cell-lines
#16
Itsuki Taniguchi, Chihiro Iwaya, Keizo Ohnaka, Hiroki Shibata, Ken Yamamoto
BACKGROUND: Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types of commonly used DNA bioresources, peripheral blood cells (PBCs) and EBV-transformed lymphoblastoid cell lines (LCLs), which are available for genetic epidemiological studies. Therefore, to extend our knowledge of the difference in DNA methylation status between LCLs and PBCs is important in human population studies that use these DNA sources to elucidate the epigenetic risks for multifactorial diseases...
May 12, 2017: Human Genomics
https://www.readbyqxmd.com/read/28472998/in-silico-prioritization-and-further-functional-characterization-of-spink1-intronic-variants
#17
Wen-Bin Zou, Hao Wu, Arnaud Boulling, David N Cooper, Zhao-Shen Li, Zhuan Liao, Jian-Min Chen, Claude Férec
BACKGROUND: SPINK1 (serine protease inhibitor, kazal-type, 1), which encodes human pancreatic secretory trypsin inhibitor, is one of the most extensively studied genes underlying chronic pancreatitis. Recently, based upon data from qualitative reverse transcription-PCR (RT-PCR) analyses of transfected HEK293T cells, we concluded that 24 studied SPINK1 intronic variants were not of pathological significance, the sole exceptions being two canonical splice site variants (i.e., c.87 + 1G > A and c...
May 4, 2017: Human Genomics
https://www.readbyqxmd.com/read/28427458/whole-exome-sequencing-identifies-novel-candidate-predisposition-genes-for-familial-polycythemia-vera
#18
Elina A M Hirvonen, Esa Pitkänen, Kari Hemminki, Lauri A Aaltonen, Outi Kilpivaara
BACKGROUND: Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe), leading to constitutive activation of JAK-STAT signaling pathway. Familial clustering is also observed occasionally, but high-penetrance predisposition genes to PV have remained unidentified. RESULTS: We studied the predisposition to PV by exome sequencing (three cases) in a Finnish PV family with four patients...
April 20, 2017: Human Genomics
https://www.readbyqxmd.com/read/28302172/transcriptome-analysis-of-bronchoalveolar-lavage-fluid-from-children-with-severe-mycoplasma-pneumoniae-pneumonia-reveals-novel-gene-expression-and-immunodeficiency
#19
Kuo Wang, Man Gao, Mingyue Yang, Fanzheng Meng, Deli Li, Ruihua Lu, Yan Wang, Huadong Zhuang, Mengyao Li, Genhong Cheng, Xiaosong Wang
BACKGROUND: A growing number of severe Mycoplasma pneumoniae pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to identify gene expression and alternative splicing profiles to provide insights into the pathogenesis of severe MPP. METHODS: RNAs of bronchoalveolar lavage fluid (BALF) samples from three severe MPP children and three mild MPP children were analyzed respectively by deep sequencing followed by computational annotation and quantification...
March 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28302154/the-israeli-national-genetic-database-a-10-year-experience
#20
Joël Zlotogora, George P Patrinos
BACKGROUND: The Israeli National and Ethnic Mutation database ( http://server.goldenhelix.org/israeli ) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar ) and ExAC ( http://exac.broadinstitute.org ) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources...
March 16, 2017: Human Genomics
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