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Human Genomics

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https://www.readbyqxmd.com/read/29221465/yale-school-of-public-health-symposium-on-lifetime-exposures-and-human-health-the-exposome-summary-and-future-reflections
#1
REVIEW
Caroline H Johnson, Toby J Athersuch, Gwen W Collman, Suraj Dhungana, David F Grant, Dean P Jones, Chirag J Patel, Vasilis Vasiliou
The exposome is defined as "the totality of environmental exposures encountered from birth to death" and was developed to address the need for comprehensive environmental exposure assessment to better understand disease etiology. Due to the complexity of the exposome, significant efforts have been made to develop technologies for longitudinal, internal and external exposure monitoring, and bioinformatics to integrate and analyze datasets generated. Our objectives were to bring together leaders in the field of exposomics, at a recent Symposium on "Lifetime Exposures and Human Health: The Exposome," held at Yale School of Public Health...
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29221463/correction-to-recessive-vars2-mutation-underlies-a-novel-syndrome-with-epilepsy-mental-retardation-short-stature-growth-hormone-deficiency-and-hypogonadism
#2
Abdulaziz Alsemari, Banan Al-Younes, Ewa Goljan, Dyala Jaroudi, Faisal BinHumaid, Brian F Meyer, Stefan T Arold, Dorota Monies
After publication of the article [1], it has been brought to our attention that there is a nomenclature issue with this article. At the time of acceptance, the VARS2 mutation was considered equivalent to the VARS2 mutation. However, this has changed so that VARS now only refers to shorter mitochondrial sequence of valyl-tRNA synthesase containing 1093 amino acids. "Therefore, in the context of this article, every usage of "VARS2" should be replaced with "VARS" when referring to the causative variant".
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29221462/ethical-frameworks-for-obtaining-informed-consent-in-tumour-profiling-an-evidence-based-case-for-singapore
#3
Yasmin Bylstra, Tamra Lysaght, Jyothi Thrivikraman, Sangeetha Watson, Patrick Tan
BACKGROUND: Genomic profiling of malignant tumours has assisted clinicians in providing targeted therapies for many serious cancer-related illnesses. Although the characterisation of somatic mutations is the primary aim of tumour profiling for treatment, germline mutations may also be detected given the heterogenous origin of mutations observed in tumours. Guidance documents address the return of germline findings that have health implications for patients and their genetic relations...
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29216901/genomic-variants-in-the-fto-gene-are-associated-with-sporadic-amyotrophic-lateral-sclerosis-in-greek-patients
#4
Konstantinos Mitropoulos, Eleni Merkouri Papadima, Georgia Xiromerisiou, Angeliki Balasopoulou, Kyriaki Charalampidou, Vasiliki Galani, Krystallia-Vassiliki Zafeiri, Efthymios Dardiotis, Styliani Ralli, Georgia Deretzi, Anne John, Kyriaki Kydonopoulou, Elpida Papadopoulou, Alba di Pardo, Fulya Akcimen, Annalisa Loizedda, Valerija Dobričić, Ivana Novaković, Vladimir S Kostić, Clint Mizzi, Brock A Peters, Nazli Basak, Sandro Orrù, Evangelos Kiskinis, David N Cooper, Spyridon Gerou, Radoje Drmanac, Marina Bartsakoulia, Evangelia-Eirini Tsermpini, Georgios M Hadjigeorgiou, Bassam R Ali, Theodora Katsila, George P Patrinos
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a devastating disease whose complex pathology has been associated with a strong genetic component in the context of both familial and sporadic disease. Herein, we adopted a next-generation sequencing approach to Greek patients suffering from sporadic ALS (together with their healthy counterparts) in order to explore further the genetic basis of sporadic ALS (sALS). RESULTS: Whole-genome sequencing analysis of Greek sALS patients revealed a positive association between FTO and TBC1D1 gene variants and sALS...
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29162152/the-peptidylglycine-%C3%AE-amidating-monooxygenase-pam-gene-rs13175330-a-g-polymorphism-is-associated-with-hypertension-in-a-korean-population
#5
Hye Jin Yoo, Minjoo Kim, Minkyung Kim, Jey Sook Chae, Sang-Hyun Lee, Jong Ho Lee
BACKGROUND: Peptidylglycine-α-amidating monooxygenase (PAM) may play a role in the secretion of atrial natriuretic peptide (ANP), which is a hormone involved in the maintenance of blood pressure (BP). The objective of the present study was to determine whether PAM is a novel candidate gene for hypertension (HTN). RESULTS: A total of 2153 Korean participants with normotension and HTN were included. Genotype data were obtained using the Korean Chip. The rs13175330 polymorphism of the PAM gene was selected from the ten single nucleotide polymorphisms (SNPs) most strongly associated with BP...
November 21, 2017: Human Genomics
https://www.readbyqxmd.com/read/29137650/recessive-vars2-mutation-underlies-a-novel-syndrome-with-epilepsy-mental-retardation-short-stature-growth-hormone-deficiency-and-hypogonadism
#6
Abdulaziz Alsemari, Banan Al-Younes, Ewa Goljan, Dyala Jaroudi, Faisal BinHumaid, Brian F Meyer, Stefan T Arold, Dorota Monies
BACKGROUND: Most mitochondrial and cytoplasmic aminoacyl-tRNA synthetases (aaRSs) are encoded by nuclear genes. Syndromic disorders resulting from mutation of aaRSs genes display significant phenotypic heterogeneity. We expand aaRSs-related phenotypes through characterization of the clinical and molecular basis of a novel autosomal-recessive syndrome manifesting severe mental retardation, ataxia, speech impairment, epilepsy, short stature, microcephaly, hypogonadism, and growth hormone deficiency...
November 14, 2017: Human Genomics
https://www.readbyqxmd.com/read/29122006/single-nucleotide-polymorphisms-in-the-angiogenic-and-lymphangiogenic-pathways-are-associated-with-lymphedema-caused-by-wuchereria-bancrofti
#7
Linda Batsa Debrah, Anna Albers, Alexander Yaw Debrah, Felix F Brockschmidt, Tim Becker, Christine Herold, Andrea Hofmann, Jubin Osei-Mensah, Yusif Mubarik, Holger Fröhlich, Achim Hoerauf, Kenneth Pfarr
BACKGROUND: Lymphedema (LE) is a chronic clinical manifestation of filarial nematode infections characterized by lymphatic dysfunction and subsequent accumulation of protein-rich fluid in the interstitial space-lymphatic filariasis. A number of studies have identified single nucleotide polymorphisms (SNPs) associated with primary and secondary LE. To assess SNPs associated with LE caused by lymphatic filariasis, a cross-sectional study of unrelated Ghanaian volunteers was designed to genotype SNPs in 285 LE patients as cases and 682 infected patients without pathology as controls...
November 9, 2017: Human Genomics
https://www.readbyqxmd.com/read/29121990/identification-of-functional-single-nucleotide-polymorphisms-in-the-branchpoint-site
#8
Hung-Lun Chiang, Jer-Yuarn Wu, Yuan-Tsong Chen
BACKGROUND: The human genome contains millions of single nucleotide polymorphisms (SNPs); many of these SNPs are intronic and have unknown functional significance. SNPs occurring within intron branchpoint sites, especially at the adenine (A), would presumably affect splicing; however, this has not been systematically studied. We employed a splicing prediction tool to identify human intron branchpoint sites and screened dbSNP for identifying SNPs located in the predicted sites to generate a genome-wide branchpoint site SNP database...
November 9, 2017: Human Genomics
https://www.readbyqxmd.com/read/29110692/identification-of-a-novel-genetic-locus-underlying-tremor-and-dystonia
#9
Dorota Monies, Hussam Abou Al-Shaar, Ewa A Goljan, Banan Al-Younes, Muna Monther Abdullah Al-Breacan, Maher Mohammed Al-Saif, Salma M Wakil, Brian F Meyer, Khalid S A Khabar, Saeed Bohlega
BACKGROUND: Five affected individuals with syndromic tremulous dystonia, spasticity, and white matter disease from a consanguineous extended family covering a period of over 24 years are presented. A positional cloning approach utilizing genome-wide linkage, homozygozity mapping and whole exome sequencing was used for genetic characterization. The impact of a calmodulin-binding transcription activator 2, (CAMTA2) isoform 2, hypomorphic mutation on mRNA and protein abundance was studied using fluorescent reporter expression cassettes...
November 6, 2017: Human Genomics
https://www.readbyqxmd.com/read/29061162/whole-transcriptome-analysis-of-human-erythropoietic-cells-during-ontogenesis-suggests-a-role-of-vegfa-gene-as-modulator-of-fetal-hemoglobin-and-pharmacogenomic-biomarker-of-treatment-response-to-hydroxyurea-in-%C3%AE-type-hemoglobinopathy-patients
#10
Vasiliki Chondrou, Petros Kolovos, Argyro Sgourou, Alexandra Kourakli, Alexia Pavlidaki, Vlasia Kastrinou, Anne John, Argiris Symeonidis, Bassam R Ali, Adamantia Papachatzopoulou, Theodora Katsila, George P Patrinos
BACKGROUND: Human erythropoiesis is characterized by distinct gene expression profiles at various developmental stages. Previous studies suggest that fetal-to-adult hemoglobin switch is regulated by a complex mechanism, in which many key players still remain unknown. Here, we report our findings from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue...
October 23, 2017: Human Genomics
https://www.readbyqxmd.com/read/29020978/precision-medicine-at-the-crossroads
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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