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Human Genomics

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https://www.readbyqxmd.com/read/29394955/the-genetic-structure-of-the-belgian-population
#1
Jimmy Van den Eynden, Tine Descamps, Els Delporte, Nancy H C Roosens, Sigrid C J De Keersmaecker, Vanessa De Wit, Joris Robert Vermeesch, Els Goetghebeur, Jean Tafforeau, Stefaan Demarest, Marc Van den Bulcke, Herman Van Oyen
BACKGROUND: National and international efforts like the 1000 Genomes Project are leading to increasing insights in the genetic structure of populations worldwide. Variation between different populations necessitates access to population-based genetic reference datasets. These data, which are important not only in clinical settings but also to potentiate future transitions towards a more personalized public health approach, are currently not available for the Belgian population. RESULTS: To obtain a representative genetic dataset of the Belgian population, participants in the 2013 National Health Interview Survey (NHIS) were invited to donate saliva samples for DNA analysis...
February 2, 2018: Human Genomics
https://www.readbyqxmd.com/read/29382385/meeting-report-of-the-2017-kidgen-renal-genetics-symposium
#2
Kushani Jayasinghe, Cathy Quinlan, Zornitza Stark, Chirag Patel, Matthew G Sampson, Moin Saleem, Andrew J Mallett
The 2017 KidGen Renal Genetics Symposium was held at the Royal Children's Hospital and Murdoch Children's Research Institute, Melbourne, from 6 to 8 December 2017. This meeting addressed clinical, diagnostic, and research aspects of inherited kidney disease. More than 100 clinicians, researchers, and patient representatives attended the conference. The overall goal was to improve the understanding and direction of genomics in renal medicine in Australia and discuss barriers to the use of genomic testing within this area...
January 30, 2018: Human Genomics
https://www.readbyqxmd.com/read/29373992/beyond-genomics-understanding-exposotypes-through-metabolomics
#3
REVIEW
Nicholas J W Rattray, Nicole C Deziel, Joshua D Wallach, Sajid A Khan, Vasilis Vasiliou, John P A Ioannidis, Caroline H Johnson
BACKGROUND: Over the past 20 years, advances in genomic technology have enabled unparalleled access to the information contained within the human genome. However, the multiple genetic variants associated with various diseases typically account for only a small fraction of the disease risk. This may be due to the multifactorial nature of disease mechanisms, the strong impact of the environment, and the complexity of gene-environment interactions. Metabolomics is the quantification of small molecules produced by metabolic processes within a biological sample...
January 26, 2018: Human Genomics
https://www.readbyqxmd.com/read/29370840/identification-of-compound-heterozygous-variants-in-the-noncoding-rnu4atac-gene-in-a-chinese-family-with-two-successive-foetuses-with-severe-microcephaly
#4
Ye Wang, Xueli Wu, Liu Du, Ju Zheng, Songqing Deng, Xin Bi, Qiuyan Chen, Hongning Xie, Claude Férec, David N Cooper, Yanmin Luo, Qun Fang, Jian-Min Chen
BACKGROUND: Whole-exome sequencing (WES) over the last few years has been increasingly employed for clinical diagnosis. However, one caveat with its use is that it inevitably fails to detect disease-causative variants that occur within noncoding RNA genes. Our experience in identifying pathogenic variants in the noncoding RNU4ATAC gene, in a Chinese family where two successive foetuses had been affected by severe microcephaly, is a case in point. These foetuses exhibited remarkably similar phenotypes in terms of their microcephaly and brain abnormalities; however, the paucity of other characteristic phenotypic features had made a precise diagnosis impossible...
January 25, 2018: Human Genomics
https://www.readbyqxmd.com/read/29351810/identify-down-syndrome-transcriptome-associations-using-integrative-analysis-of-microarray-database-and-correlation-interaction-network
#5
Min Chen, Jiayan Wang, Yingjun Luo, Kailing Huang, Xiaoshun Shi, Yanhui Liu, Jin Li, Zhengfei Lai, Shuya Xue, Haimei Gao, Allen Chen, Dunjin Chen
BACKGROUND: Long non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented...
January 19, 2018: Human Genomics
https://www.readbyqxmd.com/read/29335020/ensemble-genomic-analysis-in-human-lung-tissue-identifies-novel-genes-for-chronic-obstructive-pulmonary-disease
#6
Jarrett D Morrow, Michael H Cho, John Platig, Xiaobo Zhou, Dawn L DeMeo, Weiliang Qiu, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Edwin K Silverman, Craig P Hersh
BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context...
January 15, 2018: Human Genomics
https://www.readbyqxmd.com/read/29268782/overexpressed-hsf1-cancer-signature-genes-cluster-in-human-chromosome-8q
#7
Christopher Q Zhang, Heinric Williams, Thomas L Prince, Eric S Ho
BACKGROUND: HSF1 (heat shock factor 1) is a transcription factor that is found to facilitate malignant cancer development and proliferation. In cancer cells, HSF1 mediates a set of genes distinct from heat shock that contributes to malignancy. This set of genes is known as the HSF1 Cancer Signature genes or simply HSF1-CanSig genes. HSF1-CanSig genes function and operate differently than typical cancer-causing genes, yet it is involved in fundamental oncogenic processes. RESULTS: By utilizing expression data from 9241 cancer patients, we identified that human chromosome 8q21-24 is a location hotspot for the most frequently overexpressed HSF1-CanSig genes...
December 21, 2017: Human Genomics
https://www.readbyqxmd.com/read/29246185/early-life-adversity-and-long-term-neurobehavioral-outcomes-epigenome-as-a-bridge
#8
REVIEW
Alexander M Vaiserman, Alexander K Koliada
Accumulating evidence suggests that adversities at critical periods in early life, both pre- and postnatal, can lead to neuroendocrine perturbations, including hypothalamic-pituitary-adrenal axis dysregulation and inflammation persisting up to adulthood. This process, commonly referred to as biological embedding, may cause abnormal cognitive and behavioral functioning, including impaired learning, memory, and depressive- and anxiety-like behaviors, as well as neuropsychiatric outcomes in later life. Currently, the regulation of gene activity by epigenetic mechanisms is suggested to be a key player in mediating the link between adverse early-life events and adult neurobehavioral outcomes...
December 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/29221465/yale-school-of-public-health-symposium-on-lifetime-exposures-and-human-health-the-exposome-summary-and-future-reflections
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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