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https://read.qxmd.com/read/30900361/phenotype-comparison-among-individuals-with-developmental-delay-intellectual-disability-with-or-without-genomic-imbalances
#1
L C de Souza, A P Dos Santos, I C Sgardioli, N L Viguetti-Campos, J R Marques Prota, R P de Oliveira-Sobrinho, T P Vieira, V L Gil-da-Silva-Lopes
BACKGROUND: The chromosomal microarray analysis (CMA) is recommended as a first-tier test for individuals with developmental delay (DD)/intellectual disability (ID) and/or multiple congenital anomalies. However, owing to high costs, this technique is not widely performed for diagnostic purposes in several countries. The aim of this study was to identify clinical features that could favour the hypothesis of genomic imbalances (GIs) in individuals with DD/ID. METHODS: The sample consisted of 63 individuals, and all of them underwent a detailed evaluation by a clinical geneticist and were investigated by the CMA...
March 21, 2019: Journal of Intellectual Disability Research: JIDR
https://read.qxmd.com/read/30900102/genetic-variations-associated-with-telomere-length-confer-risk-of-gastric-cardia-adenocarcinoma
#2
Nasha Zhang, Yan Zheng, Jie Liu, Tiansui Lei, Yeyang Xu, Ming Yang
BACKGROUND: Aberrant telomere lengthening is a critical feature of malignant cells. Short leukocyte telomere length (LTL) confers elevated risk of gastric cardia adenocarcinoma (GCA). Multiple genome-wide association studies (GWAS) identified various single-nucleotide polymorphisms (SNPs) associated with LTL in different ethnic populations. However, it remains largely unexplored how these genetic variants are involved in GCA susceptibility. METHODS: We systematically screened GWAS-identified candidate SNPs and tested the impact of 30 polymorphisms in genes associated with interindividual LTL variation on GCA using two-stage case-control comparisons consisting of 1024 GCA patients and 1118 controls...
March 21, 2019: Gastric Cancer
https://read.qxmd.com/read/30899276/computational-molecular-phenotypic-analysis-of-ptpn22-w620r-il6r-d358a-and-tyk2-p1104a-gene-mutations-of-rheumatoid-arthritis
#3
Noor Ahmad Shaik, Babajan Banaganapalli
Rheumatoid arthritis (RA) is a chronic autoimmune disorder of bone joints caused by the complex interplay between several factors like body physiology, the environment with genetic background. The recent meta-analysis of GWAS has expanded the total number of RA-associated loci to more than 100, out of which approximately ∼97% (98 variants) loci are located in non-coding regions, and the other ∼3% (3 variants) are in three different non-HLA genes, i.e., TYK2 (Prp1104Ala), IL6R (Asp358Ala), and PTPN22 (Trp620Arg)...
2019: Frontiers in Genetics
https://read.qxmd.com/read/30898838/genome-wide-interrogation-of-human-cancers-identifies-egln1-dependency-in-clear-cell-ovarian-cancers
#4
Colles Price, Stanley Gill, Zandra V Ho, Shawn M Davidson, Erin Merkel, James M McFarland, Lisa Leung, Andrew Tang, Maria Kost-Alimova, Aviad Tsherniak, Oliver Jonas, Francisca Vazquez, William C Hahn
We hypothesized that candidate dependencies for which there are small molecules that are either approved or in advanced development for a non-oncology indication may represent potential therapeutic targets. To test this hypothesis, we performed genome-scale loss-of-function screens in hundreds of cancer cell lines to identify genes necessary for the proliferation and survival of certain subsets of cancer cell lines. We found that knockout of EGLN1, which encodes prolyl hydroxylase domain-containing protein 2 (PHD2), reduced the proliferation of a subset of clear cell ovarian cancer cell lines in vitro...
March 21, 2019: Cancer Research
https://read.qxmd.com/read/30898364/using-human-genetics-to-drive-drug-discovery-a-perspective
#5
Caroline S Fox
The probability of success of developing medicines to treat human disease can be improved by leveraging human genetics. Different types of genetic data and techniques, including genome-wide association, whole-exome sequencing, and whole-genome sequencing, can be used to gain insight into human disease. Layering different types of genetic evidence from Mendelian disease, coding variants, and common variation can bolster support for a genetic target. Human knockouts offer the potential to perform reverse genetic screens in humans to identify physiologically relevant targets...
March 18, 2019: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
https://read.qxmd.com/read/30898113/genome-wide-crispr-screen-reveals-psma6-to-be-an-essential-gene-in-pancreatic-cancer-cells
#6
Jesse Bakke, William C Wright, Anthony E Zamora, Peter Oladimeji, Jeremy Chase Crawford, Christopher T Brewer, Robert J Autry, William E Evans, Paul G Thomas, Taosheng Chen
BACKGROUND: Despite its relatively low incidence, pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths because of the aggressive growth/metastasis of the tumor, the lack of early symptoms, and the poor treatment options. Basic research to identify potential therapeutic targets for PDAC is greatly needed. METHODS: We used a negative-selection genome-wide CRISPR screen to identify essential genes in the PANC-1 human pancreatic carcinoma cell line...
March 21, 2019: BMC Cancer
https://read.qxmd.com/read/30896832/genome-scale-integrated-analysis-to-identify-prospective-molecular-mechanisms-and-therapeutic-targets-in-isocitrate-dehydrogenase-2-r140q-mutated-acute-myeloid-leukemia
#7
Rui Huang, Xiwen Liao, Jing Li, Jiemin Wei, Xiayun Su, Xiaoxuan Lai, Beicai Liu, Fangxiao Zhu, Yumei Huang, Qiaochuan Li
The aim of the present study was to identify potential molecular mechanisms and therapeutic targets in regards to isocitrate dehydrogenase 2 (IDH2) R140Q-mutated acute myeloid leukemia (AML). An RNA sequencing dataset of IDH2 wild-type and R140Q-mutated adult de novo AML bone marrow samples was obtained from The Cancer Genome Atlas (TCGA) database. The edgeR package was used to screen for the differentially expressed genes (DEGs), and the potential molecular mechanisms and therapeutic targets were identified using Database for Annotation, Visualization, and Integrated Discovery (DAVID) v6...
March 18, 2019: Oncology Reports
https://read.qxmd.com/read/30894498/or14i1-is-a-receptor-for-the-human-cytomegalovirus-pentameric-complex-and-defines-viral-epithelial-cell-tropism
#8
Xiaofei E, Paul Meraner, Ping Lu, Jill M Perreira, Aaron M Aker, William M McDougall, Ronghua Zhuge, Gary C Chan, Rachel M Gerstein, Patrizia Caposio, Andrew D Yurochko, Abraham L Brass, Timothy F Kowalik
A human cytomegalovirus (HCMV) pentameric glycoprotein complex (PC), gH-gL-UL128-UL130-UL131A, is necessary for viral infection of clinically relevant cell types, including epithelial cells, which are important for interhost transmission and disease. We performed genome-wide CRISPR/Cas9 screens of different cell types in parallel to identify host genes specifically required for HCMV infection of epithelial cells. This effort identified a multipass membrane protein, OR14I1, as a receptor for HCMV infection. This olfactory receptor family member is required for HCMV attachment, entry, and infection of epithelial cells and is dependent on the presence of viral PC...
March 20, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30894375/the-critical-role-of-rna-m-6-a-methylation-in-cancer
#9
REVIEW
Qing Lan, Pei Y Liu, Jacob Haase, Jessica L Bell, Stefan Hüttelmaier, Tao Liu
Since the identification of the first RNA demethylase and the establishment of methylated RNA immunoprecipitation-sequencing methodology 6 to 7 years ago, RNA methylation has emerged as a widespread phenomenon and a critical regulator of transcript expression. This new layer of regulation is termed "epitranscriptomics." The most prevalent RNA methylation, N 6 -methyladenosine (m6 A), occurs in approximately 25% of transcripts at the genome-wide level and is enriched around stop codons, in 5'- and 3'-untranslated regions, and within long internal exons...
March 20, 2019: Cancer Research
https://read.qxmd.com/read/30894373/an-interactive-resource-to-probe-genetic-diversity-and-estimated-ancestry-in-cancer-cell-lines
#10
REVIEW
Julie Dutil, Zhihua Chen, Alvaro N Monteiro, Jamie K Teer, Steven A Eschrich
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown...
March 20, 2019: Cancer Research
https://read.qxmd.com/read/30890649/genome-wide-identification-of-alternative-splicing-events-that-regulate-protein-transport-across-the-secretory-pathway
#11
Alexander Neumann, Magdalena Schindler, Didrik Olofsson, Ilka Wilhelmi, Annette Schürmann, Florian Heyd
Alternative splicing (AS) strongly increases proteome diversity and functionality in eukaryotic cells. Protein secretion is a tightly-controlled process, especially in a tissue-specific and differentiation-dependent manner. While previous work has focussed on transcriptional and post-translational regulatory mechanisms, the impact of AS on the secretory pathway remains largely unexplored. Here we integrate a published screen for modulators of protein transport and RNA-Seq analyses to identify over 200 AS events as secretion regulators...
March 19, 2019: Journal of Cell Science
https://read.qxmd.com/read/30890156/development-of-drug-inducible-crispr-cas9-systems-for-large-scale-functional-screening
#12
Ning Sun, Sakina Petiwala, Rui Wang, Charles Lu, Mufeng Hu, Sujana Ghosh, Yan Hao, Christopher P Miller, Namjin Chung
BACKGROUND: Large-scale genetic screening using CRISPR-Cas9 technology has emerged as a powerful approach to uncover and validate gene functions. The ability to control the timing of genetic perturbation during CRISPR screens will facilitate precise dissection of dynamic and complex biological processes. Here, we report the optimization of a drug-inducible CRISPR-Cas9 system that allows high-throughput gene interrogation with a temporal control. RESULTS: We designed multiple drug-inducible sgRNA expression vectors and measured their activities using an EGFP gene disruption assay in 11 human and mouse cell lines...
March 19, 2019: BMC Genomics
https://read.qxmd.com/read/30888429/mammalian-haploid-stem-cells-establishment-engineering-and-applications
#13
REVIEW
Wenteng He, Jiayu Chen, Shaorong Gao
Haploid embryonic stem cells (haESCs) contain only one set of genomes inherited from the sperm or egg and are termed AG- or PG-haESCs, respectively. Mammalian haESCs show genome-wide hypomethylation and dysregulated imprinting, whereas they can sustain genome integrity during derivation and long-term propagation. In addition, haESCs exhibit similar pluripotency to traditional diploid ESCs but are unique because they function as gametes and have been used to produce semi-cloned animals. More strikingly, unisexual reproduction has been achieved in mice by using haESCs...
March 19, 2019: Cellular and Molecular Life Sciences: CMLS
https://read.qxmd.com/read/30888413/genetic-variants-in-barrett-s-esophagus-and-esophageal-adenocarcinoma-a-literature-review
#14
Zachary M Callahan, Zhuqing Shi, Bailey Su, Jianfeng Xu, Michael Ujiki
Surveillance of Barrett's esophagus (BE) is a clinical challenge; metaplasia of the distal esophagus increases a patient's risk of esophageal adenocarcinoma (EAC) significantly but the actual percentage of patients who progress is low. The current screening recommendations require frequent endoscopy and biopsy, which has inherent risk, high cost, and operator variation. Identifying BE patients genetically who are at high risk of progressing could deemphasize the role of endoscopic screening and create an opportunity for early therapeutic intervention...
March 19, 2019: Diseases of the Esophagus: Official Journal of the International Society for Diseases of the Esophagus
https://read.qxmd.com/read/30888333/genetic-determinants-of-ototoxicity-during-and-after-childhood-cancer-treatment-protocol-for-the-pancarelife-study
#15
Eva Clemens, Annelot Jm Meijer, Linda Broer, Thorsten Langer, Anne-Lotte Lf van der Kooi, André G Uitterlinden, Andrica de Vries, Claudia E Kuehni, Maria L Garrè, Tomas Kepak, Jarmila Kruseova, Jeanette F Winther, Leontien C Kremer, Eline van Dulmen-den Broeder, Wim Je Tissing, Catherine Rechnitzer, Line Kenborg, Henrik Hasle, Desiree Grabow, Ross Parfitt, Harald Binder, Bruce C Carleton, Julianne Byrne, Peter Kaatsch, Antoinette Am Zehnhoff-Dinnesen, Oliver Zolk, Marry M van den Heuvel-Eibrink
BACKGROUND: Survival rates after childhood cancer now reach nearly 80% in developed countries. However, treatments that lead to survival and cure can cause serious adverse effects with lifelong negative impacts on survivor quality of life. Hearing impairment is a common adverse effect in children treated with cisplatin-based chemotherapy or cranial radiotherapy. Ototoxicity can extend from high-tone hearing impairment to involvement of speech frequencies. Hearing impairment can impede speech and language and neurocognitive development...
March 19, 2019: JMIR Research Protocols
https://read.qxmd.com/read/30888082/ac016405-3-a-novel-lncrna-acts-as-a-tumor-suppressor-via-modulating-of-tet2-by-mir-19a-5p-sponging-in-glioblastoma
#16
Siyang Ren, Yinghui Xu
Long non-coding RNAs (lncRNAs) are crucial regulators in various malignancies including glioblastoma multiforme (GBM). In the present study, we screened out a new lncRNA - AC016405.3 - through a previous genome-wide lncRNA microarray analysis in GBM. It showed that AC016405.3 was down-regulated in GBM tissue specimens and cell lines, and it also illustrated that the down-regulated AC016405.3 was closely correlated with several aggressive features of patients with GBM. Functionally, we displayed that overexpression of AC016405...
March 19, 2019: Cancer Science
https://read.qxmd.com/read/30887268/genome-scan-for-genomic-regions-and-genes-associated-with-growth-trait-in-pacific-white-shrimp-litopeneaus-vannamei
#17
Yang Yu, Quanchao Wang, Qian Zhang, Zheng Luo, Yue Wang, Xiaojun Zhang, Hao Huang, Jianhai Xiang, Fuhua Li
The Pacific white shrimp Litopeneaus vannmei (L. vannmei) is a predominant aquaculture shrimp species worldwide, and it is considered as the aquaculture species with the highest single output value. Advances in selective breeding have accelerated the development of L. vannmei aquaculture. Recently, the genome-wide association studies (GWAS) have been applied in aquaculture animals and markers associated with economic traits were identified. In this study, we focused on the growth trait of L. vannamei and performed GWAS to identify SNPs or genes associated with growth...
March 18, 2019: Marine Biotechnology
https://read.qxmd.com/read/30886882/targeted-sequencing-of-dcstamp-in-familial-paget-s-disease-of-bone
#18
M A Sultana, N J Pavlos, Lynley Ward, J P Walsh, S L Rea
Paget's disease of bone (PDB) has a strong genetic component. Variants in SQSTM1 are found in up to 40% of patients with a family history of the disease, where a pattern of autosomal dominance with incomplete penetrance is apparent. By contrast, SQSTM1 variants are only found in up to 10% of patients with sporadic disease. It has been hypothesised that the remaining genetic susceptibility to PDB, particularly in familial cases, could be explained by rare genetic variants in loci previously identified by Genome Wide Association Studies...
June 2019: Bone Reports
https://read.qxmd.com/read/30886426/a-genome-wide-algal-mutant-library-and-functional-screen-identifies-genes-required-for-eukaryotic-photosynthesis
#19
Xiaobo Li, Weronika Patena, Friedrich Fauser, Robert E Jinkerson, Shai Saroussi, Moritz T Meyer, Nina Ivanova, Jacob M Robertson, Rebecca Yue, Ru Zhang, Josep Vilarrasa-Blasi, Tyler M Wittkopp, Silvia Ramundo, Sean R Blum, Audrey Goh, Matthew Laudon, Tharan Srikumar, Paul A Lefebvre, Arthur R Grossman, Martin C Jonikas
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2 . Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool...
March 18, 2019: Nature Genetics
https://read.qxmd.com/read/30885195/basephasing-a-highly-efficient-approach-for-preimplantation-genetic-haplotyping-in-clinical-application-of-balanced-translocation-carriers
#20
Shuo Zhang, Dingding Zhao, Jun Zhang, Yan Mao, Lingyin Kong, Yueping Zhang, Bo Liang, Xiaoxi Sun, Congjian Xu
BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in chromosomally balanced translocation carriers to improve the clinical outcome of assisted reproduction. However, traditional methods could not further distinguish embryos carrying a translocation from those with a normal karyotype prior to implantation. METHODS: To solve this problem, we developed a method named "Chromosomal Phasing on Base level" (BasePhasing), which based on Infinium Asian Screening Array-24 v1...
March 18, 2019: BMC Medical Genomics
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