Genomics insights最新文献

{"title":"<i>De Novo</i> Duplication in the <i>CHD7</i> Gene Associated With Severe CHARGE Syndrome.","authors":"Laura Pranckėnienė,&nbsp;Eglė Preikšaitienė,&nbsp;Lucie Gueneau,&nbsp;Alexandre Reymond,&nbsp;Vaidutis Kučinskas","doi":"10.1177/1178631019839010","DOIUrl":"https://doi.org/10.1177/1178631019839010","url":null,"abstract":"<p><p>CHARGE syndrome is an autosomal dominant developmental disorder associated with a constellation of traits involving almost every organ and sensory system, in particular congenital anomalies, including choanal atresia and malformations of the heart, inner ear, and retina. Variants in <i>CHD7</i> have been shown to cause CHARGE syndrome. Here, we report the identification of a novel <i>de novo</i> p.Asp2119_Pro2120ins6 duplication variant in a conserved region of <i>CHD7</i> in a severely affected boy presenting with 3 and 5 of the CHARGE cardinal major and minor signs, respectively, combined with congenital umbilical hernia, congenital hernia at the linea alba, mildly hypoplastic inferior vermis, slight dilatation of the lateral ventricles, prominent metopic ridge, and hypoglycemic episodes.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"12 ","pages":"1178631019839010"},"PeriodicalIF":0.0,"publicationDate":"2019-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631019839010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37200685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reviewer List 2018","authors":"Weijun, Katoh-Fukui, Yuko, Glessner","doi":"10.1177/1178631019829639","DOIUrl":"https://doi.org/10.1177/1178631019829639","url":null,"abstract":"Akdag, Sa Al-Rbeawi, Salam Alizamir, M Amirian, E Amodu, Omowunmi Ao, Songjian Badoga, Sandeep Balusamy, Saravanan Banerjee, Sayandeep Bao, Zhidong Benjamin, I. Nelson Binyet, E Bu, Quan Çalık, Ahmet Cano, Antonio Cao, Zhe Chandra Babu, Jakka Sarat Chang, Tao Chang, Xiangchun Chen, Anqing Chen, Liang Chen, Shuyuan Chen, Weizhong Chen, Z.H. Cheng, Liyuan Cheng, Rui Chong, W. W. F. Cui, Huiying Dai, Cheng Devi, B. L. A. Prabhavathi Ding, Rui Ding, Xiujian Du, Shanghai Du, Shuheng Du, Xuebin El-Seesy, Ahmed I. Fan, Chaojun Feng, Bo Feng, Wenjie Fiket, Zeljka Font, Xavier Fu, Hanliang Gan, Huajun Ge, Zhaolong Ge, Shilong Genc, Mustafa Geng, Shuai Gong, Yanjie González, B. M. Gozgor, G Guler, O Guo, Chen Guo, Tiankui Guris, Burak Hamza, M He, Baojie He, Kun Hou, Dy Hou, Mingcai Hou, Xiaowei Hu, Guang Hu, Jia Hu, Jie Hu, Tao Hu, Wenxuan Hu, Xiancai Huang, Bingxiang Huang, Haiping Hudisteanu, S Huo, Aidi Hussain, Furqan Jakovljevi c, Ivan Jeong, Daein Ji, Hancheng Jiang, Bo Jiang, Guangzheng Jiang, Wei Jiang, Zaixing Jiang, Zhenxue Jiao, Kun Jirasek, J Ju, Wei Kang, Xun Kaplan, Ya Kaya, Mustafa KeRdzior, S. Kedzior, Slawomir Khan, Mi Khan, Salman Kolak, Jonathan J. Kuszewski, Hubert Lai, Jin Lee, Kyung Jae Lee, Youngsoo Levendis, Yiannis A. Li, Bo Li, Changzhu Li, Dong Li, Guiqiang Li, Guorong Li, Hao Li, J Li, Meijun Li, Qing Li, Shengli Energy Exploration & Exploitation 2019, Vol. 37(2) 884–886 ! The Author(s) 2019 DOI: 10.1177/0144598719836561 journals.sagepub.com/home/eea","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631019829639","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45400800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum.","authors":"","doi":"10.1177/1178631018801448","DOIUrl":"https://doi.org/10.1177/1178631018801448","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.4137/GEI.S32477.].</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"11 ","pages":"1178631018801448"},"PeriodicalIF":0.0,"publicationDate":"2018-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631018801448","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36480051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression Levels of Candidate Circulating microRNAs in Early-Onset Neonatal Sepsis Compared With Healthy Newborns.","authors":"Benet B Dhas,&nbsp;Vijaya R Dirisala,&nbsp;B Vishnu Bhat","doi":"10.1177/1178631018797079","DOIUrl":"https://doi.org/10.1177/1178631018797079","url":null,"abstract":"<p><p>The high mortality rate of neonatal sepsis is directly connected with time-consuming diagnostic methods that have low sensitivity and specificity. The need of the hour is to develop novel diagnostic techniques that are rapid and more specific. In this study, we estimated the expression levels of circulating microRNAs (miRNAs) that are involved in regulating immune response genes and underlying inflammatory responses, which may be used for sepsis diagnosis. The total circulating miRNA was isolated and the candidate miRNAs (miR-132, miR-146a, miR-155, and miR-223) were quantified by real-time polymerase chain reaction technique. Statistical analysis revealed that miR-132 (<i>P</i> < .01) and miR-223 (<i>P</i> < .05) were downregulated in septic newborns compared with healthy babies. The decrease in expression of miR-132 and miR-223 may be associated with increased expression of immune-related genes involved in TLR (Toll-like receptor) signaling pathway. Further case-control studies with large sample size are required to identify the potential of miRNAs in neonatal sepsis diagnosis.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"11 ","pages":"1178631018797079"},"PeriodicalIF":0.0,"publicationDate":"2018-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631018797079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36477510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of the GRADE Approach in the Development of Guidelines and Recommendations in Genomic Medicine.","authors":"Muhammad Rafiq,&nbsp;Stefania Boccia","doi":"10.1177/1178631017753360","DOIUrl":"https://doi.org/10.1177/1178631017753360","url":null,"abstract":"<p><p>A great deal of ambiguity exists in the development of guidelines for genomic applications used in clinical practice. The GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach has the potential to be applied in the guidelines and recommendations development process in genomics. Here, we discuss whether and how GRADE can be applied to address the challenges posed by the evidence-based guidelines and recommendations development process in genomics. To see how GRADE can complement to the current guidelines development in genomics, we compare and contrast GRADE with other approaches. GRADE differed from other methods by incorporating patient values and preferences and balance of consequences. We conclude that the groups trying to implement genomics into practice may gleam more information from applying the GRADE framework. However, it is not clear yet whether GRADE can address the issue of timeliness in terms of the differences between the time required for guidelines development and the rapid pace of genomics.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"11 ","pages":"1178631017753360"},"PeriodicalIF":0.0,"publicationDate":"2018-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631017753360","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35802635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights Into Upland Cotton (<i>Gossypium hirsutum</i> L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents.","authors":"Mauricio Ulloa, Amanda M Hulse-Kemp, Luis M De Santiago, David M Stelly, John J Burke","doi":"10.1177/1178631017735104","DOIUrl":"10.1177/1178631017735104","url":null,"abstract":"<p><p>High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton (<i>Gossypium hirsutum</i> L., \"2n = 52\"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F₂, a recombinant inbred line (RIL), and reciprocal RIL population, from \"Phytogen 72\" and \"Stoneville 474\" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD)₁ arisen from the merging of 2 genomes (\"A\" Old World and \"D\" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the A_t and D_t subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the D_t subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral A_t-subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of <i>Gossypium hirsutum</i>. However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid A_t and D_t subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI <i>G hirsutum</i> assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in <i>G hirsutum</i> with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"10 ","pages":"1178631017735104"},"PeriodicalIF":0.0,"publicationDate":"2017-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/82/bd/10.1177_1178631017735104.PMC5751910.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35714539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exon Mapping in Long Noncoding RNAs Using Digital Filters.","authors":"Tina P George,&nbsp;Tessamma Thomas","doi":"10.1177/1178631017732029","DOIUrl":"https://doi.org/10.1177/1178631017732029","url":null,"abstract":"<p><p>Long noncoding RNAs (lncRNAs) which were initially dismissed as \"transcriptional noise\" have become a vital area of study after their roles in biological regulation were discovered. Long noncoding RNAs have been implicated in various developmental processes and diseases. Here, we perform exon mapping of human lncRNA sequences (taken from National Center for Biotechnology Information GenBank) using digital filters. Antinotch digital filters are used to map out the exons of the lncRNA sequences analyzed. The period 3 property which is an established indicator for locating exons in genes is used here. Discrete wavelet transform filter bank is used to fine-tune the exon plots by selectively removing the spectral noise. The exon locations conform to the ranges specified in GenBank. In addition to exon prediction, G-C concentrations of lncRNA sequences are found, and the sequences are searched for START and STOP codons as these are indicators of coding potential.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"10 ","pages":"1178631017732029"},"PeriodicalIF":0.0,"publicationDate":"2017-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178631017732029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35582141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies.","authors":"Kevin H M Kuo","doi":"10.1177/1178631017721178","DOIUrl":"10.1177/1178631017721178","url":null,"abstract":"<p><p>The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"10 ","pages":"1178631017721178"},"PeriodicalIF":0.0,"publicationDate":"2017-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1f/a0/10.1177_1178631017721178.PMC5542087.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35273115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SNP Marker Discovery in Pima Cotton (<i>Gossypium barbadense</i> L.) Leaf Transcriptomes.","authors":"Pratibha Kottapalli, Mauricio Ulloa, Kameswara Rao Kottapalli, Paxton Payton, John Burke","doi":"10.4137/GEI.S40377","DOIUrl":"10.4137/GEI.S40377","url":null,"abstract":"<p><p>The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton (<i>Gossypium barbadense</i> L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6, 25,870 contigs for PS7, and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. More than 10,000 single-nucleotide polymorphisms (SNPs) were identified between the genotypes, with 100% SNP frequency and a minimum of eight sequencing reads. The most prevalent SNP substitutions were C-T and A-G in these cotton genotypes. The putative SNPs identified can be utilized for characterizing genetic diversity, genotyping, and eventually in Pima cotton breeding through marker-assisted selection.</p>","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"9 1","pages":"51-60"},"PeriodicalIF":0.0,"publicationDate":"2016-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70701389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel Approach to Analyzing MFE of Noncoding RNA Sequences","authors":"Tina P. George, T. Thomas","doi":"10.4137/GEI.S39995","DOIUrl":"https://doi.org/10.4137/GEI.S39995","url":null,"abstract":"Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"9 1","pages":"41 - 49"},"PeriodicalIF":0.0,"publicationDate":"2016-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S39995","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70701330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}