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Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
Whole Genome Sequencing Identifies Novel Structural Variant in a Large Indian Family Affected with X - Linked Agammaglobulinemia
medRxiv preprint doi: https://doi.org/10.1101/2020.10.05.20200949; this version posted October 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license . Whole Genome Sequencing identifies novel structural variant in a large Indian family affected with X - linked agammaglobulinemia 1,2,# 3,5,#,$ 3,4 3 Abhinav Jain , Geeta Madathil Govindaraj , Athulya Edavazhippurath , Nabeel Faisal , Rahul C 1 1,2 6 3 1 1 Bhoyar , Vishu Gupta , Ramya Uppuluri , Shiny Padinjare Manakkad , Atul Kashyap , Anoop Kumar , 1,2 1,2 7 7 3 Mohit Kumar Divakar , Mohamed Imran , Sneha Sawant , Aparna Dalvi , Krishnan Chakyar , 7 6 1,2,$ 1,2,$ Manisha Madkaikar , Revathi Raj , Sridhar Sivasubbu , Vinod Scaria 1 CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, Delhi, India 2 Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi, Delhi, India 3 Department of Pediatrics, Government Medical College Kozhikode, Kozhikode, Kerala, India 4 Multidisciplinary Research Unit, Government College Kozhikode, Kozhikode, Kerala, India 5 FPID Regional Diagnostic Centre, Government Medical College Kozhikode, Kozhikode, Kerala India 6 Department of Pediatric Hematology, Oncology, Blood and Marrow Transplantation, Apollo Hospitals, 320, Padma complex, Anna salai, Teynampet, Chennai, Tamil Nadu, India 7 Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, KEM Hospital, Parel, Mumbai, Maharashtra, India. # Joint first authors $ Corresponding author Vinod Scaria: [email protected] Sridhar Sivasubbu: [email protected] Geeta Madathil Govindaraj: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
Exome Sequencing and Functional Validation in Zebrafish Identify
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector REPORT Exome Sequencing and Functional Validation in Zebrafish Identify GTDC2 Mutations as a Cause of Walker-Warburg Syndrome M. Chiara Manzini,1,2 Dimira E. Tambunan,1,2 R. Sean Hill,1,2 Tim W. Yu,1,2 Thomas M. Maynard,3 Erin L. Heinzen,4 Kevin V. Shianna,4 Christine R. Stevens,5 Jennifer N. Partlow,1,2 Brenda J. Barry,1,2 Jacqueline Rodriguez,1,2 Vandana A. Gupta,1,6 Abdel-Karim Al-Qudah,7 Wafaa M. Eyaid,8 Jan M. Friedman,9,10 Mustafa A. Salih,11 Robin Clark,12 Isabella Moroni,13 Marina Mora,14 Alan H. Beggs,1,6 Stacey B. Gabriel,5 and Christopher A. Walsh1,2,5,* Whole-exome sequencing (WES), which analyzes the coding sequence of most annotated genes in the human genome, is an ideal approach to studying fully penetrant autosomal-recessive diseases, and it has been very powerful in identifying disease-causing muta- tions even when enrollment of affected individuals is limited by reduced survival. In this study, we combined WES with homozygosity analysis of consanguineous pedigrees, which are informative even when a single affected individual is available, to identify genetic mutations responsible for Walker-Warburg syndrome (WWS), a genetically heterogeneous autosomal-recessive disorder that severely affects the development of the brain, eyes, and muscle. Mutations in seven genes are known to cause WWS and explain 50%–60% of cases, but multiple additional genes are expected to be mutated because unexplained cases show suggestive linkage to diverse loci. -
Genomic Approaches for Understanding the Genetics of Complex Disease
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective Genomic approaches for understanding the genetics of complex disease William L. Lowe Jr.1 and Timothy E. Reddy2,3 1Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; 2Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27708, USA; 3Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27708, USA There are thousands of known associations between genetic variants and complex human phenotypes, and the rate of novel discoveries is rapidly increasing. Translating those associations into knowledge of disease mechanisms remains a fundamental challenge because the associated variants are overwhelmingly in noncoding regions of the genome where we have few guiding principles to predict their function. Intersecting the compendium of identified genetic associations with maps of regulatory activity across the human genome has revealed that phenotype-associated variants are highly enriched in candidate regula- tory elements. Allele-specific analyses of gene regulation can further prioritize variants that likely have a functional effect on disease mechanisms; and emerging high-throughput assays to quantify the activity of candidate regulatory elements are a promising next step in that direction. Together, these technologies have created the ability to systematically and empirically test hypotheses about the function of noncoding variants and haplotypes at the scale needed for comprehensive and system- atic follow-up of genetic association studies. Major coordinated efforts to quantify regulatory mechanisms across genetically diverse populations in increasingly realistic cell models would be highly beneficial to realize that potential. -
Robo4 Is a Vascular-Specific Receptor That Inhibits
Available online at www.sciencedirect.com R Developmental Biology 261 (2003) 251–267 www.elsevier.com/locate/ydbio Robo4 is a vascular-specific receptor that inhibits endothelial migration Kye Won Park,a,b Clayton M. Morrison,a Lise K. Sorensen,a Christopher A. Jones,a,b Yi Rao,c Chi-Bin Chien,d Jane Y. Wu,e Lisa D. Urness,f and Dean Y. Lia,b,f,* a Program in Human Molecular Biology and Genetics, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA b Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA c Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, MO 63110, USA d Department of Anatomy and Neurobiology, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA e Departments of Pediatrics and Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO 63110, USA f Division of Cardiology, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA Received for publication 4 December 2002, revised 17 April 2003, accepted 23 April 2003 Abstract Guidance and patterning of axons are orchestrated by cell-surface receptors and ligands that provide directional cues. Interactions between the Robo receptor and Slit ligand families of proteins initiate signaling cascades that repel axonal outgrowth. Although the vascular and nervous systems grow as parallel networks, the mechanisms by which the vascular endothelial cells are guided to their appropriate positions remain obscure. We have identified a putative Robo homologue, Robo4, based on its differential expression in mutant mice with defects in vascular sprouting. -
Mouse Robo4 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Robo4 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Robo4 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Robo4 gene (NCBI Reference Sequence: NM_028783 ; Ensembl: ENSMUSG00000032125 ) is located on Mouse chromosome 9. 18 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 18 (Transcript: ENSMUST00000102895). Exon 8~10 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Robo4 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-356D13 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a reporter/null allele display enhanced VEGF-induced endothelial migration, tube formation and vascular permeability, and show increased pathologic angiogenesis and vascular leak in models of oxygen-induced retinopathy and choroidal neovascularization. Exon 8 starts from about 38.85% of the coding region. The knockout of Exon 8~10 will result in frameshift of the gene. The size of intron 7 for 5'-loxP site insertion: 689 bp, and the size of intron 10 for 3'-loxP site insertion: 1706 bp. The size of effective cKO region: ~1159 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 4 5 6 7 8 9 10 11 12 18 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Robo4 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
QTL Analysis Reveals Genomic Variants Linked to High-Temperature
Wang et al. Biotechnol Biofuels (2019) 12:59 https://doi.org/10.1186/s13068-019-1398-7 Biotechnology for Biofuels RESEARCH Open Access QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast Zhen Wang1,2†, Qi Qi1,2†, Yuping Lin1*, Yufeng Guo1, Yanfang Liu1,2 and Qinhong Wang1* Abstract Background: High-temperature fermentation is desirable for the industrial production of ethanol, which requires thermotolerant yeast strains. However, yeast thermotolerance is a complicated quantitative trait. The understanding of genetic basis behind high-temperature fermentation performance is still limited. Quantitative trait locus (QTL) map- ping by pooled-segregant whole genome sequencing has been proved to be a powerful and reliable approach to identify the loci, genes and single nucleotide polymorphism (SNP) variants linked to quantitative traits of yeast. Results: One superior thermotolerant industrial strain and one inferior thermosensitive natural strain with distinct high-temperature fermentation performances were screened from 124 Saccharomyces cerevisiae strains as parent strains for crossing and segregant isolation. Based on QTL mapping by pooled-segregant whole genome sequencing as well as the subsequent reciprocal hemizygosity analysis (RHA) and allele replacement analysis, we identifed and validated total eight causative genes in four QTLs that linked to high-temperature fermentation of yeast. Interestingly, loss of heterozygosity in fve of the eight causative genes including RXT2, ECM24, CSC1, IRA2 and AVO1 exhibited posi- tive efects on high-temperature fermentation. Principal component analysis (PCA) of high-temperature fermentation data from all the RHA and allele replacement strains of those eight genes distinguished three superior parent alleles including VPS34, VID24 and DAP1 to be greatly benefcial to high-temperature fermentation in contrast to their inferior parent alleles. -
A Comprehensive Database of Putative Human Microrna Target Site
bioRxiv preprint doi: https://doi.org/10.1101/554485; this version posted May 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions Chang Li1,2, Michael D. Swartz3, Bing Yu1, Yongsheng Bai4, Xiaoming Liu1,2* 1Human Genetics Center and Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 2USF Genomics, College of Public Health, University of South Florida, Tampa, FL 3Department of Biostatistics, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 4Department of Internal Medicine, University of Michigan, Ann Arbor, MI *Correspondence: Xiaoming Liu, [email protected] Funding information: This work is supported partially by NIH funding 1UM1HG008898 and partially by the startup funding for XL from the University of South Florida. bioRxiv preprint doi: https://doi.org/10.1101/554485; this version posted May 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract microRNAs (miRNAs) are short non-coding RNAs that can repress the expression of protein coding messenger RNAs (mRNAs) by binding to the 3’UTR of the target. -
Interleukin 10 Mutant Zebrafish Have an Enhanced Interferon
www.nature.com/scientificreports OPEN Interleukin 10 mutant zebrafsh have an enhanced interferon gamma response and improved Received: 22 August 2017 Accepted: 20 June 2018 survival against a Mycobacterium Published: xx xx xxxx marinum infection Sanna-Kaisa E. Harjula1, Markus J. T. Ojanen1,2, Sinja Taavitsainen3, Matti Nykter3 & Mika Rämet1,4,5,6 Tuberculosis ranks as one of the world’s deadliest infectious diseases causing more than a million casualties annually. IL10 inhibits the function of Th1 type cells, and IL10 defciency has been associated with an improved resistance against Mycobacterium tuberculosis infection in a mouse model. Here, we utilized M. marinum infection in the zebrafsh (Danio rerio) as a model for studying Il10 in the host response against mycobacteria. Unchallenged, nonsense il10e46/e46 mutant zebrafsh were fertile and phenotypically normal. Following a chronic mycobacterial infection, il10e46/e46 mutants showed enhanced survival compared to the controls. This was associated with an increased expression of the Th cell marker cd4-1 and a shift towards a Th1 type immune response, which was demonstrated by the upregulated expression of tbx21 and ifng1, as well as the down-regulation of gata3. In addition, at 8 weeks post infection il10e46/e46 mutant zebrafsh had reduced expression levels of proinfammatory cytokines tnf and il1b, presumably indicating slower progress of the infection. Altogether, our data show that Il10 can weaken the immune defense against M. marinum infection in zebrafsh by restricting ifng1 response. Importantly, our fndings support the relevance of M. marinum infection in zebrafsh as a model for tuberculosis. Annually more than 10 million new tuberculosis cases are estimated to emerge, leading to over a million casualties1. -
Comparison of Structural and Short Variants Detectedby Linked-Read
cancers Article Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma Ashwini Kumar 1,2 , Sadiksha Adhikari 1,2, Matti Kankainen 2,3,4,5 and Caroline A. Heckman 1,2,* 1 Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Tukholmankatu 8, 00290 Helsinki, Finland; ashwini.kumar@helsinki.fi (A.K.); sadiksha.adhikari@helsinki.fi (S.A.) 2 iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland; matti.kankainen@helsinki.fi 3 Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, 00029 Helsinki, Finland 4 Translational Immunology Research Program and Department of Clinical Chemistry, University of Helsinki, 00290 Helsinki, Finland 5 Hematology Research Unit Helsinki, Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland * Correspondence: caroline.heckman@helsinki.fi; Tel.: +358-29-412-5769 Simple Summary: The wide variety of next-generation sequencing technologies requires thorough evaluation and understanding of their advantages and shortcomings of these different approaches prior to their implementation in a precision medicine setting. Here, we compared the performance of two DNA sequencing methods, whole-exome and linked-read exome sequencing, to detect large Citation: Kumar, A.; Adhikari, S.; structural variants (SVs) and short variants in eight multiple myeloma (MM) patient cases. For three Kankainen, M.; Heckman, C.A. patient cases, matched tumor-normal samples were sequenced with both methods to compare somatic Comparison of Structural and Short SVs and short variants. The methods’ clinical relevance was also evaluated, and their sensitivity Variants Detected by Linked-Read and specificity to detect MM-specific cytogenetic alterations and other short variants were measured. -
Variant Annotation
Variant annotation Theorical part V1.1 10/10/18 Ready for annotating variants!! Variant annotation and prioritization Annotation Databases Eilbeck, Karen & Quinlan, Aaron & Yandell, Mark. (2017). Settling the score: variant prioritization and Mendelian disease. Nature Reviews Genetics. 10.1038/nrg.2017.52. Genomic data repositories - 1000 Genomes The 1000 Genomes Project (abbreviated as 1KGP), launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. - ESP (NHLBI Exome Sequencing Project) Exists in 3 flavours : evs annotation data was generated from approximately 2500 exomes, evs_5400 from approximately 5400 exomes and the last one, evs_6500 from approximately 6500 exomes - ExAC (Exome Aggregation Consortium) Coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. - gnomAD (Genome Aggregation Database) Developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects. - FREX (THE FRENCH EXOME) A REFERENCE PANEL OF EXOMES FROM FRENCH REGIONS Annotation Databases Eilbeck, Karen & Quinlan, Aaron & Yandell, Mark. (2017). Settling the score: variant prioritization and Mendelian disease. Nature Reviews Genetics. 10.1038/nrg.2017.52. Databases of variant-disease and gene-disease associations -
1 Mapping Challenging Mutations by Whole-Genome Sequencing Harold
bioRxiv preprint doi: https://doi.org/10.1101/036046; this version posted January 6, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Mapping challenging mutations by whole-genome sequencing Harold E. Smith, Amy S. Fabritius, Aimee Jaramillo-Lambert, and Andy Golden National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 1 bioRxiv preprint doi: https://doi.org/10.1101/036046; this version posted January 6, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Running title: Challenging mutations by WGS Keywords: Forward genetics, variant detection, complex alleles, SNP mapping Corresponding author: Harold E. Smith 8 Center Drive Bethesda, MD 20892 301-594-6554 [email protected] 2 bioRxiv preprint doi: https://doi.org/10.1101/036046; this version posted January 6, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. ABSTRACT Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms.