Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.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[email protected] Geeta Madathil Govindaraj: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.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. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
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. -
Mixed Ancestry Analysis of Whole-Genome Sequencing Reveals
medRxiv preprint doi: https://doi.org/10.1101/2021.08.09.21261801; this version posted August 10, 2021. 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-NC-ND 4.0 International license . Mixed ancestry analysis of whole-genome sequencing reveals common, rare, and structural variants associated with posterior urethral valves Melanie MY Chan,1 Omid Sadeghi-Alavijeh,1 Horia C Stanescu,1 Catalin D Voinescu,1 Glenda M Beaman,2,3 Marcin Zaniew,4 Stefanie Weber,5 Alina C Hilger,6,7 William G Newman,2,3 Adrian S Woolf,8,9 John O Connolly,1,10 Dan Wood,10 Alexander Stuckey,11 Athanasios Kousathanas,11 Genomics England Research Consortium,11 Robert Kleta,1,12 Detlef Bockenhauer,1,12 Adam P Levine,1,13 and Daniel P Gale1* 1Department of Renal Medicine, University College London, London, NW3 2PF, UK. 2Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK. 3Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK. 4Department of Pediatrics, University of Zielona Góra, 56-417 Zielona Góra, Poland. 5Department of Pediatric Nephrology, University of Marburg, 35037 Marburg, Germany. 6Children’s Hospital, University of Bonn, 53113 Bonn, Germany. 7Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany. 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
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. -
Structural Variation in the 3D Genome
REVIEWS TRANSLATIONAL GENETICS Structural variation in the 3D genome Malte Spielmann 1, Darío G. Lupiáñez2 and Stefan Mundlos 3,4* Abstract | Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher- order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types. Structural variation The application of molecular karyotyping and, more the position and/or function of cis- regulatory elements, (SV). Genetic variation that recently, next- generation sequencing (NGS) has such as promoters and enhancers. Owing to advances in includes all structural and revealed the enormous structural complexity of the 3D genome mapping technologies, it is now becoming quantitative chromosomal human genome1–3. Structural and quantitative chromo- increasingly evident that position effects are the result of rearrangements, that is, deletions and duplications, as somal rearrangements, collectively referred to as much more complex alterations than just changes in the well as copy- number-neutral structural variation (SV), include deletions, duplications, linear genome. -
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. -
How Important Are Structural Variants for Speciation?
G C A T T A C G G C A T genes Review How Important Are Structural Variants for Speciation? Linyi Zhang 1,*, Radka Reifová 2, Zuzana Halenková 2 and Zachariah Gompert 1 1 Department of Biology, Utah State University, Logan, UT 84322, USA; [email protected] 2 Department of Zoology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; [email protected] (R.R.); [email protected] (Z.H.) * Correspondence: [email protected] Abstract: Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribu- tion of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation. Citation: Zhang, L.; Reifová, R.; Keywords: reproductive isolation; hybridization; suppressed recombination Halenková, Z.; Gompert, Z. -
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