Is It Time to Change the Reference Genome? 2 Sara Ballouz, Alexander Dobin, Jesse Gillis
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Reference Genome Sequence of the Model Plant Setaria
UC Davis UC Davis Previously Published Works Title Reference genome sequence of the model plant Setaria Permalink https://escholarship.org/uc/item/2rv1r405 Journal Nature Biotechnology, 30(6) ISSN 1087-0156 1546-1696 Authors Bennetzen, Jeffrey L Schmutz, Jeremy Wang, Hao et al. Publication Date 2012-05-13 DOI 10.1038/nbt.2196 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLES Reference genome sequence of the model plant Setaria Jeffrey L Bennetzen1,13, Jeremy Schmutz2,3,13, Hao Wang1, Ryan Percifield1,12, Jennifer Hawkins1,12, Ana C Pontaroli1,12, Matt Estep1,4, Liang Feng1, Justin N Vaughn1, Jane Grimwood2,3, Jerry Jenkins2,3, Kerrie Barry3, Erika Lindquist3, Uffe Hellsten3, Shweta Deshpande3, Xuewen Wang5, Xiaomei Wu5,12, Therese Mitros6, Jimmy Triplett4,12, Xiaohan Yang7, Chu-Yu Ye7, Margarita Mauro-Herrera8, Lin Wang9, Pinghua Li9, Manoj Sharma10, Rita Sharma10, Pamela C Ronald10, Olivier Panaud11, Elizabeth A Kellogg4, Thomas P Brutnell9,12, Andrew N Doust8, Gerald A Tuskan7, Daniel Rokhsar3 & Katrien M Devos5 We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. -
Y Chromosome Dynamics in Drosophila
Y chromosome dynamics in Drosophila Amanda Larracuente Department of Biology Sex chromosomes X X X Y J. Graves Sex chromosome evolution Proto-sex Autosomes chromosomes Sex Suppressed determining recombination Differentiation X Y Reviewed in Rice 1996, Charlesworth 1996 Y chromosomes • Male-restricted • Non-recombining • Degenerate • Heterochromatic Image from Willard 2003 Drosophila Y chromosome D. melanogaster Cen Hoskins et al. 2015 ~40 Mb • ~20 genes • Acquired from autosomes • Heterochromatic: Ø 80% is simple satellite DNA Photo: A. Karwath Lohe et al. 1993 Satellite DNA • Tandem repeats • Heterochromatin • Centromeres, telomeres, Y chromosomes Yunis and Yasmineh 1970 http://www.chrombios.com Y chromosome assembly challenges • Repeats are difficult to sequence • Underrepresented • Difficult to assemble Genome Sequence read: Short read lengths cannot span repeats Single molecule real-time sequencing • Pacific Biosciences • Average read length ~15 kb • Long reads span repeats • Better genome assemblies Zero mode waveguide Eid et al. 2009 Comparative Y chromosome evolution in Drosophila I. Y chromosome assemblies II. Evolution of Y-linked genes Drosophila genomes 2 Mya 0.24 Mya Photo: A. Karwath P6C4 ~115X ~120X ~85X ~95X De novo genome assembly • Assemble genome Iterative assembly: Canu, Hybrid, Quickmerge • Polish reference Quiver x 2; Pilon 2L 2R 3L 3R 4 X Y Assembled genome Mahul Chakraborty, Ching-Ho Chang 2L 2R 3L 3R 4 X Y Y X/A heterochromatin De novo genome assembly species Total bp # contigs NG50 D. simulans 154,317,203 161 21,495729 -
Independent Evidence for an Association Between General Cognitive Ability and a Genetic Locus for Educational Attainment J
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Hofstra Northwell Academic Works (Hofstra Northwell School of Medicine) Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2015 Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment J. W. Trampush Hofstra Northwell School of Medicine T. Lencz Hofstra Northwell School of Medicine S. Guha Northwell Health S. Mukherjee Northwell Health P. DeRosse Northwell Health See next page for additional authors Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Psychiatry Commons Recommended Citation Trampush JW, Lencz T, Guha S, Mukherjee S, DeRosse P, John M, Andreassen O, Deary I, Glahn D, Malhotra AK, . Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment. 2015 Jan 01; 168(5):Article 927 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/927. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. Authors J. W. Trampush, T. Lencz, S. Guha, S. Mukherjee, P. DeRosse, M. John, O. A. Andreassen, I. J. Deary, D. C. Glahn, A. K. Malhotra, and +41 additional authors This article is available at Donald and Barbara Zucker School of Medicine Academic Works: https://academicworks.medicine.hofstra.edu/articles/927 HHS Public Access Author manuscript Author Manuscript Author ManuscriptAm J Med Author Manuscript Genet B Neuropsychiatr Author Manuscript Genet. -
The Bacteria Genome Pipeline (BAGEP): an Automated, Scalable Workflow for Bacteria Genomes with Snakemake
The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake Idowu B. Olawoye1,2, Simon D.W. Frost3,4 and Christian T. Happi1,2 1 Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria 2 African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria 3 Microsoft Research, Redmond, WA, USA 4 London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom ABSTRACT Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Permalink https://escholarship.org/uc/item/7cx5710p Journal Nature biotechnology, 35(7) ISSN 1087-0156 Authors Mukherjee, Supratim Seshadri, Rekha Varghese, Neha J et al. Publication Date 2017-07-01 DOI 10.1038/nbt.3886 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESOU r CE OPEN 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Supratim Mukherjee1,10, Rekha Seshadri1,10, Neha J Varghese1, Emiley A Eloe-Fadrosh1, Jan P Meier-Kolthoff2 , Markus Göker2 , R Cameron Coates1,9, Michalis Hadjithomas1, Georgios A Pavlopoulos1 , David Paez-Espino1 , Yasuo Yoshikuni1, Axel Visel1 , William B Whitman3, George M Garrity4,5, Jonathan A Eisen6, Philip Hugenholtz7 , Amrita Pati1,9, Natalia N Ivanova1, Tanja Woyke1, Hans-Peter Klenk8 & Nikos C Kyrpides1 We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. -
Telomere-To-Telomere Assembly of a Complete Human X Chromosome W
https://doi.org/10.1038/s41586-020-2547-7 Accelerated Article Preview Telomere-to-telomere assembly of a W complete human X chromosome E VI Received: 30 July 2019 Karen H. Miga, Sergey Koren, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, GlennisE A. Logsdon, Accepted: 29 May 2020 Valerie A. Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Accelerated Article Preview Published Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki,R Christopher Markovic, online 14 July 2020 Valerie Maduro, Amalia Dutra, Gerard G. Bouffard, Alexander M. Chang, Nancy F. Hansen, Amy B. Wilfert, Françoise Thibaud-Nissen, Anthony D. Schmitt,P Jon-Matthew Belton, Cite this article as: Miga, K. H. et al. Siddarth Selvaraj, Megan Y. Dennis, Daniela C. Soto, Ruta Sahasrabudhe, Gulhan Kaya, Telomere-to-telomere assembly of a com- Josh Quick, Nicholas J. Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, plete human X chromosome. Nature Rosa ana Risques, Tina A. Graves Lindsay, RobertE Fulton, Ira Hall, Benedict Paten, https://doi.org/10.1038/s41586-020-2547-7 Kerstin Howe, Winston Timp, Alice Young, James C. Mullikin, Pavel A. Pevzner, (2020). Jennifer L. Gerton, Beth A. Sullivan, EvanL E. Eichler & Adam M. Phillippy C This is a PDF fle of a peer-reviewedI paper that has been accepted for publication. Although unedited, the Tcontent has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text andR fgures will undergo copyediting and a proof review before the paper is published in its fnal form. -
Genetic Influence on Cognitive Development Between Childhood
Molecular Psychiatry https://doi.org/10.1038/s41380-018-0277-0 ARTICLE Genetic influence on cognitive development between childhood and adulthood 1 1 1 2 3 Josephine Mollon ● Emma E. M. Knowles ● Samuel R. Mathias ● Ruben Gur ● Juan Manuel Peralta ● 4,5,6 4,5,6 2 3 7 1,8 Daniel J. Weiner ● Elise B. Robinson ● Raquel E. Gur ● John Blangero ● Laura Almasy ● David C. Glahn Received: 17 April 2018 / Revised: 15 August 2018 / Accepted: 11 September 2018 © Springer Nature Limited 2018 Abstract Successful cognitive development between childhood and adulthood has important consequences for future mental and physical wellbeing, as well as occupational and financial success. Therefore, delineating the genetic influences underlying changes in cognitive abilities during this developmental period will provide important insights into the biological mechanisms that govern both typical and atypical maturation. Using data from the Philadelphia Neurodevelopmental Cohort (PNC), a large population-based sample of individuals aged 8 to 21 years old (n = 6634), we used an empirical relatedness matrix to establish the heritability of general and specific cognitive functions and determine if genetic factors influence 1234567890();,: 1234567890();,: cognitive maturation (i.e., Gene × Age interactions) between childhood and early adulthood. We found that neurocognitive measures across childhood and early adulthood were significantly heritable. Moreover, genetic variance on general cognitive ability, or g, increased significantly between childhood and early adulthood. Finally, we did not find evidence for decay in genetic correlation on neurocognition throughout childhood and adulthood, suggesting that the same genetic factors underlie cognition at different ages throughout this developmental period. Establishing significant Gene × Age interactions in neurocognitive functions across childhood and early adulthood is a necessary first step in identifying genes that influence cognitive development, rather than genes that influence cognition per se. -
Whole‐Exome Sequencing in 20,197 Persons for Rare Variants In
RESEARCH PAPER Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer’s disease Neha S. Raghavan1,2, Adam M. Brickman1,2,3, Howard Andrews1,2,4, Jennifer J. Manly1,2,3, Nicole Schupf1,2,3,7, Rafael Lantigua1,6, Charles J. Wolock8, Sitharthan Kamalakaran8, Slave Petrovski8,9, Giuseppe Tosto1,2,3, Badri N. Vardarajan1,2,3,5, David B. Goldstein3,6,8, Richard Mayeux1,2,3,4,7 & The Alzheimer’s Disease Sequencing Projecta 1The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 2The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 3Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 4Department of Psychiatry, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 5Department of Systems Biology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 6Department of Medicine, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 7The Department of Epidemiology, Mailman School of Public Health, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 8Institute of Genomic Medicine, Columbia University, The New York Presbyterian Hospital, New York, New York 9AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 0AA, United Kingdom Correspondence Abstract Richard Mayeux, Department of Neurology, Objective 710 West 168th Street, Columbia University, : The genetic bases of Alzheimer’s disease remain uncertain. -
Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 'S Role in Working Memory
Neuropsychopharmacology (2017) 42, 2612–2622 © 2017 American College of Neuropsychopharmacology. All rights reserved 0893-133X/17 www.neuropsychopharmacology.org Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 's Role in Working Memory 1 1 2 3 4,5 3 Donna Cosgrove , Omar Mothersill , Kimberley Kendall , Bettina Konte , Denise Harold , Ina Giegling , 3 6 6 7 Annette Hartmann , Alex Richards , Kiran Mantripragada , The Wellcome Trust Case Control Consortium , Michael J Owen6, Michael C O’Donovan6, Michael Gill4, Dan Rujescu3, James Walters2, Aiden Corvin4, Derek W Morris1 and Gary Donohoe*,1 1 The Cognitive Genetics & Cognitive Therapy Group, The School of Psychology and Discipline of Biochemistry, The Centre for Neuroimaging & Cognitive Genomics, National University of Ireland Galway, Galway, Ireland; 2Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK; 3Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany; 4 Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; 5 6 School of Biotechnology, Dublin City University, Dublin, Ireland; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK With 4100 common variants associated with schizophrenia risk, establishing their biological significance is a priority. We sought to establish cognitive effects of -
Human Genome Reference Program (HGRP)
Frequently Asked Questions – Human Genome Reference Program (HGRP) Funding Announcements • RFA-HG-19-002: High Quality Human Reference Genomes (HQRG) • RFA-HG-19-003: Research and Development for Genome Reference Representations (GRR) • RFA-HG-19-004: Human Genome Reference Center (HGRC) • NOT-HG-19-011: Emphasizing Opportunity for Developing Comprehensive Human Genome Sequencing Methodologies Concept Clearance Slides https://www.genome.gov/pages/about/nachgr/september2018agendadocuments/sept2018council_hg _reference_program.pdf. *Note that this presentation includes a Concept for a fifth HGRP component seeking development of informatics tools for the pan-genome. Eligibility Questions 1. Are for-profit entities eligible to apply? a. Only higher education institutes, governments, and non-profits are eligible to apply for the HGRC (RFA-HG-19-004). b. For-profit entities are eligible to apply for HQRG and GRR (RFA-HG-19-002 and 003), and for the Notice for Comprehensive Human Genome Sequencing Methodologies (NOT-HG- 19-011). The Notice also allows SBIR applications. 2. Can foreign institutions apply or receive subcontracts? a. Foreign institutions are eligible to apply to the HQRG and GRR announcements, and Developing Comprehensive Sequencing Methodologies Notice. b. Foreign institutions, including non-domestic (U.S.) components of U.S. organizations, are not eligible for HGRC. However, the FOA does allow foreign components. c. For more information, please see the NIH Grants Policy Statement. 3. Will applications with multiple sites be considered? Yes, applications with multiple sites, providing they are eligible institutions, will be considered. Application Questions 1. How much funding is available for this program? NHGRI has set aside ~$10M total costs per year for the Human Genome Reference Program. -
De Novo Genome Assembly Versus Mapping to a Reference Genome
De novo genome assembly versus mapping to a reference genome Beat Wolf PhD. Student in Computer Science University of Würzburg, Germany University of Applied Sciences Western Switzerland [email protected] 1 Outline ● Genetic variations ● De novo sequence assembly ● Reference based mapping/alignment ● Variant calling ● Comparison ● Conclusion 2 What are variants? ● Difference between a sample (patient) DNA and a reference (another sample or a population consensus) ● Sum of all variations in a patient determine his genotype and phenotype 3 Variation types ● Small variations ( < 50bp) – SNV (Single nucleotide variation) – Indel (insertion/deletion) 4 Structural variations 5 Sequencing technologies ● Sequencing produces small overlapping sequences 6 Sequencing technologies ● Difference read lengths, 36 – 10'000bp (150-500bp is typical) ● Different sequencing technologies produce different data And different kinds of errors – Substitutions (Base replaced by other) – Homopolymers (3 or more repeated bases) ● AAAAA might be read as AAAA or AAAAAA – Insertion (Non existent base has been read) – Deletion (Base has been skipped) – Duplication (cloned sequences during PCR) – Somatic cells sequenced 7 Sequencing technologies ● Standardized output format: FASTQ – Contains the read sequence and a quality for every base http://en.wikipedia.org/wiki/FASTQ_format 8 Recreating the genome ● The problem: – Recreate the original patient genome from the sequenced reads ● For which we dont know where they came from and are noisy ● Solution: – Recreate the genome -
Practical Guideline for Whole Genome Sequencing Disclosure
Practical Guideline for Whole Genome Sequencing Disclosure Kwangsik Nho Assistant Professor Center for Neuroimaging Department of Radiology and Imaging Sciences Center for Computational Biology and Bioinformatics Indiana University School of Medicine • Kwangsik Nho discloses that he has no relationships with commercial interests. What You Will Learn Today • Basic File Formats in WGS • Practical WGS Analysis Pipeline • WGS Association Analysis Methods Whole Genome Sequencing File Formats WGS Sequencer Base calling FASTQ: raw NGS reads Aligning SAM: aligned NGS reads BAM Variant Calling VCF: Genomic Variation How have BIG data problems been solved in next generation sequencing? gkno.me Whole Genome Sequencing File Formats • FASTQ: text-based format for storing both a DNA sequence and its corresponding quality scores (File sizes are huge (raw text) ~300GB per sample) @HS2000-306_201:6:1204:19922:79127/1 ACGTCTGGCCTAAAGCACTTTTTCTGAATTCCACCCCAGTCTGCCCTTCCTGAGTGCCTGGGCAGGGCCCTTGGGGAGCTGCTGGTGGGGCTCTGAATGT + BC@DFDFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJHGGIGHJJJJJIJEGJHGIIJJIGGIIJHEHFBECEC@@D@BDDDDD<<?DB@BDDCDCDDC @HS2000-306_201:6:1204:19922:79127/2 GGGTAAAAGGTGTCCTCAGCTAATTCTCATTTCCTGGCTCTTGGCTAATTCTCATTCCCTGGGGGCTGGCAGAAGCCCCTCAAGGAAGATGGCTGGGGTC + BCCDFDFFHGHGHIJJJJJJJJJJJGJJJIIJCHIIJJIJIJJJJIJCHEHHIJJJJJJIHGBGIIHHHFFFDEEDED?B>BCCDDCBBDACDD8<?B09 @HS2000-306_201:4:1106:6297:92330/1 CACCATCCCGCGGAGCTGCCAGATTCTCGAGGTCACGGCTTACACTGCGGAGGGCCGGCAACCCCGCCTTTAATCTGCCTACCCAGGGAAGGAAAGCCTC + CCCFFFFFHGHHHJIJJJJJJJJIJJIIIGIJHIHHIJIGHHHHGEFFFDDDDDDDDDDD@ADBDDDDDDDDDDDDEDDDDDABCDDB?BDDBDCDDDDD