1
|
Topolska M, Beltran A, Lehner B. Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function. Nat Commun 2025; 16:2617. [PMID: 40097423 PMCID: PMC11914627 DOI: 10.1038/s41467-025-57510-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 02/21/2025] [Indexed: 03/19/2025] Open
Abstract
Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels on protein stability are not well understood. To better understand indels here we analyse new and existing large-scale deep indel mutagenesis (DIM) of structurally diverse proteins. The effects of indels on protein stability vary extensively among and within proteins and are not well predicted by existing computational methods. To address this shortcoming we present INDELi, a series of models that combine experimental or predicted substitution effects and secondary structure information to provide good prediction of the effects of indels on both protein stability and pathogenicity. Moreover, quantifying the effects of indels on protein-protein interactions suggests that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
Collapse
Affiliation(s)
- Magdalena Topolska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- University Pompeu Fabra (UPF), Barcelona, Spain
| | - Antoni Beltran
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- University Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i estudis Avançats (ICREA), Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| |
Collapse
|
2
|
Srivastava K, Yin Q, Makuria AT, Rios M, Gebremedhin A, Flegel WA. CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities. Transfusion 2024; 64:1296-1305. [PMID: 38817044 PMCID: PMC11251854 DOI: 10.1111/trf.17869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND CD59 deficiency due to rare germline variants in the CD59 gene causes disabilities, ischemic strokes, neuropathy, and hemolysis. CD59 deficiency due to common somatic variants in the PIG-A gene in hematopoietic stem cells causes paroxysmal nocturnal hemoglobinuria. The ISBT database lists one nonsense and three missense germline variants that are associated with the CD59-null phenotype. To analyze the genetic diversity of the CD59 gene, we determined long-range CD59 haplotypes among individuals from different ethnicities. METHODS We determined a 22.7 kb genomic fragment of the CD59 gene in 113 individuals using next-generation sequencing (NGS), which covered the whole NM_203330.2 mRNA transcript of 7796 base pairs. Samples came from an FDA reference repository and our Ethiopia study cohorts. The raw genotype data were computationally phased into individual haplotype sequences. RESULTS Nucleotide sequencing of the CD59 gene of 226 chromosomes identified 216 positions with single nucleotide variants. Only three haplotypes were observed in homozygous form, which allowed us to assign them unambiguously as experimentally verified CD59 haplotypes. They were also the most frequent haplotypes among both cohorts. An additional 140 haplotypes were imputed computationally. DISCUSSION We provided a large set of haplotypes and proposed three verified long-range CD59 reference sequences, based on a population approach, using a generalizable rationale for our choice. Correct long-range haplotypes are useful as template sequences for allele calling in high-throughput NGS and precision medicine approaches, thus enhancing the reliability of clinical diagnostics. Long-range haplotypes can also be used to evaluate the influence of genetic variation on the risk of transfusion reactions or diseases.
Collapse
Affiliation(s)
- Kshitij Srivastava
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
| | - Qinan Yin
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
- Present address:
Henan Engineering Research Center of Digital Pathology and Artificial Intelligence DiagnosisThe First Affiliated Hospital of Henan University of Science and TechnologyLuoyangPeople's Republic of China
- Present address:
Precision Medicine Laboratory, School of Medical Technology and EngineeringHenan University of Science and TechnologyLuoyangPeople's Republic of China
| | - Addisalem Taye Makuria
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
- Department of Pathology and Laboratory ServicesECU Health Medical CenterGreenvilleNorth CarolinaUSA
| | - Maria Rios
- Office of Blood Research and Review, Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Amha Gebremedhin
- School of MedicineCollege of Health Sciences, Addis Ababa UniversityAddis AbabaEthiopia
| | - Willy Albert Flegel
- Department of Transfusion MedicineNIH Clinical Center, National Institutes of HealthBethesdaMarylandUSA
| |
Collapse
|
3
|
Zoh MG, Bonneville JM, Laporte F, Tutagata J, Sadia CG, Fodjo BK, Mouhamadou CS, McBeath J, Schmitt F, Horstmann S, Reynaud S, David JP. Deltamethrin and transfluthrin select for distinct transcriptomic responses in the malaria vector Anopheles gambiae. Malar J 2023; 22:256. [PMID: 37667239 PMCID: PMC10476409 DOI: 10.1186/s12936-023-04673-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND The widespread use of pyrethroid insecticides in Africa has led to the development of strong resistance in Anopheles mosquitoes. Introducing new active ingredients can contribute to overcome this phenomenon and ensure the effectiveness of vector control strategies. Transfluthrin is a polyfluorinated pyrethroid whose structural conformation was thought to prevent its metabolism by cytochrome P450 monooxygenases in malaria vectors, thus representing a potential alternative for managing P450-mediated resistance occurring in the field. In this study, a controlled selection was used to compare the dynamics of resistance between transfluthrin and the widely used pyrethroid deltamethrin in the mosquito Anopheles gambiae. Then, the associated molecular mechanisms were investigated using target-site mutation genotyping and RNA-seq. METHODS A field-derived line of An. gambiae carrying resistance alleles at low frequencies was used as starting material for a controlled selection experiment. Adult females were selected across 33 generations with deltamethrin or transfluthrin, resulting in three distinct lines: the Delta-R line (selected with deltamethrin), the Transflu-R line (selected with transfluthrin) and the Tiassale-S line (maintained without selection). Deltamethrin and transfluthrin resistance levels were monitored in each selected line throughout the selection process, as well as the frequency of the L1014F kdr mutation. At generation 17, cross-resistance to other public health insecticides was investigated and transcriptomes were sequenced to compare gene transcription variations and polymorphisms associated with adaptation to each insecticide. RESULTS A rapid increase in resistance to deltamethrin and transfluthrin was observed throughout the selection process in each selected line in association with an increased frequency of the L1014F kdr mutation. Transcriptomic data support a broader response to transfluthrin selection as compared to deltamethrin selection. For instance, multiple detoxification enzymes and cuticle proteins were specifically over-transcribed in the Transflu-R line including the known pyrethroid metabolizers CYP6M2, CYP9K1 and CYP6AA1 together with other genes previously associated with resistance in An. gambiae. CONCLUSION This study confirms that recurrent exposure of adult mosquitoes to pyrethroids in a public health context can rapidly select for various resistance mechanisms. In particular, it indicates that in addition to target site mutations, the polyfluorinated pyrethroid transfluthrin can select for a broad metabolic response, which includes some P450s previously associated to resistance to classical pyrethroids. This unexpected finding highlights the need for an in-depth study on the adaptive response of mosquitoes to newly introduced active ingredients in order to effectively guide and support decision-making programmes in malaria control.
Collapse
Affiliation(s)
- Marius Gonse Zoh
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France.
- Vector Control Product Evaluation Centre (VCPEC) Institut Pierre Richet (VCPEC IPR)/INSP, Bouaké, Côte d'Ivoire.
| | - Jean-Marc Bonneville
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France
| | - Frederic Laporte
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France
| | - Jordan Tutagata
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France
| | | | - Behi K Fodjo
- Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | | | - Justin McBeath
- Envu, Milton Hall, Ely Road. Milton, Cambridge, CB24 6WZ, UK
| | - Frederic Schmitt
- Envu, 2022 Environmental Science FR S.A.S, 3 Place Giovanni Da Verrazzano, 69009, Lyon, France
| | - Sebastian Horstmann
- Envu, 2022 ES Deutschland GmbH, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
| | - Stéphane Reynaud
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA), Grenoble-Alpes University, Savoie Mont-Blanc University, CNRS, 38041, Grenoble, France
| |
Collapse
|
4
|
Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
Collapse
Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
5
|
Agarwal A, Zhao F, Jiang Y, Chen L. TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions. Bioinformatics 2023; 39:btad060. [PMID: 36707993 PMCID: PMC9900211 DOI: 10.1093/bioinformatics/btad060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Small insertion and deletion (sindel) of human genome has an important implication for human disease. One important mechanism for non-coding sindel (nc-sindel) to have an impact on human diseases and phenotypes is through the regulation of gene expression. Nevertheless, current sequencing experiments may lack statistical power and resolution to pinpoint the functional sindel due to lower minor allele frequency or small effect size. As an alternative strategy, a supervised machine learning method can identify the otherwise masked functional sindels by predicting their regulatory potential directly. However, computational methods for annotating and predicting the regulatory sindels, especially in the non-coding regions, are underdeveloped. RESULTS By leveraging labeled nc-sindels identified by cis-expression quantitative trait loci analyses across 44 tissues in Genotype-Tissue Expression (GTEx), and a compilation of both generic functional annotations and large-scale epigenomic profiles, we develop TIssue-specific Variant Annotation for Non-coding indel (TIVAN-indel), which is a supervised computational framework for predicting non-coding regulatory sindels. As a result, we demonstrate that TIVAN-indel achieves the best prediction performance in both with-tissue prediction and cross-tissue prediction. As an independent evaluation, we train TIVAN-indel from the 'Whole Blood' tissue in GTEx and test the model using 15 immune cell types from an independent study named Database of Immune Cell Expression. Lastly, we perform an enrichment analysis for both true and predicted sindels in key regulatory regions such as chromatin interactions, open chromatin regions and histone modification sites, and find biologically meaningful enrichment patterns. AVAILABILITY AND IMPLEMENTATION https://github.com/lichen-lab/TIVAN-indel. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Aman Agarwal
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Fengdi Zhao
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Yuchao Jiang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Li Chen
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| |
Collapse
|
6
|
Rajabi F, Jabalameli N, Rezaei N. The Concept of Immunogenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:1-17. [DOI: 10.1007/978-3-030-92616-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
7
|
Cattel J, Minier M, Habchi-Hanriot N, Pol M, Faucon F, Gaude T, Gaborit P, Issaly J, Ferrero E, Chandre F, Pocquet N, David JP, Dusfour I. Impact of selection regime and introgression on deltamethrin resistance in the arbovirus vector Aedes aegypti - a comparative study between contrasted situations in New Caledonia and French Guiana. PEST MANAGEMENT SCIENCE 2021; 77:5589-5598. [PMID: 34398490 DOI: 10.1002/ps.6602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Pyrethroid insecticides such as deltamethrin have been massively used against Aedes aegypti leading to the spread of resistance alleles worldwide. In an insecticide resistance management context, we evaluated the temporal dynamics of deltamethrin resistance using two distinct populations carrying resistant alleles at different frequencies. Three different scenarios were followed: a continuous selection, a full release of selection, or a repeated introgression with susceptible individuals. The responses of each population to these selection regimes were measured across five generations by bioassays and by monitoring the frequency of knockdown resistance (kdr) mutations and the transcription levels and copy number variations of key detoxification enzymes. RESULTS Knockdown resistance mutations, overexpression and copy number variations of detoxification enzymes as a mechanism of metabolic resistance to deltamethrin was found and maintained under selection across generations. On comparison, the release of insecticide pressure for five generations did not affect resistance levels and resistance marker frequencies. However, introgressing susceptible alleles drastically reduced deltamethrin resistance in only three generations. CONCLUSION The present study confirmed that strategies consisting to stop deltamethrin spraying are likely to fail when the frequencies of resistant alleles are too high and the fitness cost associated to resistance is low. In dead-end situations like in French Guiana where alternative insecticides are not available, alternative control strategies may provide a high benefit for vector control, particularly if they favor the introgression of susceptible alleles in natural populations. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Julien Cattel
- Laboratoire d'Ecologie Alpine (LECA), UMR 5553 CNRS - Université Grenoble-Alpes, Grenoble, France
- Symbiosis Technologies for Insect Control (SymbioTIC), Plateforme de Recherche Cyroi, Sainte-Clotilde, La Réunion
| | - Marine Minier
- Institut Pasteur de Nouvelle-Calédonie (IPNC), Nouméa, Nouvelle-Calédonie
| | - Nausicaa Habchi-Hanriot
- Vectopôle Amazonien Emile Abonnenc, Institut Pasteur de la Guyane, Cayenne, French Guiana
- ARS La Réunion, Sainte-Clotilde, La Réunion
| | - Morgane Pol
- Institut Pasteur de Nouvelle-Calédonie (IPNC), Nouméa, Nouvelle-Calédonie
| | - Frederic Faucon
- Laboratoire d'Ecologie Alpine (LECA), UMR 5553 CNRS - Université Grenoble-Alpes, Grenoble, France
| | - Thierry Gaude
- Laboratoire d'Ecologie Alpine (LECA), UMR 5553 CNRS - Université Grenoble-Alpes, Grenoble, France
| | - Pascal Gaborit
- Vectopôle Amazonien Emile Abonnenc, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Jean Issaly
- Vectopôle Amazonien Emile Abonnenc, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Emma Ferrero
- Vectopôle Amazonien Emile Abonnenc, Institut Pasteur de la Guyane, Cayenne, French Guiana
- Ynsect, Damparis, France
| | - Fabrice Chandre
- MIVEGEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
| | - Nicolas Pocquet
- Institut Pasteur de Nouvelle-Calédonie (IPNC), Nouméa, Nouvelle-Calédonie
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA), UMR 5553 CNRS - Université Grenoble-Alpes, Grenoble, France
| | - Isabelle Dusfour
- MIVEGEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- Département de Santé Globale, Institut Pasteur, Paris, France
- MIVEGEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| |
Collapse
|
8
|
Chen J, Guo JT. Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes. Sci Rep 2021; 11:21178. [PMID: 34707120 PMCID: PMC8551294 DOI: 10.1038/s41598-021-00583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
Insertions and deletions (Indels) represent one of the major variation types in the human genome and have been implicated in diseases including cancer. To study the features of somatic indels in different cancer genomes, we investigated the indels from two large samples of cancer types: invasive breast carcinoma (BRCA) and lung adenocarcinoma (LUAD). Besides mapping somatic indels in both coding and untranslated regions (UTRs) from the cancer whole exome sequences, we investigated the overlap between these indels and transcription factor binding sites (TFBSs), the key elements for regulation of gene expression that have been found in both coding and non-coding sequences. Compared to the germline indels in healthy genomes, somatic indels contain more coding indels with higher than expected frame-shift (FS) indels in cancer genomes. LUAD has a higher ratio of deletions and higher coding and FS indel rates than BRCA. More importantly, these somatic indels in cancer genomes tend to locate in sequences with important functions, which can affect the core secondary structures of proteins and have a bigger overlap with predicted TFBSs in coding regions than the germline indels. The somatic CDS indels are also enriched in highly conserved nucleotides when compared with germline CDS indels.
Collapse
Affiliation(s)
- Jing Chen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| |
Collapse
|
9
|
Zoh MG, Bonneville JM, Tutagata J, Laporte F, Fodjo BK, Mouhamadou CS, Sadia CG, McBeath J, Schmitt F, Horstmann S, Reynaud S, David JP. Experimental evolution supports the potential of neonicotinoid-pyrethroid combination for managing insecticide resistance in malaria vectors. Sci Rep 2021; 11:19501. [PMID: 34593941 PMCID: PMC8484614 DOI: 10.1038/s41598-021-99061-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
The introduction of neonicotinoids for managing insecticide resistance in mosquitoes is of high interest as they interact with a biochemical target not previously used in public health. In this concern, Bayer developed a combination of the neonicotinoid clothianidin and the pyrethroid deltamethrin (brand name Fludora Fusion) as a new vector control tool. Although this combination proved to be efficient against pyrethroid-resistant mosquitoes, its ability to prevent the selection of pyrethroid and neonicotinoid resistance alleles was not investigated. In this context, the objective of this work was to study the dynamics and the molecular mechanisms of resistance of An. gambiae to the separated or combined components of this combination. A field-derived An. gambiae line carrying resistance alleles to multiple insecticides at low frequencies was used as a starting for 33 successive generations of controlled selection. Resistance levels to each insecticide and target site mutation frequencies were monitored throughout the selection process. Cross resistance to other public health insecticides were also investigated. RNA-seq was used to compare gene transcription variations and polymorphisms across all lines. This study confirmed the potential of this insecticide combination to impair the selection of resistance as compared to its two separated components. Deltamethrin selection led to the rapid enrichment of the kdr L1014F target-site mutation. Clothianidin selection led to the over-transcription of multiple cytochrome P450s including some showing high homology with those conferring neonicotinoid resistance in other insects. A strong selection signature associated with clothianidin selection was also observed on a P450 gene cluster previously associated with resistance. Within this cluster, the gene CYP6M1 showed the highest selection signature together with a transcription profile supporting a role in clothianidin resistance. Modelling the impact of point mutations selected by clothianidin on CYP6M1 protein structure showed that selection retained a protein variant with a modified active site potentially enhancing clothianidin metabolism. In the context of the recent deployment of neonicotinoids for mosquito control and their frequent usage in agriculture, the present study highlights the benefit of combining them with other insecticides for preventing the selection of resistance and sustaining vector control activities.
Collapse
Affiliation(s)
- Marius Gonse Zoh
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jean-Marc Bonneville
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jordan Tutagata
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Frederic Laporte
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Behi K Fodjo
- Centre Suisse de La Recherche Scientifique (CSRS), Abidjan, Côte d'Ivoire
| | | | - Christabelle Gba Sadia
- Centre Suisse de La Recherche Scientifique (CSRS), Abidjan, Côte d'Ivoire.,University of Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Justin McBeath
- Bayer CropScience Ltd, Cambridge Science Park, Cambridge, UK
| | | | | | - Stephane Reynaud
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France.
| |
Collapse
|
10
|
Cattel J, Haberkorn C, Laporte F, Gaude T, Cumer T, Renaud J, Sutherland IW, Hertz JC, Bonneville J, Arnaud V, Fustec B, Boyer S, Marcombe S, David J. A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquito Aedes aegypti: From genomic characterization to high-throughput field detection. Evol Appl 2021; 14:1009-1022. [PMID: 33897817 PMCID: PMC8061265 DOI: 10.1111/eva.13177] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 01/06/2023] Open
Abstract
By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterize a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100-Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-color multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.
Collapse
Affiliation(s)
- Julien Cattel
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
- Present address:
Symbiosis Technologies for Insect Control (SymbioTIC)Plateforme de Recherche CyroiSte ClotildeFrance
| | - Chloé Haberkorn
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Fréderic Laporte
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Thierry Gaude
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Tristan Cumer
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Julien Renaud
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Ian W. Sutherland
- United States Navy Entomology. Center of ExcellenceNAS JacksonvilleJacksonvilleFLUSA
| | | | - Jean‐Marc Bonneville
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Victor Arnaud
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Bénédicte Fustec
- Department of MicrobiologyKhon Kaen UniversityKhon KaenThailand
- Institut de Recherche pour le DéveloppementUMR IRD 224‐CNRS 5290‐Université MontpellierMontpellier Cedex 5France
| | - Sébastien Boyer
- Medical and Veterinary EntomologyInstitut Pasteur du CambodgePhnom PenhCambodia
| | - Sébastien Marcombe
- Medical Entomology and Vector‐Borne Disease LaboratoryInstitut Pasteur du LaosVientianeLaos
| | - Jean‐Philippe David
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| |
Collapse
|
11
|
Cystic Fibrosis: A Simple and Customized Strategy for Genetic Screening Able to Detect Over 90% of Identified Mutated Alleles in Brazilian Newborns. Mol Diagn Ther 2020; 24:315-325. [PMID: 32185651 DOI: 10.1007/s40291-020-00456-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION The incorporation of molecular genetic testing into cystic fibrosis (CF) screening programs increases the specificity of the diagnostic strategy and has the potential to decrease the rate of false- positive results. In this sense, our objective was to develop a genotyping assay that could detect 25 pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with high sensitivity and that could be incorporated into the routine of newborn screening, complementing the current existing protocol used in our public health institution. METHODS A mini-sequencing assay was standardized using single-base extension in a previously genotyped control sample. This strategy was validated in a Brazilian cohort of CF patients by Sanger sequencing. RESULTS The inclusion of the 25 variants in the current newborn screening program increased the identification rates of two alleles from 33 to 52.43% in CF patients. This new approach was able to detect a total of 37 variants, which represents 93.01% of all mutated alleles described in the last CF Brazilian Register. CONCLUSIONS Mini-sequencing for the simultaneous detection of 25 CFTR gene variants improves the screening of Brazilian newborns and decreases the number of inconclusive cases. This method uses minimal hands-on time and is suited for rapid screening, which reduces sample processing costs.
Collapse
|
12
|
Li D, Kim W, Wang L, Yoon KA, Park B, Park C, Kong SY, Hwang Y, Baek D, Lee ES, Won S. Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1635-1644. [PMID: 30004886 DOI: 10.1109/tcbb.2018.2854793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Insertions and deletions (INDELs) comprise a significant proportion of human genetic variation, and recent papers have revealed that many human diseases may be attributable to INDELs. With the development of next-generation sequencing (NGS) technology, many statistical/computational tools have been developed for calling INDELs. However, there are differences among those tools, and comparisons among them have been limited. In order to better understand these inter-tool differences, five popular and publicly available INDEL calling tools-GATK HaplotypeCaller, Platypus, VarScan2, Scalpel, and GotCloud-were evaluated using simulation data, 1000 Genomes Project data, and family-based sequencing data. The accuracy of INDEL calling by each tool was mainly evaluated by concordance rates. Family-based sequencing data, which consisted of 49 individuals from eight Korean families, were used to calculate Mendelian error rates. Our comparison results show that GATK HaplotypeCaller usually performs the best and that joint calling with Platypus can lead to additional improvements in accuracy. The result of this study provides important information regarding future directions for the variant detection and the algorithms development.
Collapse
|
13
|
Hasan MS, Wu X, Zhang L. Uncovering missed indels by leveraging unmapped reads. Sci Rep 2019; 9:11093. [PMID: 31366961 PMCID: PMC6668410 DOI: 10.1038/s41598-019-47405-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/12/2019] [Indexed: 02/08/2023] Open
Abstract
In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown great accuracy in mapping short reads to the reference genome, a significant number of short reads still remain unmapped and are often excluded from downstream analyses thereby causing nonnegligible information loss in the subsequent variant calling procedure. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the original procedure. Genesis-indel is applied to the unmapped reads of 30 breast cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel identifies 72,997 novel high-quality indels previously not found, among which 16,141 have not been annotated in the widely used mutation database. Statistical analysis of these indels shows significant enrichment of indels residing in oncogenes and tumour suppressor genes. Functional annotation further reveals that these indels are strongly correlated with pathways of cancer and can have high to moderate impact on protein functions. Additionally, some of the indels overlap with the genes that do not have any indel mutations called from the originally mapped reads but have been shown to contribute to the tumorigenesis in multiple carcinomas, further emphasizing the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies.
Collapse
Affiliation(s)
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| |
Collapse
|
14
|
Genetic Study on Small Insertions and Deletions in Psoriasis Reveals a Role in Complex Human Diseases. J Invest Dermatol 2019; 139:2302-2312.e14. [PMID: 31078570 DOI: 10.1016/j.jid.2019.03.1157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 11/20/2022]
Abstract
Genetic studies based on single-nucleotide polymorphisms have provided valuable insights into the genetic architecture of complex diseases. However, a large fraction of heritability for most of these diseases remains unexplained, and the impact of small insertions and deletions (InDels) has been neglected. We performed a comprehensive screen on the exome sequence data of 1,326 genes using the SOAP-PopIndel method for InDels in 32,043 Chinese Han individuals and identified 29 unreported InDels within 25 susceptibility genes associated with psoriasis. Specifically, we identified 12 common, 9 low-frequency, and 8 rare InDels that explained approximately 1.29% of the heritability of psoriasis. Further analyses identified KIAA0319, RELN, NCAPG, ABO, AADACL2, LMAN1, FLG, HERC5, CCDC66, LEKR1, AFF3, ABCG2, ANXA7, SYTL2,GIPR, METTL1, and FYCO1 as unreported genes for psoriasis. In addition, identified InDels were associated with the following reported genes: IFIH1, ERAP1, ERAP2, LNPEP, UBLCP1, and STAT3; unreported independent associations for exonic InDels were found within GJB2 and ZNF816A. Our study enriched the genetic basis and pathogenesis of psoriasis and highlighted the non-negligible impact of InDels on complex human diseases.
Collapse
|
15
|
Banerjee A, Levy Y, Mitra P. Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database. J Proteome Res 2019; 18:1402-1410. [PMID: 30735617 DOI: 10.1021/acs.jproteome.9b00048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in vitro experimentations. In the absence of any benchmark database documenting SPDs, we curate a data set containing SPDs that lead to both folded conformations and unfolded state. We differentiate these SPD instances with the help of simple structural and physicochemical features and eventually classify the foldability resulting out of SPDs using a Random Forest classifier and an Elliptic Envelope based outlier detector. Adhering to leave one out cross validation, the accuracy of the Random Forest classifier and the Elliptic Envelope is of 99.4% and 98.1%, respectively. The newly defined database and the delineation of SPD instances based on its resulting foldability provide a head start toward finding a solution to the given problem.
Collapse
Affiliation(s)
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 76100 , Israel
| | | |
Collapse
|
16
|
Lu B, Li L, Schneider M, Hodges CA, Cotton CU, Burgess JD, Kelley TJ. Electrochemical measurement of membrane cholesterol correlates with CFTR function and is HDAC6-dependent. J Cyst Fibros 2018; 18:175-181. [PMID: 29941319 DOI: 10.1016/j.jcf.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Previous studies have demonstrated that CF epithelial cells exhibit increased cholesterol content at the plasma membrane compared to wild type controls as measured by electrochemical methods. Microtubule dysregulation that impacts intracellular transport has also been identified in CF cells and is reversible with histone deacetylase 6 (HDAC6) inhibition, a regulator of tubulin acetylation. The hypothesis of this study is that increased membrane cholesterol content in CF cells is dependent on HDAC6 regulation. METHODS Electrochemical measurement of membrane cholesterol in mouse trachea and in primary human CF bronchial epithelial cells is used to monitor CFTR correction and manipulation of cholesterol processing by HDAC6 inhibition. RESULTS Data demonstrate that induction of Cftr expression in an inducible CF mouse model restores tubulin acetylation levels and normalizes membrane cholesterol content. To test the relationship between tubulin acetylation, membrane cholesterol levels were measured in a CF mouse model depleted of Hdac6 expression (CF/HDA). CF/HDA mouse trachea have WT membrane cholesterol levels while CF mice have approximately two-fold increase in membrane cholesterol compared to WT consistent with previous studies. Pharmacological inhibition of HDAC6 in primary human CF bronchial epithelial cells also reduces membrane cholesterol levels. CONCLUSIONS This study demonstrates that elevated membrane cholesterol in CF epithelium is regulated by HDAC6 function and that the electrochemical measure of membrane cholesterol correlates with both genetic and pharmacological CFTR correction.
Collapse
Affiliation(s)
- Binyu Lu
- Department of Chemistry, Case Western Reserve University, United States
| | - Li Li
- Department of Chemistry, Case Western Reserve University, United States
| | - Molly Schneider
- Department of Pediatrics, Case Western Reserve University, United States
| | - Craig A Hodges
- Department of Pediatrics, Case Western Reserve University, United States
| | - Calvin U Cotton
- Department of Pediatrics, Case Western Reserve University, United States
| | - James D Burgess
- Department of Medical, Laboratory, Imaging and Radiologic Sciences, Augusta University, United States
| | - Thomas J Kelley
- Department of Chemistry, Case Western Reserve University, United States; Department of Pediatrics, Case Western Reserve University, United States.
| |
Collapse
|
17
|
Lin M, Whitmire S, Chen J, Farrel A, Shi X, Guo JT. Effects of short indels on protein structure and function in human genomes. Sci Rep 2017; 7:9313. [PMID: 28839204 PMCID: PMC5570956 DOI: 10.1038/s41598-017-09287-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/24/2017] [Indexed: 01/20/2023] Open
Abstract
Insertions and deletions (indels) represent the second most common type of genetic variations in human genomes. Indels can be deleterious and contribute to disease susceptibility as recent genome sequencing projects revealed a large number of indels in various cancer types. In this study, we investigated the possible effects of small coding indels on protein structure and function, and the baseline characteristics of indels in 2504 individuals of 26 populations from the 1000 Genomes Project. We found that each population has a distinct pattern in genes with small indels. Frameshift (FS) indels are enriched in olfactory receptor activity while non-frameshift (NFS) indels are enriched in transcription-related proteins. Structural analysis of NFS indels revealed that they predominantly adopt coil or disordered conformations, especially in proteins with transcription-related NFS indels. These results suggest that the annotated coding indels from the 1000 Genomes Project, while contributing to genetic variations and phenotypic diversity, generally do not affect the core protein structures and have no deleterious effect on essential biological processes. In addition, we found that a number of reference genome annotations might need to be updated due to the high prevalence of annotated homozygous indels in the general population.
Collapse
Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Sarah Whitmire
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jing Chen
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Alvin Farrel
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Xinghua Shi
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| |
Collapse
|
18
|
Jiang J, Gao Y, Hou Y, Li W, Zhang S, Zhang Q, Sun D. Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle. PLoS One 2016; 11:e0168946. [PMID: 28030618 PMCID: PMC5193355 DOI: 10.1371/journal.pone.0168946] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/08/2016] [Indexed: 11/18/2022] Open
Abstract
The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1–49 base pairs (bp)] were obtained. Among them, 3,625 indels that were polymorphic between the high and low groups of bulls were revealed and subjected to further analysis. The vast majority (76.67%) of these indels were novel. Follow-up validation assays confirmed that most (70%) of the randomly selected indels represented true variations. The indels that were polymorphic between the two groups were annotated based on the cattle genome sequence assembly (UMD3.1.69); as a result, nearly 1,137 of them were found to be located within 767 annotated genes, only 5 (0.138%) of which were located in exons. Then, by integrated analysis of the 767 genes with known quantitative trait loci (QTL); significant single-nucleotide polymorphisms (SNPs) previously identified by genome-wide association studies (GWASs) to be associated with bovine milk protein and fat traits; and the well-known pathways involved in protein, fat synthesis, and metabolism, we identified a total of 11 promising candidate genes potentially affecting milk composition traits. These were FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH. Our findings provide a basis for further study and reveal key genes for milk composition traits in dairy cattle.
Collapse
Affiliation(s)
- Jianping Jiang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yahui Gao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yali Hou
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
- * E-mail:
| |
Collapse
|
19
|
Abstract
Leptin is an adipose tissue hormone that functions as an afferent signal in a negative feedback loop that maintains homeostatic control of adipose tissue mass. This endocrine system thus serves a critical evolutionary function by protecting individuals from the risks associated with being too thin (starvation) or too obese (predation and temperature dysregulation). Mutations in leptin or its receptor cause massive obesity in mice and humans, and leptin can effectively treat obesity in leptin-deficient patients. Leptin acts on neurons in the hypothalamus and elsewhere to elicit its effects, and mutations that affect the function of this neural circuit cause Mendelian forms of obesity. Leptin levels fall during starvation and elicit adaptive responses in many other physiologic systems, the net effect of which is to reduce energy expenditure. These effects include cessation of menstruation, insulin resistance, alterations of immune function, and neuroendocrine dysfunction, among others. Some or all of these effects are also seen in patients with constitutively low leptin levels, such as occur in lipodystrophy. Leptin is an approved treatment for generalized lipodystrophy, a condition associated with severe metabolic disease, and has also shown potential for the treatment of other types of diabetes. In addition, leptin restores reproductive capacity and increases bone mineral density in patients with hypothalamic amenorrhea, an infertility syndrome in females. Most obese patients have high endogenous levels of leptin, in some instances as a result of mutations in the neural circuit on which leptin acts, though in most cases, the pathogenesis of leptin resistance is not known. Obese patients with leptin resistance show a variable response to exogenous leptin but may respond to a combination of leptin plus amylin. Overall, the identification of leptin has provided a framework for studying the pathogenesis of obesity in the general population, clarified the nature of the biologic response to starvation, and helped to advance our understanding of the neural mechanisms that control feeding.
Collapse
|
20
|
Hasan MS, Zhang L. SPAI: an interactive platform for indel analysis. BMC Genomics 2016; 17 Suppl 5:496. [PMID: 27585593 PMCID: PMC5009558 DOI: 10.1186/s12864-016-2824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Insertions and Deletions (Indels) are the most common form of structural variation in human genome. Indels not only contribute to genetic diversity but also cause diseases. Therefore assessing indels in human genome has become an interesting topic to the research community. This increasing interest on indel calling research has resulted into the development of a good number of indel calling tools. However, all of these tools are command line based and require expertise from Computer Science (CS) to execute them which makes it challenging for researchers from non-CS background. METHODS In this paper, we describe an interactive platform named SPAI which stands for Single Platform for Analyzing Indels. RESULTS Being a Graphical User Interface (GUI) tool, SPAI facilitates users to run several popular indel calling tools and perform several analyses on the indel calling results without knowing any command line programming. CONCLUSIONS SPAI is written in Java and tested in Linux operating system.
Collapse
Affiliation(s)
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
| |
Collapse
|
21
|
Porto BN, Stein RT. Neutrophil Extracellular Traps in Pulmonary Diseases: Too Much of a Good Thing? Front Immunol 2016; 7:311. [PMID: 27574522 PMCID: PMC4983612 DOI: 10.3389/fimmu.2016.00311] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
Neutrophil extracellular traps (NETs) arise from the release of granular and nuclear contents of neutrophils in the extracellular space in response to different classes of microorganisms, soluble factors, and host molecules. NETs are composed by decondensed chromatin fibers coated with antimicrobial granular and cytoplasmic proteins, such as myeloperoxidase, neutrophil elastase (NE), and α-defensins. Besides being expressed on NET fibers, NE and MPO also regulate NET formation. Furthermore, histone deimination by peptidylarginine deiminase 4 (PAD4) is a central step to NET formation. NET formation has been widely demonstrated to be an effective mechanism to fight against invading microorganisms, as deficiency in NET release or dismantling NET backbone by bacterial DNases renders the host susceptible to infections. Therefore, the primary role of NETs is to prevent microbial dissemination, avoiding overwhelming infections. However, an excess of NET formation has a dark side. The pathogenic role of NETs has been described for many human diseases, infectious and non-infectious. The detrimental effect of excessive NET release is particularly important to lung diseases, because NETs can expand more easily in the pulmonary alveoli, causing lung injury. Moreover, NETs and its associated molecules are able to directly induce epithelial and endothelial cell death. In this regard, massive NET formation has been reported in several pulmonary diseases, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, respiratory syncytial virus bronchiolitis, influenza, bacterial pneumonia, and tuberculosis, among others. Thus, NET formation must be tightly regulated in order to avoid NET-mediated tissue damage. Recent development of therapies targeting NETs in pulmonary diseases includes DNA disintegration with recombinant human DNase, neutralization of NET proteins, with anti-histone antibodies and protease inhibitors. In this review, we summarize the recent knowledge on the pathophysiological role of NETs in pulmonary diseases as well as some experimental and clinical approaches to modulate their detrimental effects.
Collapse
Affiliation(s)
- Bárbara Nery Porto
- Laboratory of Clinical and Experimental Immunology, Infant Center, Institute of Biomedical Research, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Renato Tetelbom Stein
- Laboratory of Pediatric Respirology, Infant Center, Institute of Biomedical Research, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
22
|
Wang Z, Chen Q, Liao R, Zhang Z, Zhang X, Liu X, Zhu M, Zhang W, Xue M, Yang H, Zheng Y, Wang Q, Pan Y. Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing. Anim Genet 2016; 48:38-47. [PMID: 27461929 PMCID: PMC5248613 DOI: 10.1111/age.12465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 12/24/2022]
Abstract
The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large‐effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed‐specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.
Collapse
Affiliation(s)
- Z Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Q Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - R Liao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - X Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - X Liu
- Jiangshu Station of Animal Husbandry, Nanjing, 210036, China
| | - M Zhu
- Jiangshu Station of Animal Husbandry, Nanjing, 210036, China
| | - W Zhang
- Jiangshu Station of Animal Husbandry, Nanjing, 210036, China
| | - M Xue
- National Station of Animal Husbandry, Beijing, 100125, China
| | - H Yang
- National Station of Animal Husbandry, Beijing, 100125, China
| | - Y Zheng
- National Station of Animal Husbandry, Beijing, 100125, China
| | - Q Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Y Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| |
Collapse
|
23
|
Wajnberg G, Passetti F. Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery. Expert Opin Drug Discov 2016; 11:257-68. [PMID: 26787005 DOI: 10.1517/17460441.2016.1143813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION A cancer cell is a mosaic of genomic and epigenomic alterations. Distinct cancer molecular signatures can be observed depending on tumor type or patient genetic background. One type of genomic alteration is the insertion and/or deletion (INDEL) of nucleotides in the DNA sequence, which may vary in length, and may change the encoded protein or modify protein domains. INDELs are associated to a large number of diseases and their detection is done based on low-throughput techniques. However, high-throughput sequencing has also started to be used for detection of novel disease-causing INDELs. This search may identify novel drug targets. AREAS COVERED This review presents examples of using high-throughput sequencing (DNA-Seq and RNA-Seq) to investigate the incidence of INDELs in coding regions of human genes. Some of these examples successfully utilized RNA-Seq to identify INDELs associated to diseases. In addition, other studies have described small INDELs related to chemo-resistance or poor outcome of patients, while structural variants were associated with a better clinical outcome. EXPERT OPINION On average, there is twice as much RNA-Seq data available at the most used repositories for such data compared to DNA-Seq. Therefore, using RNA-Seq data is a promising strategy for studying cancer samples with unknown mechanisms of drug resistance, aiming at the discovery of proteins with potential as novel drug targets.
Collapse
Affiliation(s)
- Gabriel Wajnberg
- a Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , RJ , Brazil
| | - Fabio Passetti
- a Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , RJ , Brazil
| |
Collapse
|
24
|
Hasan MS, Wu X, Zhang L. Performance evaluation of indel calling tools using real short-read data. Hum Genomics 2015; 9:20. [PMID: 26286629 PMCID: PMC4545535 DOI: 10.1186/s40246-015-0042-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/20/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, many indel calling tools have been developed; however, evaluation and comparison of these tools using large-scale real data are still scant. Here we evaluated seven popular and publicly available indel calling tools, GATK Unified Genotyper, VarScan, Pindel, SAMtools, Dindel, GTAK HaplotypeCaller, and Platypus, using 78 human genome low-coverage data from the 1000 Genomes project. RESULTS Comparing indels called by these tools with a known set of indels, we found that Platypus outperforms other tools. In addition, a high percentage of known indels still remain undetected and the number of common indels called by all seven tools is very low. CONCLUSION All these findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results.
Collapse
Affiliation(s)
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA.
| |
Collapse
|
25
|
Liu J, Qu J, Yang C, Tang D, Li J, Lan H, Rong T. Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data. BMC Genomics 2015; 16:601. [PMID: 26269146 PMCID: PMC4535256 DOI: 10.1186/s12864-015-1797-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 07/24/2015] [Indexed: 12/11/2022] Open
Abstract
Background Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species. Results A total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39 % of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90 %. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54. Conclusions The maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1797-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jian Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China. .,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jingtao Qu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Cong Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Dengguo Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jingwei Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China. .,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China. .,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
26
|
Faucon F, Dusfour I, Gaude T, Navratil V, Boyer F, Chandre F, Sirisopa P, Thanispong K, Juntarajumnong W, Poupardin R, Chareonviriyaphap T, Girod R, Corbel V, Reynaud S, David JP. Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing. Genome Res 2015. [PMID: 26206155 PMCID: PMC4561493 DOI: 10.1101/gr.189225.115] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The capacity of mosquitoes to resist insecticides threatens the control of diseases such as dengue and malaria. Until alternative control tools are implemented, characterizing resistance mechanisms is crucial for managing resistance in natural populations. Insecticide biodegradation by detoxification enzymes is a common resistance mechanism; however, the genomic changes underlying this mechanism have rarely been identified, precluding individual resistance genotyping. In particular, the role of copy number variations (CNVs) and polymorphisms of detoxification enzymes have never been investigated at the genome level, although they can represent robust markers of metabolic resistance. In this context, we combined target enrichment with high-throughput sequencing for conducting the first comprehensive screening of gene amplifications and polymorphisms associated with insecticide resistance in mosquitoes. More than 760 candidate genes were captured and deep sequenced in several populations of the dengue mosquito Ae. aegypti displaying distinct genetic backgrounds and contrasted resistance levels to the insecticide deltamethrin. CNV analysis identified 41 gene amplifications associated with resistance, most affecting cytochrome P450s overtranscribed in resistant populations. Polymorphism analysis detected more than 30,000 variants and strong selection footprints in specific genomic regions. Combining Bayesian and allele frequency filtering approaches identified 55 nonsynonymous variants strongly associated with resistance. Both CNVs and polymorphisms were conserved within regions but differed across continents, confirming that genomic changes underlying metabolic resistance to insecticides are not universal. By identifying novel DNA markers of insecticide resistance, this study opens the way for tracking down metabolic changes developed by mosquitoes to resist insecticides within and among populations.
Collapse
Affiliation(s)
- Frederic Faucon
- Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France
| | - Isabelle Dusfour
- Unité d'Entomologie Médicale, Institut Pasteur de la Guyane, 97306 Cayenne Cedex, France
| | - Thierry Gaude
- Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France
| | - Vincent Navratil
- Pôle Rhône Alpes de Bioinformatique, Université Lyon 1, 69100 Villeurbanne, France
| | - Frederic Boyer
- Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France
| | - Fabrice Chandre
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle (IRD 224-CNRS 5290 UM1-UM2), 34394 Montpellier Cedex 5, France
| | - Patcharawan Sirisopa
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand)
| | - Kanutcharee Thanispong
- Bureau of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Mueang, Nonthaburi 11000, Thailand
| | - Waraporn Juntarajumnong
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand)
| | - Rodolphe Poupardin
- Vector Biology Group, Liverpool School of Tropical Medicine, L35QA Liverpool, United Kingdom
| | - Theeraphap Chareonviriyaphap
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand)
| | - Romain Girod
- Unité d'Entomologie Médicale, Institut Pasteur de la Guyane, 97306 Cayenne Cedex, France
| | - Vincent Corbel
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle (IRD 224-CNRS 5290 UM1-UM2), 34394 Montpellier Cedex 5, France; Department of Entomology, Faculty of Agriculture, Kasetsart University, Lat Yao Chatuchak Bangkok 10900, Thailand; Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand)
| | - Stephane Reynaud
- Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA), CNRS, UMR 5553, 38041 Grenoble Cedex 9, France; Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France; Environmental and Systems Biology (BEeSy), Université Grenoble-Alpes, 38041 Grenoble Cedex 9, France
| |
Collapse
|
27
|
Regan JF, Kamitaki N, Legler T, Cooper S, Klitgord N, Karlin-Neumann G, Wong C, Hodges S, Koehler R, Tzonev S, McCarroll SA. A rapid molecular approach for chromosomal phasing. PLoS One 2015; 10:e0118270. [PMID: 25739099 PMCID: PMC4349636 DOI: 10.1371/journal.pone.0118270] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).
Collapse
Affiliation(s)
- John F. Regan
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
- * E-mail: (JFR); (SAM)
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Cambridge, Massachusetts, United States of America
| | - Tina Legler
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Samantha Cooper
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Niels Klitgord
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - George Karlin-Neumann
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Catherine Wong
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shawn Hodges
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Ryan Koehler
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Svilen Tzonev
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Cambridge, Massachusetts, United States of America
- * E-mail: (JFR); (SAM)
| |
Collapse
|
28
|
Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Sci Rep 2015; 5:8333. [PMID: 25660536 PMCID: PMC4321175 DOI: 10.1038/srep08333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms.
Collapse
Affiliation(s)
- Wei Chen
- 1] Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China 063000 [2] Department of Computer Science, Virginia Tech, Blacksburg VA 24060
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg VA 24060
| |
Collapse
|
29
|
Wu Z, Tembrock LR, Ge S. Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes. PLoS One 2015; 10:e0118019. [PMID: 25658309 PMCID: PMC4320078 DOI: 10.1371/journal.pone.0118019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/07/2015] [Indexed: 01/01/2023] Open
Abstract
DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.
Collapse
Affiliation(s)
- Zhiqiang Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
30
|
Analysis of indel variations in the human disease-associated genes CDKN2AIP, WDR66, USP20 and OR7C2 in a Korean population. J Genet 2014. [DOI: 10.1007/s12041-012-0129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
31
|
Nkya TE, Poupardin R, Laporte F, Akhouayri I, Mosha F, Magesa S, Kisinza W, David JP. Impact of agriculture on the selection of insecticide resistance in the malaria vector Anopheles gambiae: a multigenerational study in controlled conditions. Parasit Vectors 2014; 7:480. [PMID: 25318645 PMCID: PMC4201709 DOI: 10.1186/s13071-014-0480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/06/2014] [Indexed: 12/30/2022] Open
Abstract
Background Resistance of mosquitoes to insecticides is mainly attributed to their adaptation to vector control interventions. Although pesticides used in agriculture have been frequently mentioned as an additional force driving the selection of resistance, only a few studies were dedicated to validate this hypothesis and characterise the underlying mechanisms. While insecticide resistance is rising dramatically in Africa, deciphering how agriculture affects resistance is crucial for improving resistance management strategies. In this context, the multigenerational effect of agricultural pollutants on the selection of insecticide resistance was examined in Anopheles gambiae. Methods An urban Tanzanian An. gambiae population displaying a low resistance level was used as a parental strain for a selection experiment across 20 generations. At each generation larvae were selected with a mixture containing pesticides and herbicides classically used in agriculture in Africa. The resistance levels of adults to deltamethrin, DDT and bendiocarb were compared between the selected and non-selected strains across the selection process together with the frequency of kdr mutations. A microarray approach was used for pinpointing transcription level variations selected by the agricultural pesticide mixture at the adult stage. Results A gradual increase of adult resistance to all insecticides was observed across the selection process. The frequency of the L1014S kdr mutation rose from 1.6% to 12.5% after 20 generations of selection. Microarray analysis identified 90 transcripts over-transcribed in the selected strain as compared to the parental and the non-selected strains. Genes encoding cuticle proteins, detoxification enzymes, proteins linked to neurotransmitter activity and transcription regulators were mainly affected. RT-qPCR transcription profiling of candidate genes across multiple generations supported their link with insecticide resistance. Conclusions This study confirms the potency of agriculture in selecting for insecticide resistance in malaria vectors. We demonstrated that the recurrent exposure of larvae to agricultural pollutants can select for resistance mechanisms to vector control insecticides at the adult stage. Our data suggest that in addition to selected target-site resistance mutations, agricultural pollutants may also favor cuticle, metabolic and synaptic transmission-based resistance mechanisms. These results emphasize the need for integrated resistance management strategies taking into account agriculture activities. Electronic supplementary material The online version of this article (doi:10.1186/s13071-014-0480-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Theresia Estomih Nkya
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, BP 53, 38041, Grenoble cedex 09, France. .,Université Grenoble-Alpes, Grenoble, France. .,National Institute of Medical Research of Tanzania. Amani Medical Research Centre, P. O. Box 81, Muheza, Tanga, Tanzania.
| | - Rodolphe Poupardin
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke place, L35QA, Liverpool, UK.
| | - Frederic Laporte
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, BP 53, 38041, Grenoble cedex 09, France. .,Université Grenoble-Alpes, Grenoble, France.
| | - Idir Akhouayri
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, BP 53, 38041, Grenoble cedex 09, France. .,Université Grenoble-Alpes, Grenoble, France.
| | - Franklin Mosha
- KCM College of Tumaini University, P. O. Box. 2240, Moshi, Tanzania.
| | - Stephen Magesa
- National Institute of Medical Research of Tanzania. Amani Medical Research Centre, P. O. Box 81, Muheza, Tanga, Tanzania. .,RTI International-Tanzania, P.O.Box 369, Dar es Salaam, Tanzania.
| | - William Kisinza
- National Institute of Medical Research of Tanzania. Amani Medical Research Centre, P. O. Box 81, Muheza, Tanga, Tanzania.
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, BP 53, 38041, Grenoble cedex 09, France. .,Université Grenoble-Alpes, Grenoble, France.
| |
Collapse
|
32
|
Yan Y, Yi G, Sun C, Qu L, Yang N. Genome-wide characterization of insertion and deletion variation in chicken using next generation sequencing. PLoS One 2014; 9:e104652. [PMID: 25133774 PMCID: PMC4136736 DOI: 10.1371/journal.pone.0104652] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/10/2014] [Indexed: 12/30/2022] Open
Abstract
Insertion and deletion (INDEL) is one of the main events contributing to genetic and phenotypic diversity, which receives less attention than SNP and large structural variation. To gain a better knowledge of INDEL variation in chicken genome, we applied next generation sequencing on 12 diverse chicken breeds at an average effective depth of 8.6. Over 1.3 million non-redundant short INDELs (1-49 bp) were obtained, the vast majority (92.48%) of which were novel. Follow-up validation assays confirmed that most (88.00%) of the randomly selected INDELs represent true variations. The majority (95.76%) of INDELs were less than 10 bp. Both the detected number and affected bases were larger for deletions than insertions. In total, INDELs covered 3.8 Mbp, corresponding to 0.36% of the chicken genome. The average genomic INDEL density was estimated as 0.49 per kb. INDELs were ubiquitous and distributed in a non-uniform fashion across chromosomes, with lower INDEL density in micro-chromosomes than in others, and some functional regions like exons and UTRs were prone to less INDELs than introns and intergenic regions. Nearly 620,253 INDELs fell in genic regions, 1,765 (0.28%) of which located in exons, spanning 1,358 (7.56%) unique Ensembl genes. Many of them are associated with economically important traits and some are the homologues of human disease-related genes. We demonstrate that sequencing multiple individuals at a medium depth offers a promising way for reliable identification of INDELs. The coding INDELs are valuable candidates for further elucidation of the association between genotypes and phenotypes. The chicken INDELs revealed by our study can be useful for future studies, including development of INDEL markers, construction of high density linkage map, INDEL arrays design, and hopefully, molecular breeding programs in chicken.
Collapse
Affiliation(s)
- Yiyuan Yan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guoqiang Yi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
33
|
Fernandez L, Le Cunff L, Tello J, Lacombe T, Boursiquot JM, Fournier-Level A, Bravo G, Lalet S, Torregrosa L, This P, Martinez-Zapater JM. Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera). BMC PLANT BIOLOGY 2014; 14:209. [PMID: 25091083 PMCID: PMC4243098 DOI: 10.1186/s12870-014-0209-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/23/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Interaction between TERMINAL FLOWER 1 (TFL1) and LEAFY (LFY) seem to determine the inflorescence architecture in Arabidopsis. In a parallel way, overexpression of VvTFL1A, a grapevine TFL1 homolog, causes delayed flowering and production of a ramose cluster in the reiterated reproductive meristem (RRM) somatic variant of cultivar Carignan. To analyze the possible contribution of this gene to cluster phenotypic variation in a diversity panel of cultivated grapevine (Vitis vinifera L. subsp. vinifera) its nucleotide diversity was characterized and association analyses among detected sequence polymorphisms and phenology and cluster traits was carried out. RESULTS A total of 3.6 kb of the VvTFL1A gene, including its promoter, was sequenced in a core collection of 140 individuals designed to maximize phenotypic variation at agronomical relevant traits. Nucleotide variation for VvTFL1A within this collection was higher in the promoter and intron sequences than in the exon regions; where few polymorphisms were located in agreement with a high conservation of coding sequence. Characterization of the VvTFL1A haplotype network identified three major haplogroups, consistent with the geographic origins and the use of the cultivars that could correspond to three major ancestral alleles or evolutionary branches, based on the existence of mutations in linkage disequilibrium. Genetic association studies with cluster traits revealed the presence of major INDEL polymorphisms, explaining 16%, 13% and 25% of flowering time, cluster width and berry weight, respectively, and also structuring the three haplogroups. CONCLUSIONS At least three major VvTFL1A haplogroups are present in cultivated grapevines, which are defined by the presence of three main polymorphism LD blocks and associated to characteristic phenotypic values for flowering time, cluster width and berry size. Phenotypic differences between haplogroups are consistent with differences observed between Eastern and Western grapevine cultivars and could result from the use of different genetic pools in the domestication process as well as different selection pressures on the development of table and wine cultivars, respectively. Altogether, these results are coherent with previous classifications of grapevine phenotypic diversity mainly based on cluster and berry morphotypes as well as with recent results on the structure of genetic diversity in cultivated grapevine.
Collapse
Affiliation(s)
- Lucie Fernandez
- Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La Rioja,
Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño 26006, Spain
- current address: INRA, UMR Biologie du Fruit et Pathologie, B.P. 81,
Villenave-d’Ornon 33883, Cedex, France
| | - Loïc Le Cunff
- UMT Geno-Vigne® (IFV- INRA-SupAgro), 2 Place P. Viala 34060, Montpellier,
Cedex 1, France
| | - Javier Tello
- Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La Rioja,
Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño 26006, Spain
| | - Thierry Lacombe
- INRA-SupAgro, UMR AGAP, équipe Diversité et Adaptation de la Vigne, 2
Place P. Viala, Montpellier 34060, Cedex 1, France
- INRA, Unité Expérimentale du Domaine de Vassal, Route de Sète,
Marseillan-plage 34340, France
| | - Jean Michel Boursiquot
- INRA-SupAgro, UMR AGAP, équipe Diversité et Adaptation de la Vigne, 2
Place P. Viala, Montpellier 34060, Cedex 1, France
| | - Alexandre Fournier-Level
- Bio21 Institute, Department of Genetics, University of Melbourne, 40 Flemington
road, Melbourne 3010, Australia
| | - Gema Bravo
- CNB-CSIC, Dpto. de Genética Molecular de Plantas, Darwin 3, Madrid 28049,
Spain
| | - Sandrine Lalet
- INRA, Unité Expérimentale du Domaine de Vassal, Route de Sète,
Marseillan-plage 34340, France
| | - Laurent Torregrosa
- INRA-SupAgro, UMR AGAP, équipe Diversité et Adaptation de la Vigne, 2
Place P. Viala, Montpellier 34060, Cedex 1, France
| | - Patrice This
- INRA-SupAgro, UMR AGAP, équipe Diversité et Adaptation de la Vigne, 2
Place P. Viala, Montpellier 34060, Cedex 1, France
| | - José Miguel Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La Rioja,
Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño 26006, Spain
- CNB-CSIC, Dpto. de Genética Molecular de Plantas, Darwin 3, Madrid 28049,
Spain
| |
Collapse
|
34
|
Yang J, Wang Y, Shen H, Yang W. In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome. DNA Res 2014; 21:429-38. [PMID: 24618211 PMCID: PMC4131836 DOI: 10.1093/dnares/dsu008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/04/2014] [Indexed: 11/14/2022] Open
Abstract
Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion-deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.
Collapse
Affiliation(s)
- Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Yuanyuan Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Wencai Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| |
Collapse
|
35
|
Yoo DG, Floyd M, Winn M, Moskowitz SM, Rada B. NET formation induced by Pseudomonas aeruginosa cystic fibrosis isolates measured as release of myeloperoxidase-DNA and neutrophil elastase-DNA complexes. Immunol Lett 2014; 160:186-94. [PMID: 24670966 DOI: 10.1016/j.imlet.2014.03.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/28/2014] [Accepted: 03/12/2014] [Indexed: 01/19/2023]
Abstract
Cystic fibrosis (CF) airway disease is characterized by Pseudomonas aeruginosa infection and recruitment of neutrophil granulocytes. Neutrophil granule components (myeloperoxidase (MPO), human neutrophil elastase (HNE)), extracellular DNA and P. aeruginosa can all be found in the CF respiratory tract and have all been associated with worsening CF lung function. Pseudomonas-induced formation of neutrophil extracellular traps (NETs) offers a likely mechanism for release of MPO, HNE and DNA from neutrophils. NETs are composed of a DNA backbone decorated with granule proteins like MPO and HNE. Here we sought to examine whether CF clinical isolates of Pseudomonas are capable of inducing NET release from human neutrophil granulocytes. We used two methods to quantify NETs. We modified a previously employed ELISA that detects MPO-DNA complexes and established a new HNE-DNA ELISA. We show that these methods reliably quantify MPO-DNA and HNE-DNA complexes, measures of NET formation. We have found that CF isolates of P. aeruginosa stimulate robust respiratory burst and NET release in human neutrophils. By comparing paired "early" and "late" bacterial isolates obtained from the same CF patient we have found that early isolates induced significantly more NET release than late isolates. Our data support that Pseudomonas-induced NET release represents an important mechanism for release of neutrophil-derived CF inflammatory mediators, and confirm that decreased induction of NET formation is required for long-term adaptation of P. aeruginosa to CF airways.
Collapse
Affiliation(s)
- Dae-goon Yoo
- University of Georgia, College of Veterinary Medicine, Department of Infectious Diseases, 501 DW Brooks Drive, Athens, GA 30602, USA
| | - Madison Floyd
- University of Georgia, College of Veterinary Medicine, Department of Infectious Diseases, 501 DW Brooks Drive, Athens, GA 30602, USA
| | - Matthew Winn
- University of Georgia, College of Veterinary Medicine, Department of Infectious Diseases, 501 DW Brooks Drive, Athens, GA 30602, USA
| | - Samuel M Moskowitz
- Massachusetts General Hospital, Department of Pediatrics, 175 Cambridge Street, Boston, MA 02114, USA; Harvard Medical School, Department of Pediatrics, 25 Shattuck Street, Boston, MA 02115 USA
| | - Balázs Rada
- University of Georgia, College of Veterinary Medicine, Department of Infectious Diseases, 501 DW Brooks Drive, Athens, GA 30602, USA.
| |
Collapse
|
36
|
Nkya TE, Akhouayri I, Poupardin R, Batengana B, Mosha F, Magesa S, Kisinza W, David JP. Insecticide resistance mechanisms associated with different environments in the malaria vector Anopheles gambiae: a case study in Tanzania. Malar J 2014; 13:28. [PMID: 24460952 PMCID: PMC3913622 DOI: 10.1186/1475-2875-13-28] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/21/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Resistance of mosquitoes to insecticides is a growing concern in Africa. Since only a few insecticides are used for public health and limited development of new molecules is expected in the next decade, maintaining the efficacy of control programmes mostly relies on resistance management strategies. Developing such strategies requires a deep understanding of factors influencing resistance together with characterizing the mechanisms involved. Among factors likely to influence insecticide resistance in mosquitoes, agriculture and urbanization have been implicated but rarely studied in detail. The present study aimed at comparing insecticide resistance levels and associated mechanisms across multiple Anopheles gambiae sensu lato populations from different environments. METHODS Nine populations were sampled in three areas of Tanzania showing contrasting agriculture activity, urbanization and usage of insecticides for vector control. Insecticide resistance levels were measured in larvae and adults through bioassays with deltamethrin, DDT and bendiocarb. The distribution of An. gambiae sub-species and pyrethroid target-site mutations (kdr) were investigated using molecular assays. A microarray approach was used for identifying transcription level variations associated to different environments and insecticide resistance. RESULTS Elevated resistance levels to deltamethrin and DDT were identified in agriculture and urban areas as compared to the susceptible strain Kisumu. A significant correlation was found between adult deltamethrin resistance and agriculture activity. The subspecies Anopheles arabiensis was predominant with only few An. gambiae sensu stricto identified in the urban area of Dar es Salaam. The L1014S kdr mutation was detected at elevated frequency in An gambiae s.s. in the urban area but remains sporadic in An. arabiensis specimens. Microarrays identified 416 transcripts differentially expressed in any area versus the susceptible reference strain and supported the impact of agriculture on resistance mechanisms with multiple genes encoding pesticide targets, detoxification enzymes and proteins linked to neurotransmitter activity affected. In contrast, resistance mechanisms found in the urban area appeared more specific and more related to the use of insecticides for vector control. CONCLUSIONS Overall, this study confirmed the role of the environment in shaping insecticide resistance in mosquitoes with a major impact of agriculture activities. Results are discussed in relation to resistance mechanisms and the optimization of resistance management strategies.
Collapse
Affiliation(s)
- Theresia E Nkya
- Laboratoire d'Ecologie Alpine, UMR CNRS-Université de Grenoble 5553, BP 53, 38041, Grenoble cedex 09, France
- National Institute of Medical Research of Tanzania, Amani Medical Research Centre, P. O. Box 81, Tanga, Muheza, Tanzania
| | - Idir Akhouayri
- Laboratoire d'Ecologie Alpine, UMR CNRS-Université de Grenoble 5553, BP 53, 38041, Grenoble cedex 09, France
| | - Rodolphe Poupardin
- Liverpool School of Tropical Medicine, Vector Group. Pembroke place, Liverpool L35QA, UK
| | - Bernard Batengana
- National Institute of Medical Research of Tanzania, Amani Medical Research Centre, P. O. Box 81, Tanga, Muheza, Tanzania
| | - Franklin Mosha
- KCM College of Tumaini University, P. O. Box. 2240, Moshi, Tanzania
| | - Stephen Magesa
- RTI International-Tanzania, P.O.Box 369, Dar es Salaam, Tanzania
| | - William Kisinza
- National Institute of Medical Research of Tanzania, Amani Medical Research Centre, P. O. Box 81, Tanga, Muheza, Tanzania
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine, UMR CNRS-Université de Grenoble 5553, BP 53, 38041, Grenoble cedex 09, France
| |
Collapse
|
37
|
Oka K, Asari M, Omura T, Yoshida M, Maseda C, Yajima D, Matsubara K, Shiono H, Matsuda M, Shimizu K. Genotyping of 38 insertion/deletion polymorphisms for human identification using universal fluorescent PCR. Mol Cell Probes 2013; 28:13-8. [PMID: 24075877 DOI: 10.1016/j.mcp.2013.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/08/2013] [Accepted: 09/16/2013] [Indexed: 11/18/2022]
Abstract
Short insertion/deletion (Indel) polymorphisms of approximately 2-6 bp are useful as biallelic markers for forensic analysis, and the application of Indel genotyping as a supplementary tool would improve human identification accuracy. We examined the allele frequencies of 37 autosomal Indels in the Japanese population and developed a novel dual-color genotyping method for human identification on the basis of universal fluorescent PCR, including the sex-typing amelogenin locus. Target genomic fragment sizes for 38 Indels were 49-143 bp. We analyzed these Indels in 100 Japanese individuals using the M13(-47) sequence as a universal primer. For dual-color genotyping, we designed a novel universal primer with high amplification efficiency and specificity. Using FAM-labeled M13(-47) and HEX-labeled modified M13(-47) primers, fluorescent signals at all loci were clearly distinguished in two independent multiplex PCRs. Average minor allele frequency was 0.39, and accumulated matching probability was 2.12 × 10(-15). Complete profiles were successfully amplified with as little as 0.25 ng of DNA. This method provides robust, sensitive, and cost-effective genotyping for human identification.
Collapse
Affiliation(s)
- Kumiko Oka
- Department of Legal Medicine, Asahikawa Medical University, 2-1-1-1 Midorigaoka-higashi, Asahikawa 078-8510, Japan; Oral and Maxillofacial Surgery, Asahikawa Medical University, 2-1-1-1 Midorigaoka-higashi, Asahikawa 078-8510, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Hou LN, Xu JR, Zhao QN, Gao XL, Cui YY, Xu J, Wang H, Chen HZ. A new motif in the N-terminal of acetylcholinesterase triggers amyloid-β aggregation and deposition. CNS Neurosci Ther 2013; 20:59-66. [PMID: 23981668 DOI: 10.1111/cns.12161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/14/2013] [Accepted: 07/15/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND AND PURPOSE As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a critical role in the pathogenesis of Alzheimer's disease (AD). The peripheral anionic site (PAS) of AChE has been indicated as the amyloid-β (Aβ) binding domain. The goal of this study was to determine other motifs in AChE involved in Aβ aggregation and deposition. METHODS AND RESULTS The β-hairpin in monomeric Aβ is the key motif of nucleation-dependent Aβ self-aggregation. As AChE could induce Aβ aggregation and deposition, we searched AChE for β-hairpin structures. In A11-specific dot blot assay, AChE was detected by an oligomer-specific antibody A11, implying the existence of β-hairpin structures in AChE as β-hairpin was the core motif of oligomers. A molecular superimposing approach further revealed that the N-terminal region, from Glu7 to Ile20, in AChE (AChE 7-20) was similar to the β-hairpin domain in Aβ. The results of further dot blot assays, thioflavin T fluorescence assays, and electron microscopy imaging experiments, indicated that the N-terminal synthetic peptide AChE7-20 had nearly the same ability as AChE with regard to triggering Aβ aggregation and deposition. CONCLUSIONS AChE 7-20, a β-hairpin region in AChE, might be a new motif in AChE capable of triggering Aβ aggregation and deposition. This finding will be helpful to design new and more effective Aβ aggregation inhibitors for AD treatment.
Collapse
Affiliation(s)
- Li-Na Hou
- Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Tsui LC, Dorfman R. The cystic fibrosis gene: a molecular genetic perspective. Cold Spring Harb Perspect Med 2013; 3:a009472. [PMID: 23378595 DOI: 10.1101/cshperspect.a009472] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The positional cloning of the gene responsible for cystic fibrosis (CF) was the important first step in understanding the basic defect and pathophysiology of the disease. This study aims to provide a historical account of key developments as well as factors that contributed to the cystic fibrosis transmembrane conductance regulator (CFTR) gene identification work. A redefined gene structure based on the full sequence of the gene derived from the Human Genome Project is presented, along with brief reviews of the transcription regulatory sequences for the CFTR gene, the role of mRNA splicing in gene regulation and CF disease, and, various related sequences in the human genome and other species. Because CF mutations and genotype-phenotype correlations are covered by our colleagues (Ferec C, Cutting GR. 2012. Assessing the disease-liability of mutations in CFTR. Cold Spring Harb Perspect Med doi: 10.1101/cshperspect.a009480), we only attempt to provide an introduction of the CF mutation database here for reference purposes.
Collapse
Affiliation(s)
- Lap-Chee Tsui
- The University of Hong Kong, Hong Kong, Special Administrative Region, China.
| | | |
Collapse
|
40
|
From the conceptual basis to the discovery of leptin. Biochimie 2012; 94:2065-8. [DOI: 10.1016/j.biochi.2012.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/21/2012] [Indexed: 11/19/2022]
|
41
|
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. Population genomics of early events in the ecological differentiation of bacteria. Science 2012; 336:48-51. [PMID: 22491847 PMCID: PMC3337212 DOI: 10.1126/science.1218198] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.
Collapse
Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Jonathan Friedman
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonia C. Timberlake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gitta Szabó
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric J. Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
| |
Collapse
|
42
|
Chung CC, Boland J, Yeager M, Jacobs KB, Zhang X, Deng Z, Matthews C, Berndt SI, Chanock SJ. Comprehensive resequence analysis of a 123-kb region of chromosome 11q13 associated with prostate cancer. Prostate 2012; 72:476-86. [PMID: 22468268 PMCID: PMC3325513 DOI: 10.1002/pros.21450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine-mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region. METHODS A next generation resequence analysis of a 122.9-kb region of 11q13.3(68,642,755-68,765,690) was conducted in 78 unrelated individuals of European background,1 CEPH trio, and 1 YRI trio. RESULTS In total, 644 polymorphic loci were identified by our sequence analysis. Of these,166 variants—118 SNPs and 48 insertion-deletion polymorphisms (indels)—were novel,namely not present in the 1000 Genomes or International HapMap Projects. We identified 22,25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759,and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively. CONCLUSIONS Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010),underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region.
Collapse
Affiliation(s)
- Charles C Chung
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
Important human phenotypes like height or facial appearance run in families—that has been known for millennia. Systematic studies of the way in which crossing pea plants resulted in changes in important pea plant phenotypes such as flower color or leaf number were defined in the mid-nineteenth century by Mendel [1 ] and the chemical basis for “inherited inborn errors of metabolism” by Garrod [2 ] at the turn of the twentieth century. Thus, some of the fundamental and familiar rules that we accept in a contemporary understanding of human genetics were laid down decades ago. However, an understanding of the mechanisms whereby genetic information is transmitted from generation to generation and how this information modulates important physiologic or disease susceptibility traits has been more recent. The fundamental discovery was the double-helix structure of DNA, which immediately led to the inference that DNA replication might replicate itself [3 ]. The last 50 years has seen the development of increasingly robust techniques for sequencing DNA and for using DNA as a laboratory reagent.
Collapse
Affiliation(s)
- Dan M Roden
- Departments of Medicine and Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37232-0575, USA.
| |
Collapse
|
44
|
Williams R. Francis Collins: manning the helm with optimism. Circ Res 2010; 107:1398-9. [PMID: 21148446 DOI: 10.1161/res.0b013e318206f1a8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
45
|
|
46
|
Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 2010; 19:R131-6. [PMID: 20858594 DOI: 10.1093/hmg/ddq400] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In this review, we focus on progress that has been made with detecting small insertions and deletions (INDELs) in human genomes. Over the past decade, several million small INDELs have been discovered in human populations and personal genomes. The amount of genetic variation that is caused by these small INDELs is substantial. The number of INDELs in human genomes is second only to the number of single nucleotide polymorphisms (SNPs), and, in terms of base pairs of variation, INDELs cause similar levels of variation as SNPs. Many of these INDELs map to functionally important sites within human genes, and thus, are likely to influence human traits and diseases. Therefore, small INDEL variation will play a prominent role in personalized medicine.
Collapse
Affiliation(s)
- Julienne M Mullaney
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore Street, 615 BioPark II, Baltimore, MD 21201, USA
| | | | | | | |
Collapse
|
47
|
Zwart H. The Nobel Prize as a Reward Mechanism in the Genomics Era: Anonymous Researchers, Visible Managers and the Ethics of Excellence. JOURNAL OF BIOETHICAL INQUIRY 2010; 7:299-312. [PMID: 20730106 PMCID: PMC2917546 DOI: 10.1007/s11673-010-9248-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Accepted: 05/26/2010] [Indexed: 05/29/2023]
Abstract
The Human Genome Project (HGP) is regarded by many as one of the major scientific achievements in recent science history, a large-scale endeavour that is changing the way in which biomedical research is done and expected, moreover, to yield considerable benefit for society. Thus, since the completion of the human genome sequencing effort, a debate has emerged over the question whether this effort merits to be awarded a Nobel Prize and if so, who should be the one(s) to receive it, as (according to current procedures) no more than three individuals can be selected. In this article, the HGP is taken as a case study to consider the ethical question to what extent it is still possible, in an era of big science, of large-scale consortia and global team work, to acknowledge and reward individual contributions to important breakthroughs in biomedical fields. Is it still viable to single out individuals for their decisive contributions in order to reward them in a fair and convincing way? Whereas the concept of the Nobel prize as such seems to reflect an archetypical view of scientists as solitary researchers who, at a certain point in their careers, make their one decisive discovery, this vision has proven to be problematic from the very outset. Already during the first decade of the Nobel era, Ivan Pavlov was denied the Prize several times before finally receiving it, on the basis of the argument that he had been active as a research manager (a designer and supervisor of research projects) rather than as a researcher himself. The question then is whether, in the case of the HGP, a research effort that involved the contributions of hundreds or even thousands of researchers worldwide, it is still possible to "individualise" the Prize? The "HGP Nobel Prize problem" is regarded as an exemplary issue in current research ethics, highlighting a number of quandaries and trends involved in contemporary life science research practices more broadly.
Collapse
Affiliation(s)
- Hub Zwart
- Faculty of Science, Radboud University Nijmegen, Department of Philosophy & Science Studies, Centre for Society & Genomics Institute for Science, Innovation & Society, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
| |
Collapse
|
48
|
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res 2010; 20:249-56. [PMID: 20123915 DOI: 10.1101/gr.097956.109] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.
Collapse
Affiliation(s)
- Andrew L Young
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | |
Collapse
|
49
|
Abstract
Single nucleotide polymorphisms (SNPs) are widely distributed in the human genome and although most SNPs are the result of independent point-mutations, there are exceptions. When studying distances between SNPs, a periodic pattern in the distance between pairs of identical SNPs has been found to be heavily correlated with periodicity in short tandem repeats (STRs). STRs are short DNA segments, widely distributed in the human genome and mainly found outside known tandem repeats. Because of the biased occurrence of SNPs, special care has to be taken when analyzing SNP-variation in STRs. We present a review of STRs in the human genome and discuss molecular mechanisms related to the biased occurrence of SNPs in STRs, and its implications for genome comparisons and genetic association studies.
Collapse
Affiliation(s)
- Bo Eskerod Madsen
- AgroTech, Institute for Agri Technology and Food Innovation, Aarhus N, Denmark
| | | | | |
Collapse
|
50
|
Kann MG. Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief Bioinform 2010; 11:96-110. [PMID: 20007728 PMCID: PMC2810112 DOI: 10.1093/bib/bbp048] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 09/15/2009] [Indexed: 12/29/2022] Open
Abstract
Over a 100 years ago, William Bateson provided, through his observations of the transmission of alkaptonuria in first cousin offspring, evidence of the application of Mendelian genetics to certain human traits and diseases. His work was corroborated by Archibald Garrod (Archibald AE. The incidence of alkaptonuria: a study in chemical individuality. Lancert 1902;ii:1616-20) and William Farabee (Farabee WC. Inheritance of digital malformations in man. In: Papers of the Peabody Museum of American Archaeology and Ethnology. Cambridge, Mass: Harvard University, 1905; 65-78), who recorded the familial tendencies of inheritance of malformations of human hands and feet. These were the pioneers of the hunt for disease genes that would continue through the century and result in the discovery of hundreds of genes that can be associated with different diseases. Despite many ground-breaking discoveries during the last century, we are far from having a complete understanding of the intricate network of molecular processes involved in diseases, and we are still searching for the cures for most complex diseases. In the last few years, new genome sequencing and other high-throughput experimental techniques have generated vast amounts of molecular and clinical data that contain crucial information with the potential of leading to the next major biomedical discoveries. The need to mine, visualize and integrate these data has motivated the development of several informatics approaches that can broadly be grouped in the research area of 'translational bioinformatics'. This review highlights the latest advances in the field of translational bioinformatics, focusing on the advances of computational techniques to search for and classify disease genes.
Collapse
Affiliation(s)
- Maricel G Kann
- University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| |
Collapse
|