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Pelegri F, Mullins MC. Genetic screens for mutations affecting adult traits and parental-effect genes. Methods Cell Biol 2016; 135:39-87. [PMID: 27443920 DOI: 10.1016/bs.mcb.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Forward genetics remains an important approach for the unbiased identification of factors involved in biological pathways. Forward genetic analysis in the zebrafish has until now largely been restricted to the developmental period from zygotic genome activation through the end of embryogenesis. However, the use of the zebrafish as a model system for the analysis of late larval, juvenile and adult traits, including fertility and maternal and paternal effects, continues to gain momentum. Here, we describe two approaches, based on an F3-extended family and gynogenetic methods, that allow genetic screening for, and recovery of mutations affecting post-embryonic stages, including adult traits, fertility, and parental effects. For each approach, we also describe strategies to maintain, map, and molecularly clone the identified mutations.
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Affiliation(s)
- F Pelegri
- University of Wisconsin-Madison, Madison, WI, United States
| | - M C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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2
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Czechanski A, Kim H, Byers C, Greenstein I, Stumpff J, Reinholdt LG. Kif18a is specifically required for mitotic progression during germ line development. Dev Biol 2015; 402:253-262. [PMID: 25824710 DOI: 10.1016/j.ydbio.2015.03.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 10/23/2022]
Abstract
Genome integrity in the developing germ line is strictly required for fecundity. In proliferating somatic cells and in germ cells, there are mitotic checkpoint mechanisms that ensure accurate chromosome segregation and euploidy. There is growing evidence of mitotic cell cycle components that are uniquely required in the germ line to ensure genome integrity. We previously showed that the primary phenotype of germ cell deficient 2 (gcd2) mutant mice is infertility due to germ cell depletion during embryogenesis. Here we show that the underlying mutation is a mis-sense mutation, R308K, in the motor domain of the kinesin-8 family member, KIF18A, a protein that is expressed in a variety of proliferative tissues and is a key regulator of chromosome alignment during mitosis. Despite the conservative nature of the mutation, we show that its functional consequences are equivalent to KIF18A deficiency in HeLa cells. We also show that somatic cells progress through mitosis, despite having chromosome alignment defects, while germ cells with similar chromosome alignment defects undergo mitotic arrest and apoptosis. Our data provide evidence for differential requirements for chromosome alignment in germ and somatic cells and show that Kif18a is one of a growing number of genes that are specifically required for cell cycle progression in proliferating germ cells.
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Affiliation(s)
- Anne Czechanski
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609
| | - Haein Kim
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405
| | - Candice Byers
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609
| | - Ian Greenstein
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405
| | - Laura G Reinholdt
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609
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3
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Ma Z, Axtell MJ. Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA. PLoS One 2013; 8:e83721. [PMID: 24376739 PMCID: PMC3869802 DOI: 10.1371/journal.pone.0083721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023] Open
Abstract
Conserved plant microRNAs (miRNAs) modulate important biological processes but little is known about conserved cis-regulatory elements (CREs) surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA)-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10–20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA) from multiple species that currently don't have a full genome assembly available.
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Affiliation(s)
- Zhaorong Ma
- Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael J. Axtell
- Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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4
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del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012; 13:649. [PMID: 23171430 PMCID: PMC3526394 DOI: 10.1186/1471-2164-13-649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/15/2012] [Indexed: 11/21/2022] Open
Abstract
Background Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and occasionally incorrect genome assembly compounds this problem. To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step. Results Here we report the first use of exon capture sequencing to identify mutations in a non-mammalian, vertebrate model. We demonstrate that bulk segregant analysis coupled with exon capture sequencing is not only able to identify causative mutations but can also generate linkage information, facilitate the assembly of scaffolds, identify misassembles, and discover thousands of SNPs for fine mapping. Conclusion Exon capture sequencing and bulk segregant analysis is a rapid, inexpensive method to clone mutants identified in forward genetic screens. With sufficient meioses, this method can be generalized to any model system with a genome assembly, polished or unpolished, and in the latter case, it also provides many critical genomic resources.
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Affiliation(s)
- Florencia del Viso
- Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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5
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High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome 2012; 23:499-513. [PMID: 22991087 DOI: 10.1007/s00335-012-9424-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022]
Abstract
Phenotype-driven approaches in mice are powerful strategies for the discovery of genes and gene functions and for unravelling complex biological mechanisms. Traditional methods for mutation discovery are reliable and robust, but they can also be laborious and time consuming. Recently, high-throughput sequencing (HTS) technologies have revolutionised the process of forward genetics in mice by paving the way to rapid mutation discovery. However, successful application of HTS for mutation discovery relies heavily on the sequencing approach employed and strategies for data analysis. Here we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.
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Christopher KJ, Wang B, Kong Y, Weatherbee SD. Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling. Dev Biol 2012; 368:382-92. [PMID: 22698544 DOI: 10.1016/j.ydbio.2012.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 12/28/2022]
Abstract
Cilia are dynamic organelles that are essential for a vast array of developmental patterning events, including left-right specification, skeletal formation, neural development, and organogenesis. Despite recent advances in understanding cilia form and function, many key ciliogenesis components have yet to be identified. By using a forward genetics approach, we isolated a novel mutant allele (schlei) of the mouse Transmembrane protein 107 (Tmem107) gene, which we show here is critical for cilia formation and embryonic patterning. Tmem107 is required for normal Sonic hedgehog (Shh) signaling in the neural tube and acts in combination with Gli2 and Gli3 to pattern ventral and intermediate neuronal cell types. schlei mutants also form extra digits, and we demonstrate that Tmem107 acts in the Shh pathway to determine digit number, but not identity, by regulating a subset of Shh target genes. Phenotypically, schlei mutants share several features with other cilia mutants; however, spatial restriction of mutant phenotypes and lack of left-right patterning defects in schlei animals suggest differential requirements for Tmem107 in cilia formation in distinct tissues. Also, in contrast to mutants with complete loss of cilia, schlei mutants retain some function of both Gli activator and repressor forms. Together, these studies identify a previously unknown regulator of ciliogenesis and provide insight into how ciliary factors affect Shh signaling and cilia biogenesis in distinct tissues.
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MESH Headings
- Amino Acid Sequence
- Animals
- Body Patterning/genetics
- Cells, Cultured
- Cilia/genetics
- Embryo, Mammalian/cytology
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Extremities/embryology
- Female
- Gene Expression Regulation, Developmental
- Hedgehog Proteins/genetics
- In Situ Hybridization
- Kruppel-Like Transcription Factors/genetics
- Male
- Membrane Proteins/genetics
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Mutant Strains
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Mutation
- Nerve Tissue Proteins/genetics
- Neural Tube/embryology
- Neural Tube/metabolism
- Neural Tube/ultrastructure
- Sequence Homology, Amino Acid
- Signal Transduction/genetics
- Zinc Finger Protein Gli2
- Zinc Finger Protein Gli3
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Davisson MT, Bergstrom DE, Reinholdt LG, Donahue LR. Discovery Genetics - The History and Future of Spontaneous Mutation Research. ACTA ACUST UNITED AC 2012; 2:103-118. [PMID: 25364627 DOI: 10.1002/9780470942390.mo110200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Historically, spontaneous mutations in mice have served as valuable models of heritable human diseases, contributing substantially to our understanding of both disease mechanisms and basic biological pathways. While advances in molecular technologies have improved our ability to create mouse models of human disease through targeted mutagenesis and transgenesis, spontaneous mutations continue to provide valuable research tools for discovery of novel genes and functions. In addition, the genetic defects caused by spontaneous mutations are molecularly similar to mutations in the human genome and, therefore often produce phenotypes that more closely resemble those characteristic of human disease than do genetically engineered mutations. Due to the rarity with which spontaneous mutations arise and the animal intensive nature of their genetic analysis, large-scale spontaneous mutation analysis has traditionally been limited to large mammalian genetics institutes. More recently, ENU mutagenesis and new screening methods have increased the rate of mutant strain discovery, and high-throughput DNA sequencing has enabled rapid identification of the underlying genes and their causative mutations. Here, we discuss the continued value of spontaneous mutations for biomedical research.
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Robb EA, Delany ME. Case study of sequence capture enrichment technology: identification of variation underpinning developmental syndromes in an amniote model. Genes (Basel) 2012; 3:233-47. [PMID: 24704915 PMCID: PMC3899949 DOI: 10.3390/genes3020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/04/2012] [Accepted: 03/05/2012] [Indexed: 12/22/2022] Open
Abstract
Chicken developmental mutants are valuable for discovering sequences and pathways controlling amniote development. Herein we applied the advanced technologies of targeted sequence genomic capture enrichment and next-generation sequencing to discover the causative element for three inherited mutations affecting craniofacial, limb and/or organ development. Since the mutations (coloboma, diplopodia-1 and wingless-2) were bred into a congenic line series and previously mapped to different chromosomes, each targeted mutant causative region could be compared to that of the other two congenic partners, thereby providing internal controls on a single array. Of the ~73 million 50-bp sequence reads, ~76% were specific to the enriched targeted regions with an average target coverage of 132-fold. Analysis of the three targeted regions (2.06 Mb combined) identified line-specific single nucleotide polymorphism (SNPs) and micro (1–3 nt) indels. Sequence content for regions indicated as gaps in the reference genome was generated, thus contributing to its refinement. Additionally, Mauve alignments were constructed and indicated putative chromosomal rearrangements. This is the first report of targeted capture array technology in an avian species, the chicken, an important vertebrate model; the work highlights the utility of employing advanced technologies in an organism with only a “draft stage” reference genome sequence.
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Affiliation(s)
- Elizabeth A Robb
- Department of Animal Science, University of California, Davis, CA 95616, USA.
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, CA 95616, USA.
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9
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Abstract
ENU mutagenesis is a forward genetics strategy in which random mutagenesis and phenotypic screening is used to identify genes based on the phenotype induced when they are mutated. A modifier screen is a type of screen in which mice with a pre-existing phenotype are utilized to identify mutations that can enhance or suppress this phenotype. This approach has the potential to uncover missing pathway members, reveal novel genetic interactions, and pinpoint new drug targets. Considerations when planning a suppressor screen include current knowledge, genomic footprint, penetrance, variance, robustness, latency of the starting phenotype, viability, fertility, genetic background and ENU tolerance of starting strain, screening assay, mouse numbers required, and mutation identification strategy. Practical advice on each of these is provided in this review. Curr. Protoc. Mouse Biol. 2:75-87 © 2012 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marina R Carpinelli
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia.,Hearing Co-Operative Research Centre, Melbourne, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Rachel A Burt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia.,Hearing Co-Operative Research Centre, Melbourne, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Benjamin T Kile
- Cancer and Hematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
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10
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Kenk M, Panter S, Engler-Blum G, Bergemann J. Sensitive DNA-based allergen detection depends on food matrix and DNA isolation method. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1639-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Cohen-Zinder M, Donthu R, Larkin DM, Kumar CG, Rodriguez-Zas SL, Andropolis KE, Oliveira R, Lewin HA. Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits. Physiol Genomics 2011; 43:1185-97. [DOI: 10.1152/physiolgenomics.00253.2010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The goal of this study was to identify candidate genes and DNA polymorphisms for quantitative trait loci (QTL) affecting milk yield (MY), fat yield (FY), and protein yield (PY) previously mapped to bovine chromosome 3 (BTA3). To accomplish this, 373 half-siblings sired by three bulls previously shown to be segregating for lactation trait QTL, and 263 additional sires in the U.S. Dairy Bull DNA Repository (DBDR) were genotyped for 2,500 SNPs within a 16.3 Mbp QTL critical region on BTA3. Targeted resequencing of ∼1.8 Mbp within the QTL critical region of one of the QTL heterozygous sires identified additional polymorphisms useful for association studies. Twenty-three single nucleotide polymorphisms (SNPs) within a fine-mapped region were associated with effects on breeding values for MY, FY, or PY in DBDR sires, of which five SNPs were in strong linkage disequilibrium in the population. This multisite haplotype included SNPs located within exons or promoters of four tightly linked genes: RAP1A, ADORA3, OVGP1, and C3H1orf88. An SNP within RAP1A showed strong evidence of a recent selective sweep based on integrated haplotype score and was also associated with breeding value for PY. Because of its known function in alveolar lumen formation in the mammary gland, RAP1A is thus a strong candidate gene for QTL effects on lactation traits. Our results provide a detailed assessment of a QTL region that will be a useful guide for complex traits analysis in humans and other noninbred species.
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Affiliation(s)
| | - Ravikiran Donthu
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Denis M. Larkin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charu Gupta Kumar
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Sandra L. Rodriguez-Zas
- Institute for Genomic Biology, and
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Kalista E. Andropolis
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Rosane Oliveira
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Harris A. Lewin
- Institute for Genomic Biology, and
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
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12
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Reinholdt LG, Ding Y, Gilbert GJ, Gilbert GT, Czechanski A, Solzak JP, Roper RJ, Johnson MT, Donahue LR, Lutz C, Davisson MT. Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn. Mamm Genome 2011; 22:685-91. [PMID: 21953412 DOI: 10.1007/s00335-011-9357-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 09/05/2011] [Indexed: 11/28/2022]
Abstract
Ts65Dn is a mouse model of Down syndrome: a syndrome that results from chromosome (Chr) 21 trisomy and is associated with congenital defects, cognitive impairment, and ultimately Alzheimer's disease. Ts65Dn mice have segmental trisomy for distal mouse Chr 16, a region sharing conserved synteny with human Chr 21. As a result, this strain harbors three copies of over half of the human Chr 21 orthologs. The trisomic segment of Chr 16 is present as a translocation chromosome (Mmu17(16)), with breakpoints that have not been defined previously. To molecularly characterize the Chrs 16 and 17 breakpoints on the translocation chromosome in Ts65Dn mice, we used a selective enrichment and high-throughput paired-end sequencing approach. Analysis of paired-end reads flanking the Chr 16, Chr 17 junction on Mmu17(16) and de novo assembly of the reads directly spanning the junction provided the precise locations of the Chrs 16 and 17 breakpoints at 84,351,351 and 9,426,822 bp, respectively. These data provide the basis for low-cost, highly efficient genotyping of Ts65Dn mice. More importantly, these data provide, for the first time, complete characterization of gene dosage in Ts65Dn mice.
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13
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Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst FJ, Bergstrom DE, Murray SA, Bult C, Richardson J, Kile BT, Gut I, Hager J, Sigurdsson S, Mauceli E, Di Palma F, Lindblad-Toh K, Cunningham ML, Cox TC, Justice MJ, Spector MS, Lowe SW, Albert T, Donahue LR, Jeddeloh J, Shendure J, Reinholdt LG. Mutation discovery in mice by whole exome sequencing. Genome Biol 2011; 12:R86. [PMID: 21917142 PMCID: PMC3308049 DOI: 10.1186/gb-2011-12-9-r86] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/04/2011] [Accepted: 09/14/2011] [Indexed: 01/18/2023] Open
Abstract
We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis.
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Affiliation(s)
| | | | - Mary Barter
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Rebecca R Corrigan
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | | | - Yueming Ding
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | | | - Chao He
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | - Wenhui Huang
- Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | | | - Lucy Rowe
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Frank J Probst
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | | | | | - Carol Bult
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Joel Richardson
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Benjamin T Kile
- University of Washington, Department of Pediatrics, Division of Craniofacial Medicine and Seattle Children's Craniofacial Center, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Ivo Gut
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jorg Hager
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Snaevar Sigurdsson
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Evan Mauceli
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Federica Di Palma
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael L Cunningham
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Timothy C Cox
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Monica J Justice
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | - Mona S Spector
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | - Scott W Lowe
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | | | | | | | - Jay Shendure
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
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14
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Woollard PM, Mehta NA, Vamathevan JJ, Van Horn S, Bonde BK, Dow DJ. The application of next-generation sequencing technologies to drug discovery and development. Drug Discov Today 2011; 16:512-9. [DOI: 10.1016/j.drudis.2011.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/24/2011] [Accepted: 03/17/2011] [Indexed: 12/17/2022]
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15
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Murray SA. Mouse resources for craniofacial research. Genesis 2011; 49:190-9. [PMID: 21309071 DOI: 10.1002/dvg.20722] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/06/2011] [Accepted: 01/16/2011] [Indexed: 01/22/2023]
Abstract
The mouse, as a genetically defined and easily manipulated model organism, has played a critical role in unraveling the mechanisms of craniofacial development and dysmorphology. While numerous gene knockout strains that display craniofacial abnormalities and essential recombinase tool strains with craniofacial-specific expression have been generated, many are absent from public repositories. Large-scale, international resource-generating initiatives promise to address this concern, providing a comprehensive set of targeted mutations and a suite of new Cre driver strains. In addition, panels of genetically defined strains provide tools to dissect the multigenic, complex nature of craniofacial development, adding to the foundation of information gained from single gene studies. Continued progress will require awareness and access to these essential mouse resources. In this review, current mouse resources, large-scale efforts, and potential future directions will be outlined and discussed.
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16
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Pyrgaki C, Liu A, Niswander L. Grainyhead-like 2 regulates neural tube closure and adhesion molecule expression during neural fold fusion. Dev Biol 2011; 353:38-49. [PMID: 21377456 DOI: 10.1016/j.ydbio.2011.02.027] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/16/2011] [Accepted: 02/16/2011] [Indexed: 02/05/2023]
Abstract
Defects in closure of embryonic tissues such as the neural tube, body wall, face and eye lead to severe birth defects. Cell adhesion is hypothesized to contribute to closure of the neural tube and body wall; however, potential molecular regulators of this process have not been identified. Here we identify an ENU-induced mutation in mice that reveals a molecular pathway of embryonic closure. Line2F homozygous mutant embryos fail to close the neural tube, body wall, face, and optic fissure, and they also display defects in lung and heart development. Using a new technology of genomic sequence capture and high-throughput sequencing of a 2.5Mb region of the mouse genome, we discovered a mutation in the grainyhead-like 2 gene (Grhl2). Microarray analysis revealed Grhl2 affects the expression of a battery of genes involved in cell adhesion and E-cadherin protein is drastically reduced in tissues that require Grhl2 function. The tissue closure defects in Grhl2 mutants are similar to that of AP-2α null mutants and AP-2α has been shown to bind to the promoter of E-cadherin. Therefore, we tested for a possible interaction between these genes. However, we find that Grhl2 and AP-2α do not regulate each other's expression, E-cadherin expression is normal in AP-2α mutants during neural tube closure, and Grhl2;AP-2α trans-heterozygous embryos are morphologically normal. Taken together, our studies point to a complex regulation of neural tube fusion and highlight the importance of comparisons between these two models to understand more fully the molecular pathways of embryonic tissue closure.
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Affiliation(s)
- Christina Pyrgaki
- HHMI, Department of Pediatrics, Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus and The Children's Hospital, Aurora, CO 80045, USA
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17
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Abstract
Single nucleotide polymorphisms (SNPs) are single base differences between haplotypes. SNPs are abundant in many species and valuable as markers for genetic map construction, modern molecular breeding programs, and quantitative genetic studies. SNPs are readily mined from genomic DNA or cDNA sequence obtained from individuals having two or more distinct genotypes. While automated Sanger sequencing has become less expensive over time, it is still costly to acquire deep Sanger sequence from several genotypes. "Next-generation" DNA sequencing technologies that utilize new chemistries and massively parallel approaches have enabled DNA sequences to be acquired at extremely high depths of coverage faster and for less cost than traditional sequencing. One such method is represented by the Roche/454 Life Sciences GS-FLX Titanium Series, which currently uses pyrosequencing to produce up to 400-600 million bases of DNA sequence/run (>1 million reads, ~400 bp/read). This chapter discusses the use of high-throughput pyrosequencing for SNP discovery by focusing on 454 sequencing of maize cDNA, the development of a computational pipeline for polymorphism detection, and the subsequent identification of over 7,000 putative SNPs between Mo17 and B73 maize. In addition, alternative alignment and polymorphism detection strategies that implement Illumina short reads, data processing and visualization tools, and reduced representation techniques that reduce the sequencing of repeat DNA, thus enabling efficient analysis of genome sequence, are discussed.
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Affiliation(s)
- W Brad Barbazuk
- Department of Biology and the Genetics Institute, University of Florida, Gainesville, FL, USA.
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18
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Abnormal gonad development in Kit W-2Bao mice caused by a Kit gene missense mutation. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Amstutz U, Andrey-Zürcher G, Suciu D, Jaggi R, Häberle J, Largiadèr CR. Sequence capture and next-generation resequencing of multiple tagged nucleic acid samples for mutation screening of urea cycle disorders. Clin Chem 2010; 57:102-11. [PMID: 21068339 DOI: 10.1373/clinchem.2010.150706] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Molecular genetic testing is commonly used to confirm clinical diagnoses of inherited urea cycle disorders (UCDs); however, conventional mutation screenings encompassing only the coding regions of genes may not detect disease-causing mutations occurring in regulatory elements and introns. Microarray-based target enrichment and next-generation sequencing now allow more-comprehensive genetic screening. We applied this approach to UCDs and combined it with the use of DNA bar codes for more cost-effective, parallel analyses of multiple samples. METHODS We used sectored 2240-feature medium-density oligonucleotide arrays to capture and enrich a 199-kb genomic target encompassing the complete genomic regions of 3 urea cycle genes, OTC (ornithine carbamoyltransferase), CPS1 (carbamoyl-phosphate synthetase 1, mitochondrial), and NAGS (N-acetylglutamate synthase). We used the Genome Sequencer FLX System (454 Life Sciences) to jointly analyze 4 samples individually tagged with a 6-bp DNA bar code and compared the results with those for an individually sequenced sample. RESULTS Using a low tiling density of only 1 probe per 91 bp, we obtained strong enrichment of the targeted loci to achieve ≥90% coverage with up to 64% of the sequences covered at a sequencing depth ≥10-fold. We observed a very homogeneous sequence representation of the bar-coded samples, which yielded a >30% increase in the sequence data generated per sample, compared with an individually processed sample. Heterozygous and homozygous disease-associated mutations were correctly detected in all samples. CONCLUSIONS The use of DNA bar codes and the use of sectored oligonucleotide arrays for target enrichment enable parallel, large-scale analysis of complete genomic regions for multiple genes of a disease pathway and for multiple samples simultaneously. This approach thus may provide an efficient tool for comprehensive diagnostic screening of mutations.
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Affiliation(s)
- Ursula Amstutz
- Institute of Clinical Chemistry, Inselspital, University Hospital and University of Bern, Bern, Switzerland
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20
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Cheng Y, Wang J, Shao J, Chen Q, Mo F, Ma L, Han X, Zhang J, Chen C, Zhang C, Lin S, Yu J, Zheng S, Lin SC, Lin B. Identification of novel SNPs by next-generation sequencing of the genomic region containing the APC gene in colorectal cancer patients in China. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:315-25. [PMID: 20569184 DOI: 10.1089/omi.2010.0018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We described an approach of identifying single nucleotide polymorphisms (SNPs) in complete genomic regions of key genes including promoters, exons, introns, and downstream sequences by combining long-range polymerase chain reaction (PCR) or NimbleGen sequence capture with next-generation sequencing. Using the adenomatous polyposis coli (APC) gene as an example, we identified 210 highly reliable SNPs by next-generation sequencing analysis program MAQ and Samtools, of which 69 were novel ones, in the 123-kb APC genomic region in 27 pair of colorectal cancers and normal adjacent tissues. We confirmed all of the eight randomly selected high-quality SNPs by allele-specific PCR, suggesting that our false discovery rate is negligible. We identified 11 SNPs in the exonic region, including one novel SNP that was not previously reported. Although 10 of them are synonymous, they were predicted to affect splicing by creating or removing exonic splicing enhancers or exonic splicing silencers. We also identified seven SNPs in the upstream region of the APC gene, three of which were only identified in the cancer tissues. Six of these upstream SNPs were predicted to affect transcription factor binding. We also observed that long-range PCR was better in capturing GC-rich regions than the NimbleGen sequence capture technique.
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Affiliation(s)
- Yin Cheng
- Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, People's Republic of China
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21
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Drögemüller C, Tetens J, Sigurdsson S, Gentile A, Testoni S, Lindblad-Toh K, Leeb T. Identification of the bovine Arachnomelia mutation by massively parallel sequencing implicates sulfite oxidase (SUOX) in bone development. PLoS Genet 2010; 6. [PMID: 20865119 PMCID: PMC2928811 DOI: 10.1371/journal.pgen.1001079] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 07/22/2010] [Indexed: 11/18/2022] Open
Abstract
Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development.
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Affiliation(s)
- Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne, Switzerland
| | - Jens Tetens
- Institute for Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Snaevar Sigurdsson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Arcangelo Gentile
- Veterinary Clinical Department, University of Bologna, Bologna, Italy
| | - Stefania Testoni
- Department of Veterinary Clinical Sciences, University of Padua, Padua, Italy
| | - Kerstin Lindblad-Toh
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne, Switzerland
- * E-mail:
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22
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Gupta T, Marlow FL, Ferriola D, Mackiewicz K, Dapprich J, Monos D, Mullins MC. Microtubule actin crosslinking factor 1 regulates the Balbiani body and animal-vegetal polarity of the zebrafish oocyte. PLoS Genet 2010; 6:e1001073. [PMID: 20808893 PMCID: PMC2924321 DOI: 10.1371/journal.pgen.1001073] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 07/15/2010] [Indexed: 11/23/2022] Open
Abstract
Although of fundamental importance in developmental biology, the genetic basis for the symmetry breaking events that polarize the vertebrate oocyte and egg are largely unknown. In vertebrates, the first morphological asymmetry in the oocyte is the Balbiani body, a highly conserved, transient structure found in vertebrates and invertebrates including Drosophila, Xenopus, human, and mouse. We report the identification of the zebrafish magellan (mgn) mutant, which exhibits a novel enlarged Balbiani body phenotype and a disruption of oocyte polarity. To determine the molecular identity of the mgn gene, we positionally cloned the gene, employing a novel DNA capture method to target region-specific genomic DNA of 600 kb for massively parallel sequencing. Using this technique, we were able to enrich for the genomic region linked to our mutation within one week and then identify the mutation in mgn using massively parallel sequencing. This is one of the first successful uses of genomic DNA enrichment combined with massively parallel sequencing to determine the molecular identity of a gene associated with a mutant phenotype. We anticipate that the combination of these technologies will have wide applicability for the efficient identification of mutant genes in all organisms. We identified the mutation in mgn as a deletion in the coding sequence of the zebrafish microtubule actin crosslinking factor 1 (macf1) gene. macf1 is a member of the highly conserved spectraplakin family of cytoskeletal linker proteins, which play diverse roles in polarized cells such as neurons, muscle cells, and epithelial cells. In mgn mutants, the oocyte nucleus is mislocalized; and the Balbiani body, localized mRNAs, and organelles are absent from the periphery of the oocyte, consistent with a function for macf1 in nuclear anchoring and cortical localization. These data provide the first evidence for a role for spectraplakins in polarization of the vertebrate oocyte and egg. How the axes of the embryo are established is an important question in developmental biology. In many organisms, the axes of the embryo are established during oogenesis through the generation of a polarized egg. Very little is known regarding the mechanisms of polarity establishment and maintenance in vertebrate oocytes and eggs. We have identified a zebrafish mutant called magellan, which displays a defect in egg polarity. The gene disrupted in the magellan mutant encodes the cytoskeletal linker protein microtubule actin crosslinking factor 1 (macf1). In vertebrates, it can take years to identify the molecular nature of a mutation. We used a new technique to identify the magellan mutation, which allowed us to rapidly isolate genomic DNA linked to the mutation and sequence it. Our results describe an important new function for macf1 in polarizing the oocyte and egg and demonstrate the feasibility of this new technique for the efficient identification of mutations.
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Affiliation(s)
- Tripti Gupta
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Florence L. Marlow
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Deborah Ferriola
- Generation Biotech, Lawrenceville, New Jersey, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Katarzyna Mackiewicz
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Johannes Dapprich
- Generation Biotech, Lawrenceville, New Jersey, United States of America
| | - Dimitri Monos
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Mary C. Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS. Repeat subtraction-mediated sequence capture from a complex genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:898-909. [PMID: 20230488 DOI: 10.1111/j.1365-313x.2010.04196.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker-free, two-stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non-repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800-3000-fold enrichment and 80-98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false-positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non-reference alleles. The ability to design novel repeat-subtraction and target capture arrays makes this technology accessible in any species.
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Affiliation(s)
- Yan Fu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, Ahmed ZM, Riazuddin S, Khan SN, Riazuddin S, Friedman TB. Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. Am J Hum Genet 2010; 86:378-88. [PMID: 20170899 DOI: 10.1016/j.ajhg.2010.01.030] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 01/22/2010] [Accepted: 01/25/2010] [Indexed: 10/19/2022] Open
Abstract
Targeted genome capture combined with next-generation sequencing was used to analyze 2.9 Mb of the DFNB79 interval on chromosome 9q34.3, which includes 108 candidate genes. Genomic DNA from an affected member of a consanguineous family segregating recessive, nonsyndromic hearing loss was used to make a library of fragments covering the DFNB79 linkage interval defined by genetic analyses of four pedigrees. Homozygosity for eight previously unreported variants in transcribed sequences was detected by evaluating a library of 402,554 sequencing reads and was later confirmed by Sanger sequencing. Of these variants, six were determined to be polymorphisms in the Pakistani population, and one was in a noncoding gene that was subsequently excluded genetically from the DFNB79 linkage interval. The remaining variant was a nonsense mutation in a predicted gene, C9orf75, renamed TPRN. Evaluation of the other three DFNB79-linked families identified three additional frameshift mutations, for a total of four truncating alleles of this gene. Although TPRN is expressed in many tissues, immunolocalization of the protein product in the mouse cochlea shows prominent expression in the taper region of hair cell stereocilia. Consequently, we named the protein taperin.
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