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Fuentes R, Marlow FL, Abrams EW, Zhang H, Kobayashi M, Gupta T, Kapp LD, DiNardo Z, Heller R, Cisternas R, García-Castro P, Segovia-Miranda F, Montecinos-Franjola F, Vought W, Vejnar CE, Giraldez AJ, Mullins MC. Maternal regulation of the vertebrate oocyte-to-embryo transition. PLoS Genet 2024; 20:e1011343. [PMID: 39052672 DOI: 10.1371/journal.pgen.1011343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Maternally-loaded factors in the egg accumulate during oogenesis and are essential for the acquisition of oocyte and egg developmental competence to ensure the production of viable embryos. However, their molecular nature and functional importance remain poorly understood. Here, we present a collection of 9 recessive maternal-effect mutants identified in a zebrafish forward genetic screen that reveal unique molecular insights into the mechanisms controlling the vertebrate oocyte-to-embryo transition. Three genes, over easy, p33bjta, poached and black caviar, were found to control initial steps in yolk globule sizing and protein cleavage during oocyte maturation that act independently of nuclear maturation. The krang, kazukuram, p28tabj, and spotty genes play distinct roles in egg activation, including cortical granule biology, cytoplasmic segregation, the regulation of microtubule organizing center assembly and microtubule nucleation, and establishing the basic body plan. Furthermore, we cloned two of the mutant genes, identifying the over easy gene as a subunit of the Adaptor Protein complex 5, Ap5m1, which implicates it in regulating intracellular trafficking and yolk vesicle formation. The novel maternal protein Krang/Kiaa0513, highly conserved in metazoans, was discovered and linked to the function of cortical granules during egg activation. These mutant genes represent novel genetic entry points to decipher the molecular mechanisms functioning in the oocyte-to-embryo transition, fertility, and human disease. Additionally, our genetic adult screen not only contributes to the existing knowledge in the field but also sets the basis for future investigations. Thus, the identified maternal genes represent key players in the coordination and execution of events prior to fertilization.
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Affiliation(s)
- Ricardo Fuentes
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Florence L Marlow
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine Mount Sinai, New York, New York, United States of America
| | - Elliott W Abrams
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Purchase College, State University of New York, Purchase, New York, United States of America
| | - Hong Zhang
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Tripti Gupta
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lee D Kapp
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Zachary DiNardo
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ronald Heller
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Ruth Cisternas
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Priscila García-Castro
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Fabián Segovia-Miranda
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Felipe Montecinos-Franjola
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, Maryland, United States of America
| | - William Vought
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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2
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Fan TW, Yu HLL, Hsing IM. Conditional Displacement Hybridization Assay for Multiple SNP Phasing. Anal Chem 2017; 89:9961-9966. [DOI: 10.1021/acs.analchem.7b02300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tsz Wing Fan
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henson L. Lee Yu
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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3
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Zander J, Rothe J, Dapprich J, Nagy M. New application for haplotype-specific extraction: Separation of mitochondrial DNA mixtures. Forensic Sci Int Genet 2017; 29:242-249. [DOI: 10.1016/j.fsigen.2017.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/10/2017] [Accepted: 05/01/2017] [Indexed: 10/19/2022]
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4
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Liu S, Kandoth PK, Lakhssassi N, Kang J, Colantonio V, Heinz R, Yeckel G, Zhou Z, Bekal S, Dapprich J, Rotter B, Cianzio S, Mitchum MG, Meksem K. The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode. Nat Commun 2017; 8:14822. [PMID: 28345654 PMCID: PMC5378975 DOI: 10.1038/ncomms14822] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/06/2017] [Indexed: 12/24/2022] Open
Abstract
Two types of resistant soybean (Glycine max (L.) Merr.) sources are widely used against soybean cyst nematode (SCN, Heterodera glycines Ichinohe). These include Peking-type soybean, whose resistance requires both the rhg1-a and Rhg4 alleles, and PI 88788-type soybean, whose resistance requires only the rhg1-b allele. Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12 in one genomic segment simultaneously contribute to rhg1-b resistance. Using an integrated set of genetic and genomic approaches, we demonstrate that the rhg1-a Peking-type GmSNAP18 is sufficient for resistance to SCN in combination with Rhg4. The two SNAPs (soluble NSF attachment proteins) differ by only five amino acids. Our findings suggest that Peking-type GmSNAP18 is performing a different role in SCN resistance than PI 88788-type GmSNAP18. As such, this is an example of a pathogen resistance gene that has evolved to underlie two types of resistance, yet ensure the same function within a single plant species.
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Affiliation(s)
- Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Pramod K. Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Jingwen Kang
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Robert Heinz
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Greg Yeckel
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | | | - Bjorn Rotter
- GenXPro-GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Silvia Cianzio
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
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ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing. Sci Rep 2017; 7:44437. [PMID: 28300202 PMCID: PMC5353602 DOI: 10.1038/srep44437] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/08/2017] [Indexed: 11/21/2022] Open
Abstract
Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplification-based resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.
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6
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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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7
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Rothe J, Nagy M. Separation of Y-chromosomal haplotypes from male DNA mixtures via multiplex haplotype-specific extraction. Forensic Sci Int Genet 2015; 19:223-231. [PMID: 26275613 DOI: 10.1016/j.fsigen.2015.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 06/05/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022]
Abstract
In forensic analysis, the interpretation of DNA mixtures is the subject of ongoing debate and requires expertise knowledge. Haplotype-specific extraction (HSE) is an alternative method that enables the separation of large chromosome fragments or haplotypes by using magnetic beads in conjunction with allele-specific probes. HSE thus allows physical separation of the components of a DNA mixture. Here, we present the first multiplex HSE separation of a Y-chromosomal haplotype consisting of six Yfiler short tandem repeat markers from a mixture of male DNA.
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Affiliation(s)
- Jessica Rothe
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany
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8
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Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, Liu S, Gao P, Huang H, Sun J, Chen D, He G, Huang W, Huang Z, Li Y, Tellier LCAM, Liu X, Feng Q, Xu X, Zhang X, Bolund L, Krogh A, Kristiansen K, Drmanac R, Drmanac S, Nielsen R, Li S, Wang J, Yang H, Li Y, Wong GKS, Wang J. De novo assembly of a haplotype-resolved human genome. Nat Biotechnol 2015; 33:617-22. [PMID: 26006006 DOI: 10.1038/nbt.3200] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/16/2015] [Indexed: 12/27/2022]
Abstract
The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.
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Affiliation(s)
- Hongzhi Cao
- 1] BGI-Shenzhen, Shenzhen, China. [2] BGI-Tianjin, Tianjin, China. [3] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Honglong Wu
- 1] BGI-Shenzhen, Shenzhen, China. [2] BGI-Tianjin, Tianjin, China
| | - Ruibang Luo
- 1] BGI-Shenzhen, Shenzhen, China. [2] HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Hong Kong, China
| | - Shujia Huang
- 1] BGI-Shenzhen, Shenzhen, China. [2] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Yuhui Sun
- 1] BGI-Shenzhen, Shenzhen, China. [2] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Yinlong Xie
- 1] BGI-Shenzhen, Shenzhen, China. [2] HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Hong Kong, China. [3] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Binghang Liu
- 1] BGI-Shenzhen, Shenzhen, China. [2] HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Hong Kong, China
| | | | - Hancheng Zheng
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jian Li
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Li
- BGI-Shenzhen, Shenzhen, China
| | - Yu Wang
- 1] BGI-Shenzhen, Shenzhen, China. [2] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | | | - Siyang Liu
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Haodong Huang
- 1] BGI-Shenzhen, Shenzhen, China. [2] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | | | | | | | | | - Yue Li
- BGI-Shenzhen, Shenzhen, China
| | - Laurent C A M Tellier
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiao Liu
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qiang Feng
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | - Lars Bolund
- 1] BGI-Shenzhen, Shenzhen, China. [2] Institute of Biomedicine, University of Aarhus, Aarhus, Denmark. [3] Danish Center for Translational Breast Cancer Research, Copenhagen, Denmark
| | - Anders Krogh
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karsten Kristiansen
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Rasmus Nielsen
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Integrative Biology, University of California, Berkeley, California, USA. [3] Department of Statistics, University of California, Berkeley, California, USA
| | | | - Jian Wang
- 1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Huanming Yang
- 1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Sciences, Hangzhou, China. [3] Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yingrui Li
- 1] BGI-Shenzhen, Shenzhen, China. [2] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Gane Ka-Shu Wong
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada. [3] Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jun Wang
- 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. [4] Macau University of Science and Technology, Taipa, Macau, China. [5] Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
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Park Y, Yoon CE, Kwon OJ, Kim YS, Kim HS. Resolution of ambiguous HLA genotyping in korean by multi-group-specific sequence-based typing. Yonsei Med J 2014; 55:1005-13. [PMID: 24954331 PMCID: PMC4075361 DOI: 10.3349/ymj.2014.55.4.1005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To evaluate a multi-group-specific sequence-based typing (SBT) method for resolving ambiguous results from human leukocyte antigen (HLA) genotyping. MATERIALS AND METHODS A total of 50 samples that showed ambiguous genotypes for at least two HLA loci from HLA-A, -B, -C and -DRB1 by the conventional SBT assay were evaluated using a new SBT test, the AVITA plus assay. The most likely HLA genotypes for the respective samples considering allele frequencies in Korean were concordant between the AVITA and conventional SBT assays. RESULTS An average of 3.3 loci among the HLA-A, -B, -C and -DRB1 loci per sample gave results with two or more possible allele combinations with the conventional SBT, and 48 (96.0%) out of 50 showed reduced numbers of possible genotypes for at least one HLA locus with the AVITA. A total of 41, 43, 42, and 38 cases among the 50 samples showed ambiguous results for HLA-A, -B, -C, and -DRB1 typing by the conventional SBT, respectively. The average numbers of possible allele combinations for the respective four HLA loci were 8.2, 6.7, 5.9, and 3.2, and they were reduced to 1.5, 2.2, 4.4, and 1.8, respectively, by the AVITA. Ambiguity was resolved by the AVITA in 33 (80.5%), 31 (72.1%), 17 (40.5%) and 28 (73.7%) samples among the ambiguous cases from the conventional SBT for HLA-A, -B, -C, and -DRB1 typing, respectively. CONCLUSION The multi-group-specific SBT method considerably reduced the number of ambiguous results, and thus may be useful for accurate HLA typing in clinical laboratories.
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Affiliation(s)
- Yongjung Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | | | - Oh-Joong Kwon
- College of Animal Bioscience & Technology, Konkuk University, Seoul, Korea
| | - Yu-Seun Kim
- Division of Transplantation Surgery, Department of Surgery,The Research Institute for Transplantation, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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10
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Murphy NM, Pouton CW, Irving HR. Human leukocyte antigen haplotype phasing by allele-specific enrichment with peptide nucleic acid probes. Mol Genet Genomic Med 2014; 2:245-53. [PMID: 24936514 PMCID: PMC4049365 DOI: 10.1002/mgg3.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 12/22/2022] Open
Abstract
Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe–target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb separating the HLA-DRB1 and the HLA-DQA1 genes, potentially spanning a total distance of at least 130 kb. Allele-specific target enrichment with PNA probes is a straightforward technique that has the capability to improve the resolution of DNA and whole genome sequencing technologies by allowing haplotyping of enriched DNA and crucially, retaining the DNA methylation profile.
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Affiliation(s)
- Nicholas M Murphy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia ; Department of Preimplantation Genetic Diagnosis, Melbourne IVF 344 Victoria Parade, East Melbourne, Australia
| | - Colin W Pouton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
| | - Helen R Irving
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
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11
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Tyson J, Armour JAL. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR. BMC Genomics 2012; 13:693. [PMID: 23231411 PMCID: PMC3543183 DOI: 10.1186/1471-2164-13-693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/07/2012] [Indexed: 12/26/2022] Open
Abstract
Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.
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Affiliation(s)
- Jess Tyson
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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12
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New prediction model for probe specificity in an allele-specific extension reaction for haplotype-specific extraction (HSE) of Y chromosome mixtures. PLoS One 2012; 7:e45955. [PMID: 23049901 PMCID: PMC3457965 DOI: 10.1371/journal.pone.0045955] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/23/2012] [Indexed: 01/30/2023] Open
Abstract
Allele-specific extension reactions (ASERs) use 3′ terminus-specific primers for the selective extension of completely annealed matches by polymerase. The ability of the polymerase to extend non-specific 3′ terminal mismatches leads to a failure of the reaction, a process that is only partly understood and predictable, and often requires time-consuming assay design. In our studies we investigated haplotype-specific extraction (HSE) for the separation of male DNA mixtures. HSE is an ASER and provides the ability to distinguish between diploid chromosomes from one or more individuals. Here, we show that the success of HSE and allele-specific extension depend strongly on the concentration difference between complete match and 3′ terminal mismatch. Using the oligonucleotide-modeling platform Visual Omp, we demonstrated the dependency of the discrimination power of the polymerase on match- and mismatch-target hybridization between different probe lengths. Therefore, the probe specificity in HSE could be predicted by performing a relative comparison of different probe designs with their simulated differences between the duplex concentration of target-probe match and mismatches. We tested this new model for probe design in more than 300 HSE reactions with 137 different probes and obtained an accordance of 88%.
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Tissue-specific temporal exome capture revealed muscle-specific genes and SNPs in Indian buffalo (Bubalus bubalis). GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:107-13. [PMID: 22768984 PMCID: PMC5054198 DOI: 10.1016/j.gpb.2012.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/28/2011] [Indexed: 11/20/2022]
Abstract
Whole genome sequencing of buffalo is yet to be completed, and in the near future it may not be possible to identify an exome (coding region of genome) through bioinformatics for designing probes to capture it. In the present study, we employed in solution hybridization to sequence tissue specific temporal exomes (TST exome) in buffalo. We utilized cDNA prepared from buffalo muscle tissue as a probe to capture TST exomes from the buffalo genome. This resulted in a prominent reduction of repeat sequences (up to 40%) and an enrichment of coding sequences (up to 60%). Enriched targets were sequenced on a 454 pyro-sequencing platform, generating 101,244 reads containing 24,127,779 high quality bases. The data revealed 40,100 variations, of which 403 were indels and 39,218 SNPs containing 195 nonsynonymous candidate SNPs in protein-coding regions. The study has indicated that 80% of the total genes identified from capture data were expressed in muscle tissue. The present study is the first of its kind to sequence TST exomes captured by use of cDNA molecules for SNPs found in the coding region without any prior sequence information of targeted molecules.
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Rothe J, Nagy M. Strategies for excluding false Y-chromosomal SNP entries from human genome databases. Electrophoresis 2012; 33:1488-91. [PMID: 22648820 DOI: 10.1002/elps.201100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Current human genome databases for public single nucleotide polymorphisms (SNPs) still contain a substantial fraction of false entries. The main reasons for errors include sequencing or assembly errors, paralogous sequence-, and private variants. In the course of our studies on the Y chromosome, we established a set of internal laboratory guidelines for reliably identifying false SNP entries in databases.
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Affiliation(s)
- Jessica Rothe
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany.
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15
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Rapid retrieval of DNA target sequences by primer extension capture. Methods Mol Biol 2012. [PMID: 22065436 DOI: 10.1007/978-1-61779-228-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
There is a widespread need for methods to enrich DNA samples for sequences of interest prior to high-throughput sequencing and to reduce the costs associated with a shotgun approach. While useful for targeting megabase-sized regions in a few samples, hybridization capture approaches such as those using microarrays currently involve bulky handling steps, long incubation times, and high per-sample costs. In contrast, the primer extension capture (PEC) method allows direct selection of small genomic regions from DNA sources within 2 h, with low costs for use with parallel samples. PEC promises useful applications in studies such as ancient DNA or forensic sequencing, taxonomic surveying of metagenomic samples, or genomic mapping of repetitive elements.
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Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:215653. [PMID: 21647313 PMCID: PMC3106376 DOI: 10.1155/2011/215653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 02/17/2011] [Accepted: 02/24/2011] [Indexed: 11/23/2022]
Abstract
Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172 was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.
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Rothe J, Roewer L, Nagy M. Individual specific extraction of DNA from male mixtures--First evaluation studies. Forensic Sci Int Genet 2010; 5:117-21. [PMID: 21115416 DOI: 10.1016/j.fsigen.2010.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In forensic work, the interpretation of DNA profiles becomes complicated when samples contain more than one contributor because the simultaneous amplification of individual identification markers results in mixed profiles. To overcome this problem, we present haplotype-specific extraction (HSE) as a more straightforward method to analyze a DNA mixture. HSE has been developed to clarify ambiguous HLA alleles by separating diploid samples into their haploid components to facilitate HLA typing. We have started to establish new protocols and strategies to adapt HSE for the separation of male DNA mixtures in forensic analysis. First results have shown an improved enrichment of male DNA from a single contributor. We have also evaluated a new, optimized buffer composition by testing different concentrations of its components. Improved separation of a male DNA mixture is detected using AmpFℓSTR(®) Yfiler short tandem repeat analysis.
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Affiliation(s)
- Jessica Rothe
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany.
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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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Danzer M, Polin H, Stabentheiner S, Hartmann CC, Lennartz K, Gabriel C. Comprehensive polymorphism analysis of ABO using allele-specific separation by bead technology and subsequent sequencing. Vox Sang 2010; 98:451-4. [DOI: 10.1111/j.1423-0410.2009.01269.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mir KU. Sequencing genomes: from individuals to populations. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2010; 8:367-78. [PMID: 19808932 DOI: 10.1093/bfgp/elp040] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whole genome sequences of Jim Watson and Craig Venter are early examples of personalized genomics, which promises to change how we approach healthcare in the future. Before personal sequencing can have practical medical benefits, however, and before it should be advocated for implementation at the population-scale, there needs to be a better understanding of which genetic variants influence which traits and how their effects are modified by epigenetic factors. Nonetheless, for forging links between DNA sequence and phenotype, efforts to sequence the genomes of individuals need to continue; this includes sequencing sub-populations for association studies which analyse the difference in sequence between disease affected and unaffected individuals. Such studies can only be applied on a large enough scale to be effective if the massive strides in sequencing technology that have recently occurred also continue.
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Affiliation(s)
- Kalim U Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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21
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Affiliation(s)
- W. BABIK
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30‐387 Kraków, Poland
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22
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Abstract
The past few years have seen enormous advances in genotyping technology, including chips that accommodate in excess of 1 million SNP assays. In addition, the cost per genotype has been driven down to levels unimagined only a few years ago. These developments have resulted in an explosion of positive whole-genome association studies and the identification of many new genes for common diseases. Here I review high-throughput genotyping platforms as well as other approaches for lower numbers of assays but high sample throughput, which play an important role in genotype validation and study replication. Further, the utility of SNP arrays for detecting structural variation through the development of genotyping algorithms is reviewed and methods for long-range haplotyping are presented. It is anticipated that in the future, sample throughput and cost savings will be increased further through the combination of automation, microfluidics, and nanotechnologies.
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Affiliation(s)
- Jiannis Ragoussis
- Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom.
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Vandiedonck C, Knight JC. The human Major Histocompatibility Complex as a paradigm in genomics research. BRIEFINGS IN FUNCTIONAL GENOMICS & PROTEOMICS 2009; 8:379-94. [PMID: 19468039 PMCID: PMC2987720 DOI: 10.1093/bfgp/elp010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became the first genomic region to be entirely re-sequenced for common haplotypes, while studies mapping gene expression phenotypes across the genome have strongly implicated variation in the MHC. This review shows how the MHC continues to provide new insights and remains in the vanguard of contemporary research in human genomics.
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Affiliation(s)
- Claire Vandiedonck
- Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, UK.
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Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 2009; 70:960-4. [PMID: 19706315 DOI: 10.1016/j.humimm.2009.08.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 08/07/2009] [Accepted: 08/18/2009] [Indexed: 12/19/2022]
Abstract
Transplantation and, notably, hematopoietic stem cell transplantation require high-resolution human leukocyte antigen (HLA) typing and, because of the heterozygous genomic DNA samples, are dependent on clonal analytical methods. High-resolution HLA typing is a necessity for accomplishing the best possible histocompatibility match between donor and recipient, because mismatches strongly increase the risk of severe acute graft-versus-host disease. We describe the development and first application in a clinical setting of a novel, HLA sequence-based typing method by exploring the next-generation sequencing technology as provided by the Genome Sequencer FLX system (Roche/454 Life Sciences, Branford, CT). The developed system allows for ambiguity-free, high-throughput, high-resolution HLA-A and -B typing with the potential for automation. Primers and Genome Sequencer FLX specific adapters were lengthened with donor-identifying barcode sequences to identify each of eight Caucasian reference donors within one single multiplex sequencing run. Compared with normal SBT HLA typing, results indicate that every patient was identified correctly with an average of 1000 reads per amplicon. Furthermore, current investments for increased read lengths and fully automated molecular diagnostic software tools, using original GS-FLX data file formats, will enhance this novel HLA typing strategy in the near future.
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Affiliation(s)
- Christian Gabriel
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, 4017 Linz, Austria
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