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insertion calls  (BioNano Genomics)

 
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    Structured Review

    BioNano Genomics insertion calls
    Insertion Calls, supplied by BioNano Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/insertion+calls/pm33127893-339-13-13?v=BioNano+Genomics
    Average 90 stars, based on 1 article reviews
    insertion calls - by Bioz Stars, 2026-06
    90/100 stars

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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
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    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
    Tungsten Carbide Milling Insert With 15 Rake Face Angle, Chamfer Width (Also Called As T Land), supplied by Kennametal Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    deletion and insertion calls  (Illumina Inc)
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    Illumina Inc deletion and insertion calls
    ( A ) Ribbon diagram of the <t>AAV9</t> viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).
    Deletion And Insertion Calls, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/insertion+calls/pmc06467913__41467_2018_8148_MOESM1_ESM-312-3-11?v=Illumina+Inc
    Average 90 stars, based on 1 article reviews
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    Image Search Results


    ( A ) Ribbon diagram of the AAV9 viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).

    Journal: Viruses

    Article Title: Natural Adeno-Associated Virus Serotypes and Engineered Adeno-Associated Virus Capsid Variants: Tropism Differences and Mechanistic Insights

    doi: 10.3390/v16030442

    Figure Lengend Snippet: ( A ) Ribbon diagram of the AAV9 viral protein monomer colored by chain and with labelled β-sheet strands, α helix, VRs, and C/N-terminus. VR location within protein chains: VR-I (blue), VR-II (teal), VR-III (dark blue), VR-IV (green), VR-V and VR-VI (yellow), VR-VII (dark yellow), VR-VIII (orange), and VR-IX (red). ( B ) Adeno-associated virus (AAV) capsid surface model illustrates the location of variable regions (VR)-IV, V, and VIII (left panel). Representation of the AAV9 capsid zoomed-in (right panels), showing VR-IV at AA452-460 (red) and VR-VIII at AA581-593 (green) from a monomer and VR-V at AA488-505 (blue) from the adjacent monomer of the three-fold axis. ( C ) Comparison of VP1 amino acid sequences from AAV serotypes 1, 2, 3, 4, 6, 7, 8, and 9. VRs are highlighted in red boxes. Multi-sequence alignment in ( C ) performed with Clustal Omega (available at: https://www.ebi.ac.uk/Tools/msa/clustalo/ ). Images in ( A , B ) constructed with PyMOL Molecular Graphics System Version 2.5.5, Schrodinger, LLC (Boston, MA, USA).

    Article Snippet: These novel CNS variants include the following: 9P801, also called TTD-001 (586-AQ-587 substituted with 586-PL-587 and NGAVHLY inserted after AAV9 AA588) [ ], which was screened and characterized in cynomolgus macaque, mice, and human brain microvascular endothelial cells using the TRACER platform; VCAP-101 and VCAP-102 (peptide insertion into AAV9 VR-IV), screened and characterized in adult African green monkeys, cynomolgus macaques, marmoset, and C57BL/6 and BALB/c mice (Voyager Therapeutics, ASGCT 2023); CGN2, screened in mice using the TRADE platform and characterized in cynomolgus macaque (Capsigen, ASGCT 2023); bCap 1, characterized in NHP (Dyno Therapeutics, ASGCT 2023); and a GEN5 capsid variant from Capsida Biotherapeutics, screened in adult cynomolgus macaques (ASGCT 2023).

    Techniques: Virus, Comparison, Sequencing, Construct

    Primary receptors and secondary co-receptors of commonly used AAV serotypes.

    Journal: Viruses

    Article Title: Natural Adeno-Associated Virus Serotypes and Engineered Adeno-Associated Virus Capsid Variants: Tropism Differences and Mechanistic Insights

    doi: 10.3390/v16030442

    Figure Lengend Snippet: Primary receptors and secondary co-receptors of commonly used AAV serotypes.

    Article Snippet: These novel CNS variants include the following: 9P801, also called TTD-001 (586-AQ-587 substituted with 586-PL-587 and NGAVHLY inserted after AAV9 AA588) [ ], which was screened and characterized in cynomolgus macaque, mice, and human brain microvascular endothelial cells using the TRACER platform; VCAP-101 and VCAP-102 (peptide insertion into AAV9 VR-IV), screened and characterized in adult African green monkeys, cynomolgus macaques, marmoset, and C57BL/6 and BALB/c mice (Voyager Therapeutics, ASGCT 2023); CGN2, screened in mice using the TRADE platform and characterized in cynomolgus macaque (Capsigen, ASGCT 2023); bCap 1, characterized in NHP (Dyno Therapeutics, ASGCT 2023); and a GEN5 capsid variant from Capsida Biotherapeutics, screened in adult cynomolgus macaques (ASGCT 2023).

    Techniques: