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Akademický článek

A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing

Autor: Josefin Johansson, Sarah Lidéus, Ida Höijer, Adam Ameur, Sanna Gudmundsson, Göran Annerén, Marie-Louise Bondeson, Maria Wilbe

Publikováno v: Scientific Reports, Vol 13, Iss 1, Pp 1-9 (2023)

Abstract X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford

Externí odkaz: https://doaj.org/article/1a5f041a671a44b5858911c375c525c1

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Akademický článek

CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations

Autor: Ida Höijer, Anastasia Emmanouilidou, Rebecka Östlund, Robin van Schendel, Selma Bozorgpana, Marcel Tijsterman, Lars Feuk, Ulf Gyllensten, Marcel den Hoed, Adam Ameur

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)

CRISPR-Cas9 can introduce unintended off-target effects. Here authors show that unintended mutations produced by in vivo of zebrafish can be inherited by their off-spring.

Externí odkaz: https://doaj.org/article/c9926fdc297c499ead1e48efd9227591

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Akademický článek

Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

Autor: Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-19 (2020)

Abstract Background One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMR

Externí odkaz: https://doaj.org/article/faeeee05357040f48367202efe662786

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Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

Autor: Esben Bjoern Madsen, Ida Höijer, Adam Ameur, Thomas Kvist, Marie Just Mikkelsen

Publikováno v: Human Mutation

Long‐read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome‐gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::67aa98242d11280e0c5e29852a41038a
https://doi.org/10.1002/humu.24063

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CRISPR-Cas9 induces large structural variants at on-target and off-target sitesin vivothat segregate across generations

Autor: Adam Ameur, Anastasia Emmanouilidou, Rebecka Östlund, Selma Bozorgpana, Robin van Schendel, Ulf Gyllensten, Ida Höijer, Lars Feuk, Marcel den Hoed

To investigate the extent and distribution of unintended mutations induced by CRISPR-Cas9in vivo,we edited the genome of fertilized zebrafish eggs and investigated DNA from >1100 larvae, juvenile and adult fish in the F0 and F1 generations. Four guid

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::c88783bfa2e898727b15577d08477946
https://doi.org/10.1101/2021.10.05.463186

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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

Autor: Benedikt von der Heyde, Sitaf Jumaa, Marcel den Hoed, Hannah L. Brooke, Eugenia Mazzaferro, Olga Dethlefsen, Harold Snieder, Amin Allalou, Anastasia Emmanouilidou, Silvia Vicenzi, Erik Ingelsson, Adam Ameur, Eco J. C. de Geus, Ida Höijer, Tiffany Klingström

Publikováno v: Scientific Reports, Vol 10, Iss 1, Pp 1-18 (2020)
Scientific Reports, 10(1):11831. Nature Publishing Group
Scientific Reports
von der Heyde, B, Emmanouilidou, A, Mazzaferro, E, Vicenzi, S, Höijer, I, Klingström, T, Jumaa, S, Dethlefsen, O, Snieder, H, de Geus, E, Ameur, A, Ingelsson, E, Allalou, A, Brooke, H L & den Hoed, M 2020, ' Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image-and CRISPR/Cas9-based approach ', Scientific Reports, vol. 10, no. 1, 11831, pp. 1-18 . https://doi.org/10.1038/s41598-020-68567-1
Scientific Reports, 10(1):11831, 1-18. Nature Publishing Group

A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::21ac858e1d917bb4b3fa2029de2915c4
https://doi.org/10.1038/s41598-020-68567-1

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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

Autor: Susana Häggqvist, Ulf Gyllensten, Marie-Louise Bondeson, Anastasia Emmanouilidou, Sanna Gudmundsson, Adam Ameur, Ida Höijer, Marcel den Hoed, Josefin Johansson, Ignas Bunikis, Chen-Shan Chin, Lars Feuk, Maria Wilbe

Publikováno v: Genome Biology
Genome Biology, Vol 21, Iss 1, Pp 1-19 (2020)

BackgroundOne ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMRT-OTS and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b9c0f13f6fa0134bf6beceffa5672c5a
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-428344

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Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

Autor: Jochen B. W. Wolf, Matthias H. Weissensteiner, Olga Vinnere-Petterson, Andy Wing Chun Pang, Ida Höijer, Alexander Suh, Ignas Bunikis

Publikováno v: Genome Research. 27:697-708

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DN

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f920203eee0985f8e956b1f010107a76
https://doi.org/10.1101/gr.215095.116

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De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Autor: Johan Dahlberg, Adam Ameur, Susana Häggqvist, Jessica Nordlund, Ulf Gyllensten, Ida Höijer, Marcel Martin, Huiwen Che, Francesco Vezzi, Ignas Bunikis, Pall I Olason, Lars Feuk

Publikováno v: Genes, Vol 9, Iss 10, p 486 (2018)
Genes
Volume 9
Issue 10

The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we perfo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e2560d3c0aabfd40ca8669778eb10b6
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-369762

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Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

Autor: Ida, Höijer, Yu-Chih, Tsai, Tyson A, Clark, Paul, Kotturi, Niklas, Dahl, Eva-Lena, Stattin, Marie-Louise, Bondeson, Lars, Feuk, Ulf, Gyllensten, Adam, Ameur

Publikováno v: Human Mutation

Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine–cytosine (GC) content

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::46ca84264178504d90b0c154bc293e0c
https://pubmed.ncbi.nlm.nih.gov/29932473

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