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1. Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders

Author

Zhou, Bo, Arthur, Joseph G., Guo, Hanmin, Kim, Taeyoung, Huang, Yiling, Pattni, Reenal, Wang, Tao, Kundu, Soumya, Luo, Jay X.J., Lee, HoJoon, Nachun, Daniel C., Purmann, Carolin, Monte, Emma M., Weimer, Annika K., Qu, Ping-Ping, Shi, Minyi, Jiang, Lixia, Yang, Xinqiong, Fullard, John F., Bendl, Jaroslav, Girdhar, Kiran, Kim, Minsu, Chen, Xi, Greenleaf, William J., Duncan, Laramie, Ji, Hanlee P., Zhu, Xiang, Song, Giltae, Montgomery, Stephen B., Palejev, Dean, zu Dohna, Heinrich, Roussos, Panos, Kundaje, Anshul, Hallmayer, Joachim F., Snyder, Michael P., Wong, Wing H., and Urban, Alexander E.

Published
2024
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2. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

Author

Replogle, Joseph M, Norman, Thomas M, Xu, Albert, Hussmann, Jeffrey A, Chen, Jin, Cogan, J Zachery, Meer, Elliott J, Terry, Jessica M, Riordan, Daniel P, Srinivas, Niranjan, Fiddes, Ian T, Arthur, Joseph G, Alvarado, Luigi J, Pfeiffer, Katherine A, Mikkelsen, Tarjei S, Weissman, Jonathan S, and Adamson, Britt

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Genetics, Biological Sciences, Human Genome, Biotechnology, Prevention, Generic health relevance, CRISPR-Cas Systems, Gene Expression Regulation, Gene Targeting, HEK293 Cells, High-Throughput Nucleotide Sequencing, Humans, Nucleic Acid Amplification Techniques, RNA, Guide, Kinetoplastida, Single-Cell Analysis, Transcriptome
Abstract

Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.

Published
2020

4. A loss-of-function variant in ALOX15 protects against nasal polyps and chronic rhinosinusitis

Author

Kristjansson, Ragnar P., Benonisdottir, Stefania, Davidsson, Olafur B., Oddsson, Asmundur, Tragante, Vinicius, Sigurdsson, Jon K., Stefansdottir, Lilja, Jonsson, Stefan, Jensson, Brynjar O., Arthur, Joseph G., Arnadottir, Gudny A., Sulem, Gerald, Halldorsson, Bjarni V., Gunnarsson, Bjarni, Halldorsson, Gisli H., Stefansson, Olafur A., Oskarsson, Gudjon R., Deaton, Aimee M., Olafsson, Isleifur, Eyjolfsson, Gudmundur I., Sigurdardottir, Olof, Onundarson, Pall T., Gislason, David, Gislason, Thorarinn, Ludviksson, Bjorn R., Ludviksdottir, Dora, Olafsdottir, Thorunn A., Rafnar, Thorunn, Masson, Gisli, Zink, Florian, Bjornsdottir, Gyda, Magnusson, Olafur Th., Bjornsdottir, Unnur S., Thorleifsson, Gudmar, Norddahl, Gudmundur L., Gudbjartsson, Daniel F., Thorsteinsdottir, Unnur, Jonsdottir, Ingileif, Sulem, Patrick, and Stefansson, Kari

Published
2019
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5. Automatic Detection of Complex Structural Genome Variation Across Human Populations and in Brains of Individuals with Psychiatric Disorders

Author

Zhou, Bo, primary, Arthur, Joseph G., additional, Guo, Hanmin, additional, Kim, Taeyoung, additional, Huang, Yiling, additional, Pattni, Reenal, additional, Kundu, Soumya, additional, Luo, Jay X. J., additional, Lee, HoJoon, additional, Wang, Tao, additional, Purmann, Carolin, additional, Monte, Emma M., additional, Weimer, Annika, additional, Qu, Pingping, additional, Shi, Minyi, additional, Jiang, Lixia, additional, Yang, Xinqiong, additional, Fullard, John, additional, Bendl, Jaroslav, additional, Girdhar, Kiran, additional, Chen, Xi, additional, Consortium, PsychENCODE, additional, Duncan, Laramie, additional, Ji, Hanlee P., additional, Dohna, Heinrich zu, additional, Palajev, Dean, additional, Song, Giltae, additional, Zhu, Xiang, additional, Rousos, Panos, additional, Kundaje, Anshul, additional, Hallmayer, Joachim F., additional, Snyder, Michael, additional, Wong, Wing H., additional, and Urban, Alexander E., additional

Published
2023
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8. Sequence variants associating with urinary biomarkers

Author

Onderzoek Precision medicine, Circulatory Health, Team Medisch, Benonisdottir, Stefania, Kristjansson, Ragnar P, Oddsson, Asmundur, Steinthorsdottir, Valgerdur, Mikaelsdottir, Evgenia, Kehr, Birte, Jensson, Brynjar O, Arnadottir, Gudny A, Sulem, Gerald, Sveinbjornsson, Gardar, Kristmundsdottir, Snaedis, Ivarsdottir, Erna V, Vogel, Lotte K, Tragante, Vinicius, Gunnarsson, Bjarni, Runolfsdottir, Hrafnhildur Linnet, Arthur, Joseph G, Deaton, Aimee M, Eyjolfsson, Gudmundur I, Davidsson, Olafur B, Asselbergs, Folkert W, Hreidarsson, Astradur B, Rafnar, Thorunn, Thorleifsson, Gudmar, Edvardsson, Vidar, Sigurdsson, Gunnar, Helgadottir, Anna, Halldorsson, Bjarni V, Masson, Gisli, Holm, Hilma, Onundarson, Pall T, Indridason, Olafur S, Benediktsson, Rafn, Palsson, Runolfur, Gudbjartsson, Daniel F, Olafsson, Isleifur, Thorsteinsdottir, Unnur, Sulem, Patrick, Stefansson, Kari, Onderzoek Precision medicine, Circulatory Health, Team Medisch, Benonisdottir, Stefania, Kristjansson, Ragnar P, Oddsson, Asmundur, Steinthorsdottir, Valgerdur, Mikaelsdottir, Evgenia, Kehr, Birte, Jensson, Brynjar O, Arnadottir, Gudny A, Sulem, Gerald, Sveinbjornsson, Gardar, Kristmundsdottir, Snaedis, Ivarsdottir, Erna V, Vogel, Lotte K, Tragante, Vinicius, Gunnarsson, Bjarni, Runolfsdottir, Hrafnhildur Linnet, Arthur, Joseph G, Deaton, Aimee M, Eyjolfsson, Gudmundur I, Davidsson, Olafur B, Asselbergs, Folkert W, Hreidarsson, Astradur B, Rafnar, Thorunn, Thorleifsson, Gudmar, Edvardsson, Vidar, Sigurdsson, Gunnar, Helgadottir, Anna, Halldorsson, Bjarni V, Masson, Gisli, Holm, Hilma, Onundarson, Pall T, Indridason, Olafur S, Benediktsson, Rafn, Palsson, Runolfur, Gudbjartsson, Daniel F, Olafsson, Isleifur, Thorsteinsdottir, Unnur, Sulem, Patrick, and Stefansson, Kari

Published
2019

9. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

Author

Zhou, Bo, primary, Ho, Steve S, additional, Greer, Stephanie U, additional, Spies, Noah, additional, Bell, John M, additional, Zhang, Xianglong, additional, Zhu, Xiaowei, additional, Arthur, Joseph G, additional, Byeon, Seunggyu, additional, Pattni, Reenal, additional, Saha, Ishan, additional, Huang, Yiling, additional, Song, Giltae, additional, Perrin, Dimitri, additional, Wong, Wing H, additional, Ji, Hanlee P, additional, Abyzov, Alexej, additional, and Urban, Alexander E, additional

Published
2019
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10. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Author

Zhou, Bo, primary, Ho, Steve S., additional, Greer, Stephanie U., additional, Zhu, Xiaowei, additional, Bell, John M., additional, Arthur, Joseph G., additional, Spies, Noah, additional, Zhang, Xianglong, additional, Byeon, Seunggyu, additional, Pattni, Reenal, additional, Ben-Efraim, Noa, additional, Haney, Michael S., additional, Haraksingh, Rajini R., additional, Song, Giltae, additional, Ji, Hanlee P., additional, Perrin, Dimitri, additional, Wong, Wing H., additional, Abyzov, Alexej, additional, and Urban, Alexander E., additional

Published
2019
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12. Detection of complex structural variation from paired-end sequencing data

Author

Arthur, Joseph G., Chen, Xi, Zhou, Bo, Urban, Alexander E., and Wong, Wing Hung

Abstract

Detecting structural variants (SVs) from sequencing data is key to genome analysis, but methods using standard whole-genome sequencing (WGS) data are typically incapable of resolving complex SVs with multiple co-located breakpoints. We introduce the ARC-SV method, which uses a probabilistic model to detect arbitrary local rearrangements from WGS data. Our method performs well on simple SVs while surpassing state-of-the-art methods in complex SV detection.

Published
2017
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13. Sequence variants associating with urinary biomarkers

Author

Benonisdottir, Stefania, primary, Kristjansson, Ragnar P, additional, Oddsson, Asmundur, additional, Steinthorsdottir, Valgerdur, additional, Mikaelsdottir, Evgenia, additional, Kehr, Birte, additional, Jensson, Brynjar O, additional, Arnadottir, Gudny A, additional, Sulem, Gerald, additional, Sveinbjornsson, Gardar, additional, Kristmundsdottir, Snaedis, additional, Ivarsdottir, Erna V, additional, Tragante, Vinicius, additional, Gunnarsson, Bjarni, additional, Runolfsdottir, Hrafnhildur Linnet, additional, Arthur, Joseph G, additional, Deaton, Aimee M, additional, Eyjolfsson, Gudmundur I, additional, Davidsson, Olafur B, additional, Asselbergs, Folkert W, additional, Hreidarsson, Astradur B, additional, Rafnar, Thorunn, additional, Thorleifsson, Gudmar, additional, Edvardsson, Vidar, additional, Sigurdsson, Gunnar, additional, Helgadottir, Anna, additional, Halldorsson, Bjarni V, additional, Masson, Gisli, additional, Holm, Hilma, additional, Onundarson, Pall T, additional, Indridason, Olafur S, additional, Benediktsson, Rafn, additional, Palsson, Runolfur, additional, Gudbjartsson, Daniel F, additional, Olafsson, Isleifur, additional, Thorsteinsdottir, Unnur, additional, Sulem, Patrick, additional, and Stefansson, Kari, additional

Published
2018
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14. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

Author

Zhou, Bo, primary, Ho, Steve S., additional, Greer, Stephanie U., additional, Spies, Noah, additional, Bell, John M., additional, Zhang, Xianglong, additional, Zhu, Xiaowei, additional, Arthur, Joseph G., additional, Byeon, Seunggyu, additional, Pattni, Reenal, additional, Saha, Ishan, additional, Huang, Yiling, additional, Song, Giltae, additional, Perrin, Dimitri, additional, Wong, Wing H., additional, Ji, Hanlee P., additional, Abyzov, Alexej, additional, and Urban, Alexander E., additional

Published
2018
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15. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Author

Zhou, Bo, primary, Ho, Steve S., additional, Greer, Stephanie U., additional, Zhu, Xiaowei, additional, Bell, John M., additional, Arthur, Joseph G., additional, Spies, Noah, additional, Zhang, Xianglong, additional, Byeon, Seunggyu, additional, Pattni, Reenal, additional, Ben-Efraim, Noa, additional, Haney, Michael S., additional, Haraksingh, Rajini R., additional, Ji, Hanlee P., additional, Song, Giltae, additional, Perrin, Dimitri, additional, Wong, Wing H., additional, Abyzov, Alexej, additional, and Urban, Alexander E., additional

Published
2017
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16. Automatic detection of complex structural genome variation across world populations

Author

Zhou, Bo, primary, Arthur, Joseph G., additional, Guo, Hanmin, additional, Hughes, Christopher R., additional, Kim, Taeyoung, additional, Huang, Yiling, additional, Pattni, Reenal, additional, Lee, HoJoon, additional, Ji, Hanlee P., additional, Song, Giltae, additional, Palejev, Dean, additional, Zhu, Xiang, additional, Wong, Wing H., additional, and Urban, Alexander E., additional

Published
2017
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18. Sequence variants associating with urinary biomarkers.

Author

Benonisdottir, Stefania, Kristjansson, Ragnar P, Oddsson, Asmundur, Steinthorsdottir, Valgerdur, Mikaelsdottir, Evgenia, Kehr, Birte, Jensson, Brynjar O, Arnadottir, Gudny A, Sulem, Gerald, Sveinbjornsson, Gardar, Kristmundsdottir, Snaedis, Ivarsdottir, Erna V, Tragante, Vinicius, Gunnarsson, Bjarni, Runolfsdottir, Hrafnhildur Linnet, Arthur, Joseph G, Deaton, Aimee M, Eyjolfsson, Gudmundur I, Davidsson, Olafur B, and Asselbergs, Folkert W

Published
2019
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19. A loss-of-function variant in ALOX15protects against nasal polyps and chronic rhinosinusitis

Author

Kristjansson, Ragnar P., Benonisdottir, Stefania, Davidsson, Olafur B., Oddsson, Asmundur, Tragante, Vinicius, Sigurdsson, Jon K., Stefansdottir, Lilja, Jonsson, Stefan, Jensson, Brynjar O., Arthur, Joseph G., Arnadottir, Gudny A., Sulem, Gerald, Halldorsson, Bjarni V., Gunnarsson, Bjarni, Halldorsson, Gisli H., Stefansson, Olafur A., Oskarsson, Gudjon R., Deaton, Aimee M., Olafsson, Isleifur, Eyjolfsson, Gudmundur I., Sigurdardottir, Olof, Onundarson, Pall T., Gislason, David, Gislason, Thorarinn, Ludviksson, Bjorn R., Ludviksdottir, Dora, Olafsdottir, Thorunn A., Rafnar, Thorunn, Masson, Gisli, Zink, Florian, Bjornsdottir, Gyda, Magnusson, Olafur Th., Bjornsdottir, Unnur S., Thorleifsson, Gudmar, Norddahl, Gudmundur L., Gudbjartsson, Daniel F., Thorsteinsdottir, Unnur, Jonsdottir, Ingileif, Sulem, Patrick, and Stefansson, Kari

Abstract

Nasal polyps (NP) are lesions on the nasal and paranasal sinus mucosa and are a risk factor for chronic rhinosinusitis (CRS). We performed genome-wide association studies on NP and CRS in Iceland and the UK (using UK Biobank data) with 4,366 NP cases, 5,608 CRS cases, and >700,000 controls. We found 10 markers associated with NP and 2 with CRS. We also tested 210 markers reported to associate with eosinophil count, yielding 17 additional NP associations. Of the 27 NP signals, 7 associate with CRS and 13 with asthma. Most notably, a missense variant in ALOX15that causes a p.Thr560Met alteration in arachidonate 15-lipoxygenase (15-LO) confers large genome-wide significant protection against NP (P=8.0 × 10−27, odds ratio = 0.32; 95% confidence interval = 0.26, 0.39) and CRS (P=1.1 × 10−8, odds ratio = 0.64; 95% confidence interval = 0.55, 0.75). p.Thr560Met, carried by around 1 in 20 Europeans, was previously shown to cause near total loss of 15-LO enzymatic activity. Our findings identify 15-LO as a potential target for therapeutic intervention in NP and CRS.

Published
2019
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