1
|
Cameron P, Fuller CK, Donohoue PD, Jones BN, Thompson MS, Carter MM, Gradia S, Vidal B, Garner E, Slorach EM, Lau E, Banh LM, Lied AM, Edwards LS, Settle AH, Capurso D, Llaca V, Deschamps S, Cigan M, Young JK, May AP. Author Correction: Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat Methods 2023:10.1038/s41592-023-02114-4. [PMID: 37945910 DOI: 10.1038/s41592-023-02114-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
| | | | | | - Brittnee N Jones
- Caribou Biosciences, Berkeley, California, USA
- Omicia, Inc., Oakland, California, USA
| | | | | | | | | | | | | | - Elaine Lau
- Caribou Biosciences, Berkeley, California, USA
| | | | | | | | | | | | | | | | - Mark Cigan
- DuPont Pioneer, Johnston, Iowa, USA
- Genus Research, DeForest, Wisconsin, USA
| | | | - Andrew P May
- Caribou Biosciences, Berkeley, California, USA.
- Chan Zuckerberg Biohub, San Francisco, California, USA.
| |
Collapse
|
2
|
Zheng M, Tian SZ, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu JJ, Li Z, Wong CH, Ngan CY, Wang P, Ruan X, Wei CL, Ruan Y. Multiplex chromatin interactions with single-molecule precision. Nature 2019; 566:558-562. [PMID: 30778195 DOI: 10.1038/s41586-019-0949-1] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 01/16/2019] [Indexed: 12/25/2022]
Abstract
The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus1. Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C)2, and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)3, have revealed topologically associating domains4 with frequent chromatin contacts, and have identified chromatin loops mediated by specific protein factors for insulation and regulation of transcription5-7. However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C8 potentially overcomes this issue, this method may be limited by the sparsity of data that is inherent to current single-cell assays. Recent advances in microfluidics have opened opportunities for droplet-based genomic analysis9 but this approach has not yet been adapted for chromatin interaction analysis. Here we describe a strategy for multiplex chromatin-interaction analysis via droplet-based and barcode-linked sequencing, which we name ChIA-Drop. We demonstrate the robustness of ChIA-Drop in capturing complex chromatin interactions with single-molecule precision, which has not been possible using methods based on population-level pairwise contacts. By applying ChIA-Drop to Drosophila cells, we show that chromatin topological structures predominantly consist of multiplex chromatin interactions with high heterogeneity; ChIA-Drop also reveals promoter-centred multivalent interactions, which provide topological insights into transcription.
Collapse
Affiliation(s)
- Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Daniel Capurso
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Emaly Piecuch
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jacqueline Jufen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Zhihui Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Chee Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. .,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA. .,Huazhong Agricultural University, Wuhan, China.
| |
Collapse
|
3
|
Gernone G, Montemurro M, Capurso D, Colucci G, Dell'Anna D, Detomaso F, La Rosa R, La Volpe M, Partipilo F, Pepe V, Ripa E. SP489MID-TERM EVALUATION OF THE NEW MEDIUM CUT-OFF FILTER (THERANOVA) ON REMOVAL EFFICIENCY AND QUALITY OF LIFE. Nephrol Dial Transplant 2018. [DOI: 10.1093/ndt/gfy104.sp489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Giuseppe Gernone
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - M Montemurro
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - D Capurso
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - G Colucci
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - D Dell'Anna
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - F Detomaso
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - R La Rosa
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - M La Volpe
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - F Partipilo
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - V Pepe
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| | - E Ripa
- Nephrology and Dialisys of "Santa Maria degli Angeli" Hospital, ASL BA - Bari, Putignano, Italy
| |
Collapse
|
4
|
Cameron P, Fuller CK, Donohoue PD, Jones BN, Thompson MS, Carter MM, Gradia S, Vidal B, Garner E, Slorach EM, Lau E, Banh LM, Lied AM, Edwards LS, Settle AH, Capurso D, Llaca V, Deschamps S, Cigan M, Young JK, May AP. Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat Methods 2017; 14:600-606. [PMID: 28459459 DOI: 10.1038/nmeth.4284] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/06/2017] [Indexed: 12/22/2022]
Abstract
RNA-guided CRISPR-Cas9 endonucleases are widely used for genome engineering, but our understanding of Cas9 specificity remains incomplete. Here, we developed a biochemical method (SITE-Seq), using Cas9 programmed with single-guide RNAs (sgRNAs), to identify the sequence of cut sites within genomic DNA. Cells edited with the same Cas9-sgRNA complexes are then assayed for mutations at each cut site using amplicon sequencing. We used SITE-Seq to examine Cas9 specificity with sgRNAs targeting the human genome. The number of sites identified depended on sgRNA sequence and nuclease concentration. Sites identified at lower concentrations showed a higher propensity for off-target mutations in cells. The list of off-target sites showing activity in cells was influenced by sgRNP delivery, cell type and duration of exposure to the nuclease. Collectively, our results underscore the utility of combining comprehensive biochemical identification of off-target sites with independent cell-based measurements of activity at those sites when assessing nuclease activity and specificity.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Elaine Lau
- Caribou Biosciences, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, Russ C, Reece-Hoyes JS, Nye C, Gradia S, Vidal B, Zheng J, Hoffman GR, Fuller CK, May AP. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks. Mol Cell 2016; 63:633-646. [PMID: 27499295 DOI: 10.1016/j.molcel.2016.06.037] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 12/16/2022]
Abstract
The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.
Collapse
Affiliation(s)
| | | | | | | | - Elizabeth Frias
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John S Reece-Hoyes
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Scott Gradia
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA
| | | | | | - Gregory R Hoffman
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Andrew P May
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA.
| |
Collapse
|
6
|
Capurso D, Bengtsson H, Segal MR. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res 2016; 44:2028-35. [PMID: 26869583 PMCID: PMC4797302 DOI: 10.1093/nar/gkw070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/25/2016] [Indexed: 11/14/2022] Open
Abstract
The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions.
Collapse
Affiliation(s)
- Daniel Capurso
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| |
Collapse
|
7
|
Capurso D, Segal MR. Distance-based assessment of the localization of functional annotations in 3D genome reconstructions. BMC Genomics 2014; 15:992. [PMID: 25407917 PMCID: PMC4254257 DOI: 10.1186/1471-2164-15-992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 11/04/2014] [Indexed: 11/20/2022] Open
Abstract
Background Recent studies used the contact data or three-dimensional (3D) genome reconstructions from Hi-C (chromosome conformation capture with next-generation sequencing) to assess the co-localization of functional genomic annotations in the nucleus. These analyses dichotomized data point pairs belonging to a functional annotation as “close” or “far” based on some threshold and then tested for enrichment of “close” pairs. We propose an alternative approach that avoids dichotomization of the data and instead directly estimates the significance of distances within the 3D reconstruction. Results We applied this approach to 3D genome reconstructions for Plasmodium falciparum, the causative agent of malaria, and Saccharomyces cerevisiae and compared the results to previous approaches. We found significant 3D co-localization of centromeres, telomeres, virulence genes, and several sets of genes with developmentally regulated expression in P. falciparum; and significant 3D co-localization of centromeres and long terminal repeats in S. cerevisiae. Additionally, we tested the experimental observation that telomeres form three to seven clusters in P. falciparum and S. cerevisiae. Applying affinity propagation clustering to telomere coordinates in the 3D reconstructions yielded six telomere clusters for both organisms. Conclusions Distance-based assessment replicated key findings, while avoiding dichotomization of the data (which previously yielded threshold-sensitive results). Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-992) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94107, USA.
| |
Collapse
|
8
|
Abstract
It is widely recognized that the three-dimensional (3D) architecture of eukaryotic chromatin plays an important role in processes such as gene regulation and cancer-driving gene fusions. Observing or inferring this 3D structure at even modest resolutions had been problematic, since genomes are highly condensed and traditional assays are coarse. However, recently devised high-throughput molecular techniques have changed this situation. Notably, the development of a suite of chromatin conformation capture (CCC) assays has enabled elicitation of contacts-spatially close chromosomal loci-which have provided insights into chromatin architecture. Most analysis of CCC data has focused on the contact level, with less effort directed toward obtaining 3D reconstructions and evaluating the accuracy and reproducibility thereof. While questions of accuracy must be addressed experimentally, questions of reproducibility can be addressed statistically-the purpose of this paper. We use a constrained optimization technique to reconstruct chromatin configurations for a number of closely related yeast datasets and assess reproducibility using four metrics that measure the distance between 3D configurations. The first of these, Procrustes fitting, measures configuration closeness after applying reflection, rotation, translation, and scaling-based alignment of the structures. The others base comparisons on the within-configuration inter-point distance matrix. Inferential results for these metrics rely on suitable permutation approaches. Results indicate that distance matrix-based approaches are preferable to Procrustes analysis, not because of the metrics per se but rather on account of the ability to customize permutation schemes to handle within-chromosome contiguity. It has recently been emphasized that the use of constrained optimization approaches to 3D architecture reconstruction are prone to being trapped in local minima. Our methods of reproducibility assessment provide a means for comparing 3D reconstruction solutions so that we can discern between local and global optima by contrasting solutions under perturbed inputs.
Collapse
Affiliation(s)
- Mark R Segal
- Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
| | - Hao Xiong
- Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
| | - Daniel Capurso
- Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
| | - Mariel Vazquez
- Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
| | - Javier Arsuaga
- Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, San Francisco, CA 94143, USADepartment of Mathematics, San Francisco State University, San Francisco, CA 94132, USA
| |
Collapse
|
9
|
Capurso D, Xiong H, Segal MR. A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome. BMC Genomics 2012; 13:630. [PMID: 23153121 PMCID: PMC3559892 DOI: 10.1186/1471-2164-13-630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/09/2012] [Indexed: 02/05/2023] Open
Abstract
Background Applying supervised learning/classification techniques to epigenomic data may reveal properties that differentiate histone modifications. Previous analyses sought to classify nucleosomes containing histone H2A/H4 arginine 3 symmetric dimethylation (H2A/H4R3me2s) or H2A.Z using human CD4+ T-cell chromatin immunoprecipitation sequencing (ChIP-Seq) data. However, these efforts only achieved modest accuracy with limited biological interpretation. Here, we investigate the impact of using appropriate data pre-processing —deduplication, normalization, and position- (peak-) finding to identify stable nucleosome positions — in conjunction with advanced classification algorithms, notably discriminatory motif feature selection and random forests. Performance assessments are based on accuracy and interpretative yield. Results We achieved dramatically improved accuracy using histone modification features (99.0%; previous attempts, 68.3%) and DNA sequence features (94.1%; previous attempts, <60%). Furthermore, the algorithms elicited interpretable features that withstand permutation testing, including: the histone modifications H4K20me3 and H3K9me3, which are components of heterochromatin; and the motif TCCATT, which is part of the consensus sequence of satellite II and III DNA. Downstream analysis demonstrates that satellite II and III DNA in the human genome is occupied by stable nucleosomes containing H2A/H4R3me2s, H4K20me3, and/or H3K9me3, but not 18 other histone methylations. These results are consistent with the recent biochemical finding that H4R3me2s provides a binding site for the DNA methyltransferase (Dnmt3a) that methylates satellite II and III DNA. Conclusions Classification algorithms applied to appropriately pre-processed ChIP-Seq data can accurately discriminate between histone modifications. Algorithms that facilitate interpretation, such as discriminatory motif feature selection, have the added potential to impart information about underlying biological mechanism.
Collapse
Affiliation(s)
- Daniel Capurso
- Department of Bioengineering and Therapeutic Sciences, San Francisco, CA, USA
| | | | | |
Collapse
|
10
|
Torgerson DG, Capurso D, Ampleford EJ, Li X, Moore WC, Gignoux CR, Hu D, Eng C, Mathias RA, Busse WW, Castro M, Erzurum SC, Fitzpatrick AM, Gaston B, Israel E, Jarjour NN, Teague WG, Wenzel SE, Rodríguez-Santana JR, Rodríguez-Cintrón W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C, Nicolae DL. Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects. J Allergy Clin Immunol 2012; 130:622-629.e9. [PMID: 22607992 DOI: 10.1016/j.jaci.2012.03.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 02/22/2012] [Accepted: 03/06/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genetic variants that contribute to asthma susceptibility might be present at varying frequencies in different populations, which is an important consideration and advantage for performing genetic association studies in admixed populations. OBJECTIVE We sought to identify asthma-associated loci in African American subjects. METHODS We compared local African and European ancestry estimated from dense single nucleotide polymorphism genotype data in African American adults with asthma and nonasthmatic control subjects. Allelic tests of association were performed within the candidate regions identified, correcting for local European admixture. RESULTS We identified a significant ancestry association peak on chromosome 6q. Allelic tests for association within this region identified a single nucleotide polymorphism (rs1361549) on 6q14.1 that was associated with asthma exclusively in African American subjects with local European admixture (odds ratio, 2.2). The risk allele is common in Europe (42% in the HapMap population of Utah residents with Northern and Western European ancestry from the Centre d'Etude du Polymorphisme Humain collection) but absent in West Africa (0% in the HapMap population of Yorubans in Ibadan, Nigeria), suggesting the allele is present in African American subjects because of recent European admixture. We replicated our findings in Puerto Rican subjects and similarly found that the signal of association is largely specific to subjects who are heterozygous for African and non-African ancestry at 6q14.1. However, we found no evidence for association in European American or Puerto Rican subjects in the absence of local African ancestry, suggesting that the association with asthma at rs1361549 is due to an environmental or genetic interaction. CONCLUSION We identified a novel asthma-associated locus that is relevant to admixed populations with African ancestry and highlight the importance of considering local ancestry in genetic association studies of admixed populations.
Collapse
Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Il 60637, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedón JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KC, Ober C, Nicolae DL. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet 2011; 43:887-92. [PMID: 21804549 PMCID: PMC3445408 DOI: 10.1038/ng.888] [Citation(s) in RCA: 637] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 06/16/2011] [Indexed: 11/09/2022]
Abstract
Asthma is a common disease with a complex risk architecture including both genetic and environmental factors. We performed a meta-analysis of North American genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of European American, African American or African Caribbean, and Latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. We identified five susceptibility loci. Four were at previously reported loci on 17q21, near IL1RL1, TSLP and IL33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. In addition, we identified a new asthma susceptibility locus at PYHIN1, with the association being specific to individuals of African descent (P = 3.9 × 10(-9)). These results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma.
Collapse
Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Bagchi A, Papazoglu C, Wu Y, Capurso D, Brodt M, Francis D, Bredel M, Vogel H, Mills AA. CHD5 is a tumor suppressor at human 1p36. Cell 2007; 128:459-75. [PMID: 17289567 DOI: 10.1016/j.cell.2006.11.052] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 10/24/2006] [Accepted: 11/27/2006] [Indexed: 01/25/2023]
Abstract
Cancer gene discovery has relied extensively on analyzing tumors for gains and losses to reveal the location of oncogenes and tumor suppressor genes, respectively. Deletions of 1p36 are extremely common genetic lesions in human cancer, occurring in malignancies of epithelial, neural, and hematopoietic origin. Although this suggests that 1p36 harbors a gene that drives tumorigenesis when inactivated, the identity of this tumor suppressor has remained elusive. Here we use chromosome engineering to generate mouse models with gain and loss of a region corresponding to human 1p36. This approach functionally identifies chromodomain helicase DNA binding domain 5 (Chd5) as a tumor suppressor that controls proliferation, apoptosis, and senescence via the p19(Arf)/p53 pathway. We demonstrate that Chd5 functions as a tumor suppressor in vivo and implicate deletion of CHD5 in human cancer. Identification of this tumor suppressor provides new avenues for exploring innovative clinical interventions for cancer.
Collapse
Affiliation(s)
- Anindya Bagchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Morrone LF, Capurso D, D'Elia F, Di Paolo S, Grandaliano G, Marangi AL, Schena A, Stallone G, Tarantino G. [Herpetic viruses and renal transplantation]. G Ital Nefrol 2002; 19:316-25. [PMID: 12195400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Over the last few years emerging evidence indicate the involvement of herpes viruses in the pathogenesis of several medical complications in transplanted patients. Herpes viruses are transmitted via inter-human contact and cause a primary infection, which commonly fails to give clinical signs and may persist even for years in a latent state in healthy subjects. In transplanted patients, herpes viruses may be transmitted through the transplanted organ or may be reactivated because of the use of powerful immunosuppressive drugs. Moreover, the persistence of immunosuppression greatly favours the clinical expression and severity of virus infection. Thus, herpes viruses seem to be involved in both acute and chronic deterioration of graft function, in the pathogenesis of post-transplant lymphoproliferative disorders and Kaposi sarcoma, and even in vessel atherosclerosis. This review will focus on relevant clinical aspects of herpes-virus infection, namely cytomegalovirus, EBV, herpes simplex 1 and 2, varicella zoster virus, HHV-6, HHV-7 and HHV-8, in kidney transplanted patients.
Collapse
Affiliation(s)
- L F Morrone
- U.O. Nefrologia e Dialisi Policlinico di Bari.
| | | | | | | | | | | | | | | | | |
Collapse
|