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Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M. A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment. Sci Rep 2024; 14:5583. [PMID: 38448490 PMCID: PMC10917763 DOI: 10.1038/s41598-024-56402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024] Open
Abstract
In this report, we present OLAF-Seq, a novel strategy to construct a long-read sequencing library such that adjacent fragments are linked with end-terminal duplications. We use the CRISPR-Cas9 nickase enzyme and a pool of multiple sgRNAs to perform non-random fragmentation of targeted long DNA molecules (> 300kb) into smaller library-sized fragments (about 20 kbp) in a manner so as to retain physical linkage information (up to 1000 bp) between adjacent fragments. DNA molecules targeted for fragmentation are preferentially ligated with adaptors for sequencing, so this method can enrich targeted regions while taking advantage of the long-read sequencing platforms. This enables the sequencing of target regions with significantly lower total coverage, and the genome sequence within linker regions provides information for assembly and phasing. We demonstrated the validity and efficacy of the method first using phage and then by sequencing a panel of 100 full-length cancer-related genes (including both exons and introns) in the human genome. When the designed linkers contained heterozygous genetic variants, long haplotypes could be established. This sequencing strategy can be readily applied in both PacBio and Oxford Nanopore platforms for both long and short genes with an easy protocol. This economically viable approach is useful for targeted enrichment of hundreds of target genomic regions and where long no-gap contigs need deep sequencing.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Christina Huan Shi
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Danielle Piazza
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Kevin Y Yip
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA.
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Schmidt M, Kutzner A. MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads. Genome Biol 2023; 24:170. [PMID: 37461107 DOI: 10.1186/s13059-023-03009-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA .
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Affiliation(s)
- Markus Schmidt
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-Ro, Seongdong-Gu, Seoul, 133-791, Republic of Korea.
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3
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Cleal K, Baird DM. Dysgu: efficient structural variant calling using short or long reads. Nucleic Acids Res 2022; 50:e53. [PMID: 35100420 PMCID: PMC9122538 DOI: 10.1093/nar/gkac039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/20/2021] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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4
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Jadhao S, Davison CL, Roulis EV, Schoeman EM, Divate M, Haring M, Williams C, Shankar AJ, Lee S, Pecheniuk NM, Irving DO, Hyland CA, Flower RL, Nagaraj SH. RBCeq: A robust and scalable algorithm for accurate genetic blood typing. EBioMedicine 2022; 76:103759. [PMID: 35033986 PMCID: PMC8763639 DOI: 10.1016/j.ebiom.2021.103759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
Background While blood transfusion is an essential cornerstone of hematological care, patients requiring repetitive transfusion remain at persistent risk of alloimmunization due to the diversity of human blood group polymorphisms. Despite the promise, user friendly methods to accurately identify blood types from next-generation sequencing data are currently lacking. To address this unmet need, we have developed RBCeq, a novel genetic blood typing algorithm to accurately identify 36 blood group systems. Methods RBCeq can predict complex blood groups such as RH, and ABO that require identification of small indels and copy number variants. RBCeq also reports clinically significant, rare, and novel variants with potential clinical relevance that may lead to the identification of novel blood group alleles. Findings The RBCeq algorithm demonstrated 99·07% concordance when validated on 402 samples which included 29 antigens with serology and 9 antigens with SNP-array validation in 14 blood group systems and 59 antigens validation on manual predicted phenotype from variant call files. We have also developed a user-friendly web server that generates detailed blood typing reports with advanced visualization (https://www.rbceq.org/). Interpretation RBCeq will assist blood banks and immunohematology laboratories by overcoming existing methodological limitations like scalability, reproducibility, and accuracy when genotyping and phenotyping in multi-ethnic populations. This Amazon Web Services (AWS) cloud based platform has the potential to reduce pre-transfusion testing time and to increase sample processing throughput, ultimately improving quality of patient care. Funding This work was supported in part by Advance Queensland Research Fellowship, MRFF Genomics Health Futures Mission (76,757), and the Australian Red Cross LifeBlood. The Australian governments fund the Australian Red Cross Lifeblood for the provision of blood, blood products and services to the Australian community.
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Affiliation(s)
- Sudhir Jadhao
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Candice L Davison
- Australian Red Cross Lifeblood Research and Development, Brisbane, Queensland, Australia
| | - Eileen V Roulis
- Australian Red Cross Lifeblood Research and Development, Brisbane, Queensland, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Elizna M Schoeman
- Australian Red Cross Lifeblood Research and Development, Brisbane, Queensland, Australia
| | - Mayur Divate
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Mitchel Haring
- Office of eResearch, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Chris Williams
- Office of eResearch, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Arvind Jaya Shankar
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Simon Lee
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Natalie M Pecheniuk
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - David O Irving
- Research and Development, Australian Red Cross Blood Service, Sydney, New South Wales, Australia
| | - Catherine A Hyland
- Australian Red Cross Lifeblood Research and Development, Brisbane, Queensland, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Robert L Flower
- Australian Red Cross Lifeblood Research and Development, Brisbane, Queensland, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia; Translational Research Institute, Brisbane, Australia.
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5
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Ramachandran A, Lumetta SS, Klee EW, Chen D. HELLO: improved neural network architectures and methodologies for small variant calling. BMC Bioinformatics 2021; 22:404. [PMID: 34391391 PMCID: PMC8364080 DOI: 10.1186/s12859-021-04311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning have enabled the application of Deep Neural Networks to variant calling, surpassing the accuracy of classical approaches in many settings. DeepVariant, arguably the most popular among such methods, transforms the problem of variant calling into one of image recognition where a Deep Neural Network analyzes sequencing data that is formatted as images, achieving high accuracy. In this paper, we explore an alternative approach to designing Deep Neural Networks for variant calling, where we use meticulously designed Deep Neural Network architectures and customized variant inference functions that account for the underlying nature of sequencing data instead of converting the problem to one of image recognition. RESULTS Results from 27 whole-genome variant calling experiments spanning Illumina, PacBio and hybrid Illumina-PacBio settings suggest that our method allows vastly smaller Deep Neural Networks to outperform the Inception-v3 architecture used in DeepVariant for indel and substitution-type variant calls. For example, our method reduces the number of indel call errors by up to 18%, 55% and 65% for Illumina, PacBio and hybrid Illumina-PacBio variant calling respectively, compared to a similarly trained DeepVariant pipeline. In these cases, our models are between 7 and 14 times smaller. CONCLUSIONS We believe that the improved accuracy and problem-specific customization of our models will enable more accurate pipelines and further method development in the field. HELLO is available at https://github.com/anands-repo/hello.
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Affiliation(s)
- Anand Ramachandran
- Department of Electrical and Computer Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, 61801, USA
| | - Steven S Lumetta
- Department of Electrical and Computer Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eric W Klee
- Biomedical Statistics and Informatics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Deming Chen
- Department of Electrical and Computer Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, 61801, USA.
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6
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van Belzen IAEM, Schönhuth A, Kemmeren P, Hehir-Kwa JY. Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. NPJ Precis Oncol 2021; 5:15. [PMID: 33654267 PMCID: PMC7925608 DOI: 10.1038/s41698-021-00155-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
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Affiliation(s)
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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7
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Chen L, Pryce JE, Hayes BJ, Daetwyler HD. Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle. Animals (Basel) 2021; 11:ani11020541. [PMID: 33669735 PMCID: PMC7922624 DOI: 10.3390/ani11020541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Structural variants are large changes to the DNA sequences that differ from individual to individual. We discovered and quality-controlled a set of 24,908 structural variants and used a technique called imputation to infer them into 35,588 Holstein and Jersey cattle. We then investigated whether the structural variants affected key dairy cattle traits such as milk production, fertility and overall conformation. Structural variants explained generally less than 10 percent of the phenotypic variation in these traits. Four of the structural variants were significantly associated with dairy cattle production traits. However, the inclusion of the structural variants in the genomic prediction model did not increase genomic prediction accuracy. Abstract Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.
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Affiliation(s)
- Long Chen
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (L.C.); (J.E.P.); (B.J.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Jennie E. Pryce
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (L.C.); (J.E.P.); (B.J.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Ben J. Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (L.C.); (J.E.P.); (B.J.H.)
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (L.C.); (J.E.P.); (B.J.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
- Correspondence:
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8
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Zhou X, Zhang L, Weng Z, Dill DL, Sidow A. Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads. Nat Commun 2021; 12:1077. [PMID: 33597536 PMCID: PMC7889865 DOI: 10.1038/s41467-021-21395-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023] Open
Abstract
We introduce Aquila, a new approach to variant discovery in personal genomes, which is critical for uncovering the genetic contributions to health and disease. Aquila uses a reference sequence and linked-read data to generate a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. The contigs of the assemblies from our libraries cover >95% of the human reference genome, with over 98% of that in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased Variant Call Format (VCF) file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective approach that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.
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Affiliation(s)
- Xin Zhou
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Lu Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ziming Weng
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Arend Sidow
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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9
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A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. Genes (Basel) 2020; 11:genes11111350. [PMID: 33202901 PMCID: PMC7697454 DOI: 10.3390/genes11111350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022] Open
Abstract
The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still elusive. Here, we juxtaposed GRCh38 with a high-contiguity genome assembly of one Korean (AK1) to show that a part of AK1 genome is missing in GRCh38 and that the missing regions harbored ~1390 putative coding elements. Furthermore, we found that multiple populations shared some certain parts in the missing genome when we analyzed the “unmapped” (to GRCh38) reads of fourteen individuals (five East-Asians, four Europeans, and five Africans), amounting to ~5.3 Mb (~0.2% of AK1) of the total genomic regions. The recovered AK1 regions from the “unmapped reads”, which were the estimated missing regions that did not exist in GRCh38, harbored candidate coding elements. We verified that most of the common (shared by ≥7 individuals) missing regions exist in human and chimpanzee DNA. Moreover, we further identified the occurrence mechanism and ethnic heterogeneity as well as the presence of the common missing regions. This study illuminates a potential advantage of using a pangenome reference and brings up the need for further investigations on the various features of regions globally missed in GRCh38.
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10
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Wohlers I, Künstner A, Munz M, Olbrich M, Fähnrich A, Calonga-Solís V, Ma C, Hirose M, El-Mosallamy S, Salama M, Busch H, Ibrahim S. An integrated personal and population-based Egyptian genome reference. Nat Commun 2020; 11:4719. [PMID: 32948767 PMCID: PMC7501257 DOI: 10.1038/s41467-020-17964-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/24/2020] [Indexed: 02/05/2023] Open
Abstract
A small number of de novo assembled human genomes have been reported to date, and few have been complemented with population-based genetic variation, which is particularly important for North Africa, a region underrepresented in current genome-wide references. Here, we combine long- and short-read whole-genome sequencing data with recent assembly approaches into a de novo assembly of an Egyptian genome. The assembly demonstrates well-balanced quality metrics and is complemented with variant phasing via linked reads into haploblocks, which we associate with gene expression changes in blood. To construct an Egyptian genome reference, we identify genome-wide genetic variation within a cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genome references. Thus, the Egyptian genome reference will be a valuable resource for precision medicine.
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Affiliation(s)
- Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Matthias Munz
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Michael Olbrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Verónica Calonga-Solís
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Brazil
| | - Caixia Ma
- Novogene (UK) Company Limited, 25 Cambridge Science Park, Milton Road, CB4 0FW, Cambridge, UK
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Shaaban El-Mosallamy
- Medical Experimental Research Center (MERC), Mansoura University, Elgomhouria St., Dakahlia Governorate, 35516, Mansoura, Egypt
| | - Mohamed Salama
- Medical Experimental Research Center (MERC), Mansoura University, Elgomhouria St., Dakahlia Governorate, 35516, Mansoura, Egypt
- Institute of Global Health and Human Ecology, The American University in Cairo, AUC avenue, 11835, Cairo, Egypt
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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11
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Yang L. A Practical Guide for Structural Variation Detection in the Human Genome. CURRENT PROTOCOLS IN HUMAN GENETICS 2020; 107:e103. [PMID: 32813322 PMCID: PMC7738216 DOI: 10.1002/cphg.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Profiling genetic variants-including single nucleotide variants, small insertions and deletions, copy number variations, and structural variations (SVs)-from both healthy individuals and individuals with disease is a key component of genetic and biomedical research. SVs are large-scale changes in the genome and involve breakage and rejoining of DNA fragments. They may affect thousands to millions of nucleotides and can lead to loss, gain, and reshuffling of genes and regulatory elements. SVs are known to impact gene expression and potentially result in altered phenotypes and diseases. Therefore, identifying SVs from the human genomes is particularly important. In this review, I describe advantages and disadvantages of the available high-throughput assays for the discovery of SVs, which are the most challenging genetic alterations to detect. A practical guide is offered to suggest the most suitable strategies for discovering different types of SVs including common germline, rare, somatic, and complex variants. I also discuss factors to be considered, such as cost and performance, for different strategies when designing experiments. Last, I present several approaches to identify potential SV artifacts caused by samples, experimental procedures, and computational analysis. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- Lixing Yang
- Ben May Department for Cancer Research, Department of Human Genetics, University of Chicago, Chicago, Illinois
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12
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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13
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Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol 2019; 20:246. [PMID: 31747936 PMCID: PMC6868818 DOI: 10.1186/s13059-019-1828-7] [Citation(s) in RCA: 298] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/19/2019] [Indexed: 02/08/2023] Open
Abstract
Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution—giving rise to the differences within populations and among species. Nevertheless, characterizing SVs and determining the optimal approach for a given experimental design remains a computational and scientific challenge. Multiple approaches have emerged to target various SV classes, zygosities, and size ranges. Here, we review these approaches with respect to their ability to infer SVs across the full spectrum of large, complex variations and present computational methods for each approach.
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Affiliation(s)
- Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
| | - Nastassia Gobet
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Diana Ivette Cruz-Dávalos
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ninon Mounier
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Christophe Dessimoz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London, UK. .,Department of Computer Science, University College London, London, UK.
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA.
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14
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Haghshenas E, Sahinalp SC, Hach F. lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinformatics 2019; 35:20-27. [PMID: 30561550 DOI: 10.1093/bioinformatics/bty544] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 06/28/2018] [Indexed: 02/01/2023] Open
Abstract
Motivation Recent advances in genomics and precision medicine have been made possible through the application of high throughput sequencing (HTS) to large collections of human genomes. Although HTS technologies have proven their use in cataloging human genome variation, computational analysis of the data they generate is still far from being perfect. The main limitation of Illumina and other popular sequencing technologies is their short read length relative to the lengths of (common) genomic repeats. Newer (single molecule sequencing - SMS) technologies such as Pacific Biosciences and Oxford Nanopore are producing longer reads, making it theoretically possible to overcome the difficulties imposed by repeat regions. Unfortunately, because of their high sequencing error rate, reads generated by these technologies are very difficult to work with and cannot be used in many of the standard downstream analysis pipelines. Note that it is not only difficult to find the correct mapping locations of such reads in a reference genome, but also to establish their correct alignment so as to differentiate sequencing errors from real genomic variants. Furthermore, especially since newer SMS instruments provide higher throughput, mapping and alignment need to be performed much faster than before, maintaining high sensitivity. Results We introduce lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint. Availability and implementation lordFAST is implemented in C++ and supports multi-threading. The source code of lordFAST is available at https://github.com/vpc-ccg/lordfast. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ehsan Haghshenas
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - S Cenk Sahinalp
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.,School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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15
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Whitford W, Lehnert K, Snell RG, Jacobsen JC. Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data. J Biomed Inform 2019; 94:103174. [PMID: 30965134 DOI: 10.1016/j.jbi.2019.103174] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/12/2019] [Accepted: 04/06/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Whole genome sequencing (WGS) has increased in popularity and decreased in cost over the past decade, rendering this approach as a viable and sensitive method for variant detection. In addition to its utility for single nucleotide variant detection, WGS data has the potential to detect Copy Number Variants (CNV) to fine resolution. Many CNV detection software packages have been developed exploiting four main types of data: read pair, split read, read depth, and assembly based methods. The aim of this study was to evaluate the efficiency of each of these main approaches in detecting germline deletions. METHODS WGS data and high confidence deletion calls for the individual NA12878 from the Genome in a Bottle consortium were the benchmark dataset. The performance of BreakDancer, CNVnator, Delly, FermiKit, and Pindel was assessed by comparing the accuracy and sensitivity of each software package in detecting deletions exceeding 1 kb. RESULTS There was considerable variability in the outputs of the different WGS CNV detection programs. The best performance was seen from BreakDancer and Delly, with 92.6% and 96.7% sensitivity, respectively and 34.5% and 68.5% false discovery rate (FDR), respectively. In comparison, Pindel, CNVnator, and FermiKit were less effective with sensitivities of 69.1%, 66.0%, and 15.8%, respectively and FDR of 91.3%, 69.0%, and 31.7%, respectively. Concordance across software packages was poor, with only 27 of the total 612 benchmark deletions identified by all five methodologies. CONCLUSIONS The WGS based CNV detection tools evaluated show disparate performance in identifying deletions ≥1 kb, particularly those utilising different input data characteristics. Software that exploits read pair based data had the highest sensitivity, namely BreakDancer and Delly. BreakDancer also had the second lowest false discovery rate. Therefore, in this analysis read pair methods (BreakDancer in particular) were the best performing approaches for the identification of deletions ≥1 kb, balancing accuracy and sensitivity. There is potential for improvement in the detection algorithms, particularly for reducing FDR. This analysis has validated the utility of WGS based CNV detection software to reliably identify deletions, and these findings will be of use when choosing appropriate software for deletion detection, in both research and diagnostic medicine.
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Affiliation(s)
- Whitney Whitford
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Klaus Lehnert
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Russell G Snell
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
| | - Jessie C Jacobsen
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; Centre for Brain Research, The University of Auckland, New Zealand.
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16
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Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat Commun 2019; 10:1025. [PMID: 30833565 PMCID: PMC6399254 DOI: 10.1038/s41467-019-08992-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 01/10/2023] Open
Abstract
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome. Large structural variants (SV) are understudied in human genetics research because of the difficulty to detect them in the routinely generated short-read sequencing data. Here, the authors generate optical genome maps of 154 individuals from 26 populations that allow comprehensive examination of large SVs.
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17
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Hehir-Kwa JY, Tops BBJ, Kemmeren P. The clinical implementation of copy number detection in the age of next-generation sequencing. Expert Rev Mol Diagn 2018; 18:907-915. [PMID: 30221560 DOI: 10.1080/14737159.2018.1523723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.
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Affiliation(s)
- Jayne Y Hehir-Kwa
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Bastiaan B J Tops
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Patrick Kemmeren
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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18
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Affiliation(s)
- Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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19
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Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res 2018. [PMID: 29535149 PMCID: PMC5880247 DOI: 10.1101/gr.221028.117] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA's performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs and substantially improves detection performance for variants in the 20–300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (<1000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types and found that short templated-sequence insertions occur in ∼4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized (50–300 bp) SVs.
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Affiliation(s)
- Jeremiah A Wala
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Bioinformatics and Integrative Genomics, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pratiti Bandopadhayay
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Noah F Greenwald
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Ryan O'Rourke
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Ted Sharpe
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Chip Stewart
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Steve Schumacher
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Yilong Li
- Seven Bridges Genomics, Cambridge, Massachusetts 02142, USA.,Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Joachim Weischenfeldt
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Xiaotong Yao
- Tri-Institutional PhD Program in Computational Biology and Medicine, New York, New York 10065, USA.,New York Genome Center, New York, New York 10013, USA
| | - Chad Nusbaum
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Bioinformatics and Integrative Genomics, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Bioinformatics and Integrative Genomics, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cheng-Zhong Zhang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marcin Imielinski
- New York Genome Center, New York, New York 10013, USA.,Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
| | - Rameen Beroukhim
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Bioinformatics and Integrative Genomics, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
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