1
|
Walton NA, Hafen B, Graceffo S, Sutherland N, Emmerson M, Palmquist R, Formea CM, Purcell M, Heale B, Brown MA, Danford CJ, Rachamadugu SI, Person TN, Shortt KA, Christensen GB, Evans JM, Raghunath S, Johnson CP, Knight S, Le VT, Anderson JL, Van Meter M, Reading T, Haslem DS, Hansen IC, Batcher B, Barker T, Sheffield TJ, Yandava B, Taylor DP, Ranade-Kharkar P, Giauque CC, Eyring KR, Breinholt JW, Miller MR, Carter PR, Gillman JL, Gunn AW, Knowlton KU, Bonkowsky JL, Stefansson K, Nadauld LD, McLeod HL. The Development of an Infrastructure to Facilitate the Use of Whole Genome Sequencing for Population Health. J Pers Med 2022; 12:jpm12111867. [PMID: 36579594 PMCID: PMC9693138 DOI: 10.3390/jpm12111867] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The clinical use of genomic analysis has expanded rapidly resulting in an increased availability and utility of genomic information in clinical care. We have developed an infrastructure utilizing informatics tools and clinical processes to facilitate the use of whole genome sequencing data for population health management across the healthcare system. Our resulting framework scaled well to multiple clinical domains in both pediatric and adult care, although there were domain specific challenges that arose. Our infrastructure was complementary to existing clinical processes and well-received by care providers and patients. Informatics solutions were critical to the successful deployment and scaling of this program. Implementation of genomics at the scale of population health utilizes complicated technologies and processes that for many health systems are not supported by current information systems or in existing clinical workflows. To scale such a system requires a substantial clinical framework backed by informatics tools to facilitate the flow and management of data. Our work represents an early model that has been successful in scaling to 29 different genes with associated genetic conditions in four clinical domains. Work is ongoing to optimize informatics tools; and to identify best practices for translation to smaller healthcare systems.
Collapse
Affiliation(s)
- Nephi A. Walton
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
- Correspondence:
| | - Brent Hafen
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Sara Graceffo
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Nykole Sutherland
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Melanie Emmerson
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Rachel Palmquist
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84108, USA
- Center for Personalized Medicine, Primary Children’s Hospital, Intermountain Healthcare, Salt Lake City, UT 84113, USA
| | - Christine M. Formea
- Department of Pharmacy, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Maricel Purcell
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Bret Heale
- Humanized Health Consulting, Salt Lake City, UT 84102, USA
| | | | | | - Sumathi I. Rachamadugu
- Department of Bioinformatics and Genomics, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas N. Person
- John Hopkins Genomics—DNA Diagnostics Laboratory, Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - G. Bryce Christensen
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Jared M. Evans
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Sharanya Raghunath
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Christopher P. Johnson
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Stacey Knight
- Department of Cardiology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Viet T. Le
- Department of Cardiology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Jeffrey L. Anderson
- Department of Cardiology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Margaret Van Meter
- Department of Medical Oncology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Teresa Reading
- Department of Surgery, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Derrick S. Haslem
- Department of Cardiology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Ivy C. Hansen
- School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Betsey Batcher
- Department of Endocrinology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Tyler Barker
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Travis J. Sheffield
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Bhaskara Yandava
- Digital Technology Services, Intermountain Healthcare, Salt Lake City, UT 84130, USA
| | - David P. Taylor
- Digital Technology Services, Intermountain Healthcare, Salt Lake City, UT 84130, USA
| | | | - Christopher C. Giauque
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Kenneth R. Eyring
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Jesse W. Breinholt
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Mickey R. Miller
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Payton R. Carter
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Jason L. Gillman
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Andrew W. Gunn
- Center for Personalized Medicine, Primary Children’s Hospital, Intermountain Healthcare, Salt Lake City, UT 84113, USA
| | - Kirk U. Knowlton
- Department of Cardiology, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Joshua L. Bonkowsky
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84108, USA
- Center for Personalized Medicine, Primary Children’s Hospital, Intermountain Healthcare, Salt Lake City, UT 84113, USA
| | | | - Lincoln D. Nadauld
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| | - Howard L. McLeod
- Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT 84107, USA
| |
Collapse
|
2
|
Teo CHY, Norhisham NHB, Lee OF, Png S, Chai CN, Yan G, Tang JW, Lee CK. Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting. Viruses 2022; 14:2208. [PMID: 36298763 DOI: 10.3390/v14102208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022] Open
Abstract
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar's test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.
Collapse
|
3
|
Webster AK, Hung A, Moore BT, Guzman R, Jordan JM, Kaplan REW, Hibshman JD, Tanny RE, Cook DE, Andersen E, Baugh LR. Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance. G3 (Bethesda) 2019; 9:3477-3488. [PMID: 31444297 PMCID: PMC6778785 DOI: 10.1534/g3.119.400617] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022]
Abstract
To understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the globe and whole-genome sequenced. As a result, hundreds of wild strains with known genome sequences can be used for genome-wide association studies (GWAS). However, phenotypic analysis of these strains can be laborious, particularly for quantitative traits requiring multiple measurements per strain. Starvation resistance is likely a fitness-proximal trait for nematodes, and it is related to metabolic disease risk in humans. However, natural variation in C. elegans starvation resistance has not been systematically characterized, and precise measurement of the trait is time-intensive. Here, we developed a population-selection-and-sequencing-based approach to phenotype starvation resistance in a pool of 96 wild strains. We used restriction site-associated DNA sequencing (RAD-seq) to infer the frequency of each strain among survivors in a mixed culture over time during starvation. We used manual starvation survival assays to validate the trait data, confirming that strains that increased in frequency over time are starvation-resistant relative to strains that decreased in frequency. Further, we found that variation in starvation resistance is significantly associated with variation at a region on chromosome III. Using a near-isogenic line (NIL), we showed the importance of this genomic interval for starvation resistance. This study demonstrates the feasibility of using population selection and sequencing in an animal model for phenotypic analysis of quantitative traits, documents natural variation of starvation resistance in C. elegans, and identifies a genomic region that contributes to such variation.
Collapse
Affiliation(s)
- Amy K Webster
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Anthony Hung
- Department of Biology, Duke University, Durham, NC
| | - Brad T Moore
- Department of Biology, Duke University, Durham, NC
| | - Ryan Guzman
- Department of Biology, Duke University, Durham, NC
| | | | - Rebecca E W Kaplan
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Jonathan D Hibshman
- Department of Biology, Duke University, Durham, NC
- University Program in Genetics and Genomics, Duke University, Durham, NC, and
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Erik Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC
| |
Collapse
|
4
|
Minosse C, Selleri M, Giombini E, Bartolini B, Capobianchi MR, Cerilli S, Loiacono L, Taibi C, D'Offizi G, McPhee F, Garbuglia A. Clinical and virological properties of hepatitis C virus genotype 4 infection in patients treated with different direct-acting antiviral agents. Infect Drug Resist 2018; 11:2117-2127. [PMID: 30464554 PMCID: PMC6223400 DOI: 10.2147/idr.s179158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The efficacy of direct-acting antivirals (DAAs) depends on the hepatitis C virus (HCV) genotype 4 (GT4) subtype which are used in the treatment of HCV. We aimed to retrospectively investigate the baseline prevalence of HCV NS5A and NS5B polymorphisms and their impact on virological outcome in GT4-infected patients treated with various DAA regimens. Patients and methods Available plasma samples from HCV GT4-infected patients treated with different DAA regimens were analyzed at baseline and after treatment failure, where applicable. Sanger sequencing of patient-derived NS5A and NS5B regions was performed on all available samples, while ultradeep pyrosequencing (UDPS) of NS5A and NS5B regions was performed only on samples from treatment failures at different time points. Results Sustained virological response (SVR) was achieved by 96% (48/50) of patients. Of 16 patients with baseline NS5A sequence, polymorphisms at amino acid positions associated with drug resistance were detected only at position 58: P58 (69.2%) and T58 (30.8%). Of 21 patients with baseline NS5B sequence, N142S was detected only in the two treatment failures, both with GT4d were treated with sofosbuvir (SOF)-based regimens, suggesting a potential involvement in SOF efficacy. Two patients (patient 1 [Pt1] and patient 2 [Pt2]) relapsed. In Pt1, NS5A-T56I and NS5A-Y93H/S emerged. In Pt2, NS5A-L28F emerged and a novel NS5B resistance-associated substitution (RAS), L204F, representing 1.5% of the viral population at baseline, enriched to 71% and 91.6% during and after treatment failure, respectively. UDPS of NS5B from Pt2 indicated a mixed infection of approximately 1:5, GT1a:GT4d, at baseline and GT4d during failure. Phylogenetic analysis of NS5A sequences indicated no clustering of HCV strains from patients achieving SVR vs patients who relapsed. The mean genetic distance in NS5A sequences was 5.8%, while a lower genetic distance (3.1%) was observed in NS5B sequences. Conclusion Results from these analyses confirm the importance of UDPS in the analysis of viral quasispecies variability and the identification of novel RASs potentially associated with DAA treatment failure in HCV GT4-infected patients.
Collapse
Affiliation(s)
- Claudia Minosse
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Marina Selleri
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Emanuela Giombini
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Barbara Bartolini
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Maria Rosaria Capobianchi
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Stefano Cerilli
- Clinical Department, Infectious Disease-Hepatology Unit, National Institute for Infectious Diseases, "Lazzaro Spallanzani" - IRCCS, Rome, Italy,
| | - Laura Loiacono
- Clinical Department, Infectious Disease-Hepatology Unit, National Institute for Infectious Diseases, "Lazzaro Spallanzani" - IRCCS, Rome, Italy,
| | - Chiara Taibi
- Clinical Department, Infectious Disease-Hepatology Unit, National Institute for Infectious Diseases, "Lazzaro Spallanzani" - IRCCS, Rome, Italy,
| | - Gianpiero D'Offizi
- Clinical Department, Infectious Disease-Hepatology Unit, National Institute for Infectious Diseases, "Lazzaro Spallanzani" - IRCCS, Rome, Italy,
| | - Fiona McPhee
- Bristol-Myers Squibb Research and Development, Wallingford, CT, USA
| | - AnnaRosa Garbuglia
- Department of Pre-clinical Research Epidemiology and Advanced Diagnostics, Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| |
Collapse
|
5
|
Ameur A, Che H, Martin M, Bunikis I, Dahlberg J, Höijer I, Häggqvist S, Vezzi F, Nordlund J, Olason P, Feuk L, Gyllensten U. De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data. Genes (Basel) 2018; 9:E486. [PMID: 30304863 DOI: 10.3390/genes9100486] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/21/2018] [Accepted: 10/05/2018] [Indexed: 12/16/2022] Open
Abstract
The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.
Collapse
|
6
|
Cheng CY, Tsai MS, Yang CJ, Cheng SH, Sun HY, Chang SF, Su LH, Su YC, Hung CC, Chang SY. Patterns of emergent resistance-associated mutations after initiation of non-nucleoside reverse-transcriptase inhibitor-containing antiretroviral regimens in Taiwan: a multicenter cohort study. Infect Drug Resist 2018; 11:849-859. [PMID: 29892199 PMCID: PMC5993039 DOI: 10.2147/idr.s158341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Increasing trends of resistance-associated mutations (RAMs) to non-nucleoside reverse-transcriptase inhibitors (nNRTIs) have raised concerns about the effectiveness of the regimens in the national HIV treatment programs in resource-limited countries. We aimed to retrospectively investigate the incidence and patterns of emergent RAMs of HIV-1 in HIV-positive adults experiencing virological failure to first-line nNRTI-containing combination antiretroviral therapy (cART) in Taiwan. Patients and methods Between June 2012 and March 2016, 1138 antiretroviral-naïve HIV-positive adults without baseline RAMs who initiated nNRTI-containing regimens were included for analysis. Virological failure was defined as plasma viral load (PVL) ≥200 copies/mL after 6 months of cART or confirmed PVL ≥200 copies/mL after achieving PVL <50 copies/mL. Population sequencing was retrospectively performed to detect baseline and emergent RAMs. RAMs were interpreted using the International AIDS Society-USA 2016 mutations list. Results Seventy-one patients (6.2%) developed virological failure, which occurred in 14.8% (43/291), 3.9% (26/675), and 1.2% (2/172) of patients receiving 2 nucleoside reverse-transcriptase inhibitors (NRTIs) plus nevirapine, efavirenz, and rilpivirine, respectively. Among those, 53 (74.6%) had emergent RAMs identified, which included 43 (81.1%), 53 (100.0%), and 1 (1.9%) with RAMs to NRTIs, nNRTIs, and protease inhibitors, respectively; and 43 (81.1%) had multi-drug resistance. The most common emergent RAMs to NRTIs were M184V/I (42.3%) and K65R (28.2%), and those to nNRTIs were Y181C (42.3%), K103N (15.5%), G190A/E/Q (12.7%), V179D/E (12.7%), and V108I (9.9%). Conclusion While the rates of virological failure varied with the nNRTI used, the rate of emergent RAMs of HIV-1 to NRTIs and nNRTIs among the antiretroviral-naïve patients who failed nNRTI-containing cART remained low.
Collapse
Affiliation(s)
- Chien-Yu Cheng
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.,School of Public Health, National Yang-Ming University, Taipei, Taiwan
| | - Mao-Song Tsai
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Chia-Jui Yang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shu-Hsing Cheng
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.,School of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Hsin-Yun Sun
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Fang Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Hsin Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ching Su
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Parasitology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,China Medical University, Taichung, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
7
|
Zhu YO, Sherlock G, Petrov DA. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3 (Bethesda) 2016; 6:2421-34. [PMID: 27317778 DOI: 10.1534/g3.116.029397] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker's/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.
Collapse
|
8
|
Abstract
In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus each sample archived in this way, consists of many unique genotypes and phenotypes. The effect of archiving on such a heterogeneous population is unknown. Here, we identified optimal archiving conditions for E. coli. We also used genome sequencing of archived samples to study the effects that archiving has on genomic population diversity. We observed no allele substitutions and mostly small changes in allele frequency. Nevertheless, principal component analysis of genome-scale allelic diversity shows that archiving affects diversity across many loci. We showed that this change in diversity is due to selection rather than drift. In addition, ∼1% of rare alleles that occurred at low frequencies were lost after treatment. Our observations imply that archived populations may be used to conduct fitness or other phenotypic assays of populations, in which the loss of a rare allele may have negligible effects. However, caution is appropriate when sequencing populations restarted from glycerol stocks, as well as when using glycerol stocks to restart or replay evolution. This is because the loss of rare alleles can alter the future evolutionary trajectory of a population if the lost alleles were strongly beneficial.
Collapse
Affiliation(s)
- Kathleen Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - José Aguilar-Rodríguez
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland The Santa Fe Institute, Santa Fe, NM, USA
| |
Collapse
|
9
|
Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Song J, Garcia JF, Sonstegard TS, Van Tassell CP, Schnabel RD, Taylor JF, Lewin HA, Liu GE. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res 2016; 23:253-62. [PMID: 27085184 PMCID: PMC4909312 DOI: 10.1093/dnares/dsw013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/29/2016] [Indexed: 11/14/2022] Open
Abstract
The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.
Collapse
Affiliation(s)
- Derek M Bickhart
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Lingyang Xu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Jana L Hutchison
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - John B Cole
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Daniel J Null
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | | | - Tad S Sonstegard
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | | | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Harris A Lewin
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - George E Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| |
Collapse
|
10
|
Dierynck I, Thys K, Ghys A, Sullivan JC, Kieffer TL, Aerssens J, Picchio G, De Meyer S. Deep-sequencing analysis of the gene encoding the hepatitis C virus nonstructural 3-4A protease confirms a low prevalence of telaprevir-resistant variants at baseline and the end of the REALIZE study. J Infect Dis 2014; 210:1871-80. [PMID: 24943725 DOI: 10.1093/infdis/jiu340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Population sequencing (PS) has shown that telaprevir-resistant variants are not typically detectable at baseline (prevalence, ≤5% of patients), and most variants present at the time of treatment failure are no longer detectable at the end of the study. METHODS To gain insight into the evolution of telaprevir-resistant variants, their baseline prevalence and persistence after treatment was investigated using a more sensitive, deep-sequencing (DS) technique in a large number of treatment-experienced patients from the REALIZE study who were infected with hepatitis C virus genotype 1. RESULTS Before treatment initiation, telaprevir-resistant variants (T54A, T54S, or R155K in 1%-2% of the viral population) were detected by DS in a fraction (2%) of patients for whom PS failed to detect resistance; these variants were not necessarily detected at the time of treatment failure. Of 49 patients in whom telaprevir-resistant variants were detected by PS at the time of treatment failure but not at the end of the study, DS revealed the presence of variants (V36A/L/M, T54S, or R155K in 1%-36% of the viral population) in 16 patients (33%) at the end of the study. CONCLUSIONS Similar to PS findings, DS analysis revealed that the frequency of telaprevir-resistant variants before treatment was also low, and variants detected at the time of treatment failure were no longer detectable in the majority of patients during follow-up.
Collapse
Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases, Beerse, Belgium
| | - Anne Ghys
- Janssen Infectious Diseases, Beerse, Belgium
| | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
| | | |
Collapse
|
11
|
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 2013; 76:718-27. [PMID: 23998490 PMCID: PMC4298792 DOI: 10.1111/tpj.12319] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/07/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
Collapse
Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
- For correspondence (e-mails ; )
| | - Gary J Muehlbauer
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
- University of Minnesota, Department of Plant BiologySt Paul, MN 55108, USA
- For correspondence (e-mails ; )
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA, 94720, USA
| | - Jarrod Chapman
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - María Muñoz-Amatriaín
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
| | - Timothy J Close
- Department of Botany & Plant Sciences, University of CaliforniaRiverside, CA, 92521, USA
| | - Roger P Wise
- US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State UniversityAmes, IA, 50011–1020, USA
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki/MTT Agrifood ResearchPO Box 65, 00014, Helsinki, Finland
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Klaus FX Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum MünchenD–85764, Neuherberg, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Jesse A Poland
- US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State UniversityManhattan, KS, 65506, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
| |
Collapse
|