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  1. AU="Munugala, Chetan"
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  1. Article: Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction.

    Boocock, James / Alexander, Noah / Tapia, Leslie Alamo / Walter-McNeill, Laura / Munugala, Chetan / Bloom, Joshua S / Kruglyak, Leonid

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene ... ...

    Abstract Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in
    Language English
    Publishing date 2023-12-21
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.07.570640
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA.

    Guo, Longhua / Boocock, James / Hilt, Evann E / Chandrasekaran, Sukantha / Zhang, Yi / Munugala, Chetan / Sathe, Laila / Alexander, Noah / Arboleda, Valerie A / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Yang, Shangxin / Garner, Omai B / Yin, Yi / Bloom, Joshua S / Kruglyak, Leonid

    BMC genomics

    2022  Volume 23, Issue 1, Page(s) 260

    Abstract: Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide ... ...

    Abstract Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks.
    Methods: The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020.
    Results: We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region.
    Conclusion: Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.
    MeSH term(s) COVID-19/epidemiology ; Disease Outbreaks ; Genomics ; Humans ; Los Angeles/epidemiology ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-04-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08488-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Genomic epidemiology of the Los Angeles COVID-19 outbreak

    Guo, Longhua / Boocock, James / Hilt, Evann / Chandrasekaran, Sukantha / Zhang, Yi / Munugala, Chetan / Sathe, Laila / Alexander, Noah / Arboleda, Valerie A. / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Yang, Shangxin / Garner, Omai B / Yin, Yi / Bloom, Joshua S / Kruglyak, Leonid

    medRxiv

    Abstract: Los Angeles (LA) County has sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history of SARS-CoV-2 in LA County, we sequenced 142 viral genomes from unique patients seeking care ... ...

    Abstract Los Angeles (LA) County has sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history of SARS-CoV-2 in LA County, we sequenced 142 viral genomes from unique patients seeking care at UCLA Health System. 86 of these genomes are from samples collected before April 19, 2020. We found that the early outbreak in LA, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a US-specific strain, B.1.43, which has been found predominantly in California and Washington State. While samples from LA County carry the ancestral B.1.43 genome, viral genomes from neighbouring counties in California and from counties in Washington State carry additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but may have been undermined by the many introductions of SARS-CoV-2 into the region. Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the U.S. to have coordinated inter-state responses to the pandemic.
    Keywords covid19
    Language English
    Publishing date 2020-09-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.09.15.20194712
    Database COVID19

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  4. Article: Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing.

    Bloom, Joshua S / Sathe, Laila / Munugala, Chetan / Jones, Eric M / Gasperini, Molly / Lubock, Nathan B / Yarza, Fauna / Thompson, Erin M / Kovary, Kyle M / Park, Jimin / Marquette, Dawn / Kay, Stephania / Lucas, Mark / Love, TreQuan / Booeshaghi, A Sina / Brandenberg, Oliver F / Guo, Longhua / Boocock, James / Hochman, Myles /
    Simpkins, Scott W / Lin, Isabella / LaPierre, Nathan / Hong, Duke / Zhang, Yi / Oland, Gabriel / Choe, Bianca Judy / Chandrasekaran, Sukantha / Hilt, Evann E / Butte, Manish J / Damoiseaux, Robert / Kravit, Clifford / Cooper, Aaron R / Yin, Yi / Pachter, Lior / Garner, Omai B / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Kosuri, Sriram / Kruglyak, Leonid / Arboleda, Valerie A

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of ... ...

    Abstract The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission
    Keywords covid19
    Language English
    Publishing date 2021-03-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.08.04.20167874
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.

    Bloom, Joshua S / Sathe, Laila / Munugala, Chetan / Jones, Eric M / Gasperini, Molly / Lubock, Nathan B / Yarza, Fauna / Thompson, Erin M / Kovary, Kyle M / Park, Jimin / Marquette, Dawn / Kay, Stephania / Lucas, Mark / Love, TreQuan / Sina Booeshaghi, A / Brandenberg, Oliver F / Guo, Longhua / Boocock, James / Hochman, Myles /
    Simpkins, Scott W / Lin, Isabella / LaPierre, Nathan / Hong, Duke / Zhang, Yi / Oland, Gabriel / Choe, Bianca Judy / Chandrasekaran, Sukantha / Hilt, Evann E / Butte, Manish J / Damoiseaux, Robert / Kravit, Clifford / Cooper, Aaron R / Yin, Yi / Pachter, Lior / Garner, Omai B / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Kosuri, Sriram / Kruglyak, Leonid / Arboleda, Valerie A

    Nature biomedical engineering

    2021  Volume 5, Issue 7, Page(s) 657–665

    Abstract: Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing ... ...

    Abstract Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.
    MeSH term(s) High-Throughput Nucleotide Sequencing ; Humans ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Saliva/virology ; Sensitivity and Specificity
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-07-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-021-00754-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

    Bloom, Joshua S. / Jones, Eric M. / Gasperini, Molly / Lubock, Nathan B. / Sathe, Laila / Munugala, Chetan / Booeshaghi, A. Sina / Brandenberg, Oliver F. / Guo, Longhua / Simpkins, Scott W. / Lin, Isabella / LaPierre, Nathan / Hong, Duke / Zhang, Yi / Oland, Gabriel / Choe, Bianca Judy / Chandrasekaran, Sukantha / Hilt, Evann E. / Butte, Manish J. /
    Damoiseaux, Robert / Cooper, Aaron R. / Yin, Yi / Pachter, Lior / Garner, Omai B. / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Kosuri, Sriram / Kruglyak, Leonid / Arboleda, Valerie A.

    medRxiv

    Abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission. Frequent, widespread testing of the asymptomatic population for ... ...

    Abstract The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.
    Keywords covid19
    Language English
    Publishing date 2020-08-06
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.08.04.20167874
    Database COVID19

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  7. Article ; Online: Swab-Seq

    Bloom, Joshua / Jones, Eric / Gasperini, Molly / Lubock, Nathan / Sathe, Laila / Munugala, Chetan / Booeshaghi, Sina / Brandenberg, Oliver / Guo, Longhua / Boocock, James / Simpkins, Scott / Lin, Isabella / LaPierre, Nathan / Hong, Duke / Zhang, Yi / Oland, Gabriel / Choe, Bianca Judy / Chandrasekaran, Sukantha / Hilt, Evann /
    Butte, Manish / Damoiseaux, Robert / Cooper, Aaron / Yin, Yi / Pachter, Lior / Garner, Omai / Flint, Jonathan / Eskin, Eleazar / Luo, Chongyuan / Kosuri, Sriram / Kruglyak, Leonid / Arboleda, Valerie

    A high-throughput platform for massively scaled up SARS-CoV-2 testing

    2020  

    Abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission. Frequent, widespread testing of the asymptomatic population for ... ...

    Abstract The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.
    Keywords covid19
    Publishing date 2020-08-06
    Publisher eScholarship, University of California
    Publishing country us
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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