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  1. Article ; Online: The Michigan Genomics Initiative

    Matthew Zawistowski / Lars G. Fritsche / Anita Pandit / Brett Vanderwerff / Snehal Patil / Ellen M. Schmidt / Peter VandeHaar / Cristen J. Willer / Chad M. Brummett / Sachin Kheterpal / Xiang Zhou / Michael Boehnke / Gonçalo R. Abecasis / Sebastian Zöllner

    Cell Genomics, Vol 3, Iss 2, Pp 100257- (2023)

    A biobank linking genotypes and electronic clinical records in Michigan Medicine patients

    2023  

    Abstract: Summary: Biobanks of linked clinical patient histories and biological samples are an efficient strategy to generate large cohorts for modern genetics research. Biobank recruitment varies by factors such as geographic catchment and sampling strategy, ... ...

    Abstract Summary: Biobanks of linked clinical patient histories and biological samples are an efficient strategy to generate large cohorts for modern genetics research. Biobank recruitment varies by factors such as geographic catchment and sampling strategy, which affect biobank demographics and research utility. Here, we describe the Michigan Genomics Initiative (MGI), a single-health-system biobank currently consisting of >91,000 participants recruited primarily during surgical encounters at Michigan Medicine. The surgical enrollment results in a biobank enriched for many diseases and ideally suited for a disease genetics cohort. Compared with the much larger population-based UK Biobank, MGI has higher prevalence for nearly all diagnosis-code-based phenotypes and larger absolute case counts for many phenotypes. Genome-wide association study (GWAS) results replicate known findings, thereby validating the genetic and clinical data. Our results illustrate that opportunistic biobank sampling within single health systems provides a unique and complementary resource for exploring the genetics of complex diseases.
    Keywords Genetics ; QH426-470 ; Internal medicine ; RC31-1245
    Subject code 610
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

    Liron Ganel / Lei Chen / Ryan Christ / Jagadish Vangipurapu / Erica Young / Indraniel Das / Krishna Kanchi / David Larson / Allison Regier / Haley Abel / Chul Joo Kang / Alexandra Scott / Aki Havulinna / Charleston W. K. Chiang / Susan Service / Nelson Freimer / Aarno Palotie / Samuli Ripatti / Johanna Kuusisto /
    Michael Boehnke / Markku Laakso / Adam Locke / Nathan O. Stitziel / Ira M. Hall

    Human Genomics, Vol 15, Iss 1, Pp 1-

    2021  Volume 17

    Abstract: Abstract Background Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a ... ...

    Abstract Abstract Background Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combination of the number of mitochondria per cell and cell-type composition. Here, we studied MT-CN variation in blood-derived DNA from 19184 Finnish individuals using a combination of genome (N = 4163) and exome sequencing (N = 19034) data as well as imputed genotypes (N = 17718). Results We identified two loci significantly associated with MT-CN variation: a common variant at the MYB-HBS1L locus (P = 1.6 × 10−8), which has previously been associated with numerous hematological parameters; and a burden of rare variants in the TMBIM1 gene (P = 3.0 × 10−8), which has been reported to protect against non-alcoholic fatty liver disease. We also found that MT-CN is strongly associated with insulin levels (P = 2.0 × 10−21) and other metabolic syndrome (metS)-related traits. Using a Mendelian randomization framework, we show evidence that MT-CN measured in blood is causally related to insulin levels. We then applied an MT-CN polygenic risk score (PRS) derived from Finnish data to the UK Biobank, where the association between the PRS and metS traits was replicated. Adjusting for cell counts largely eliminated these signals, suggesting that MT-CN affects metS via cell-type composition. Conclusion These results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.
    Keywords Metabolic syndrome ; Mitochondrial content ; Human genetics ; Human genome sequencing ; Genome-wide association studies ; Mendelian randomization ; Medicine ; R ; Genetics ; QH426-470
    Subject code 610
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans

    Jedidiah Carlson / Adam E. Locke / Matthew Flickinger / Matthew Zawistowski / Shawn Levy / Richard M. Myers / Michael Boehnke / Hyun Min Kang / Laura J. Scott / Jun Z. Li / Sebastian Zöllner / The BRIDGES Consortium

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 13

    Abstract: Germline mutation rate is a critical parameter in the study of genetics and evolution. Here, Carlson et al. infer fine-scale patterns of human mutation rate heterogeneity by analyzing ~36 million singleton variants from 3560 whole-genome sequences. ...

    Abstract Germline mutation rate is a critical parameter in the study of genetics and evolution. Here, Carlson et al. infer fine-scale patterns of human mutation rate heterogeneity by analyzing ~36 million singleton variants from 3560 whole-genome sequences.
    Keywords Science ; Q
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans

    Jedidiah Carlson / Adam E. Locke / Matthew Flickinger / Matthew Zawistowski / Shawn Levy / Richard M. Myers / Michael Boehnke / Hyun Min Kang / Laura J. Scott / Jun Z. Li / Sebastian Zöllner / The BRIDGES Consortium

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 13

    Abstract: Germline mutation rate is a critical parameter in the study of genetics and evolution. Here, Carlson et al. infer fine-scale patterns of human mutation rate heterogeneity by analyzing ~36 million singleton variants from 3560 whole-genome sequences. ...

    Abstract Germline mutation rate is a critical parameter in the study of genetics and evolution. Here, Carlson et al. infer fine-scale patterns of human mutation rate heterogeneity by analyzing ~36 million singleton variants from 3560 whole-genome sequences.
    Keywords Science ; Q
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Identification of genetic effects underlying type 2 diabetes in South Asian and European populations

    Marie Loh / Weihua Zhang / Hong Kiat Ng / Katharina Schmid / Amel Lamri / Lin Tong / Meraj Ahmad / Jung-Jin Lee / Maggie C. Y. Ng / Lauren E. Petty / Cassandra N. Spracklen / Fumihiko Takeuchi / Md. Tariqul Islam / Farzana Jasmine / Anuradhani Kasturiratne / Muhammad Kibriya / Karen L. Mohlke / Guillaume Paré / Gauri Prasad /
    Mohammad Shahriar / Miao Ling Chee / H. Janaka de Silva / James C. Engert / Hertzel C. Gerstein / K. Radha Mani / Charumathi Sabanayagam / Marijana Vujkovic / Ananda R. Wickremasinghe / Tien Yin Wong / Chittaranjan S. Yajnik / Salim Yusuf / Habibul Ahsan / Dwaipayan Bharadwaj / Sonia S. Anand / Jennifer E. Below / Michael Boehnke / Donald W. Bowden / Giriraj R. Chandak / Ching-Yu Cheng / Norihiro Kato / Anubha Mahajan / Xueling Sim / Mark I. McCarthy / Andrew P. Morris / Jaspal S. Kooner / Danish Saleheen / John C. Chambers

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Marie Loh, Weihua Zhang et al. use a genome-wide association study meta-analysis to examine variants associated with Type 2 diabetes (T2D) in South Asian and European ancestry cohorts. Their results provide further insights into the genetic mechanisms ... ...

    Abstract Marie Loh, Weihua Zhang et al. use a genome-wide association study meta-analysis to examine variants associated with Type 2 diabetes (T2D) in South Asian and European ancestry cohorts. Their results provide further insights into the genetic mechanisms underlying T2D across ancestral populations.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci

    Xianyong Yin / Lap Sum Chan / Debraj Bose / Anne U. Jackson / Peter VandeHaar / Adam E. Locke / Christian Fuchsberger / Heather M. Stringham / Ryan Welch / Ketian Yu / Lilian Fernandes Silva / Susan K. Service / Daiwei Zhang / Emily C. Hector / Erica Young / Liron Ganel / Indraniel Das / Haley Abel / Michael R. Erdos /
    Lori L. Bonnycastle / Johanna Kuusisto / Nathan O. Stitziel / Ira M. Hall / Gregory R. Wagner / FinnGen / Jian Kang / Jean Morrison / Charles F. Burant / Francis S. Collins / Samuli Ripatti / Aarno Palotie / Nelson B. Freimer / Karen L. Mohlke / Laura J. Scott / Xiaoquan Wen / Eric B. Fauman / Markku Laakso / Michael Boehnke

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 14

    Abstract: The Finnish population is enriched for genetic variants which are rare in other populations. Here, the authors find new genetic loci associated with 1391 circulating metabolites in 6136 Finnish men, demonstrating that metabolite genetic associations can ... ...

    Abstract The Finnish population is enriched for genetic variants which are rare in other populations. Here, the authors find new genetic loci associated with 1391 circulating metabolites in 6136 Finnish men, demonstrating that metabolite genetic associations can help elucidate disease mechanisms.
    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Author Correction

    Marie Loh / Weihua Zhang / Hong Kiat Ng / Katharina Schmid / Amel Lamri / Lin Tong / Meraj Ahmad / Jung-Jin Lee / Maggie C. Y. Ng / Lauren E. Petty / Cassandra N. Spracklen / Fumihiko Takeuchi / Md. Tariqul Islam / Farzana Jasmine / Anuradhani Kasturiratne / Muhammad Kibriya / Karen L. Mohlke / Guillaume Paré / Gauri Prasad /
    Mohammad Shahriar / Miao Ling Chee / H. Janaka de Silva / James C. Engert / Hertzel C. Gerstein / K. Radha Mani / Charumathi Sabanayagam / Marijana Vujkovic / Ananda R. Wickremasinghe / Tien Yin Wong / Chittaranjan S. Yajnik / Salim Yusuf / Habibul Ahsan / Dwaipayan Bharadwaj / Sonia S. Anand / Jennifer E. Below / Michael Boehnke / Donald W. Bowden / Giriraj R. Chandak / Ching-Yu Cheng / Norihiro Kato / Anubha Mahajan / Xueling Sim / Mark I. McCarthy / Andrew P. Morris / Jaspal S. Kooner / Danish Saleheen / John C. Chambers

    Communications Biology, Vol 5, Iss 1, Pp 1-

    Identification of genetic effects underlying type 2 diabetes in South Asian and European populations

    2022  Volume 1

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

    David Z. Pan / Kristina M. Garske / Marcus Alvarez / Yash V. Bhagat / James Boocock / Elina Nikkola / Zong Miao / Chelsea K. Raulerson / Rita M. Cantor / Mete Civelek / Craig A. Glastonbury / Kerrin S. Small / Michael Boehnke / Aldons J. Lusis / Janet S. Sinsheimer / Karen L. Mohlke / Markku Laakso / Päivi Pajukanta / Arthur Ko

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 11

    Abstract: GWAS have identified numerous genetic loci for BMI and related traits. Here, Pan et al. generate Promoter Capture Hi-C data for human white adipocytes and integrate these with data of transcription factor motifs, RNA-seq and GWAS to identify eQTL-eGene ... ...

    Abstract GWAS have identified numerous genetic loci for BMI and related traits. Here, Pan et al. generate Promoter Capture Hi-C data for human white adipocytes and integrate these with data of transcription factor motifs, RNA-seq and GWAS to identify eQTL-eGene relationships mediated by chromosomal interactions.
    Keywords Science ; Q
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Author Correction

    David Z. Pan / Kristina M. Garske / Marcus Alvarez / Yash V. Bhagat / James Boocock / Elina Nikkola / Zong Miao / Chelsea K. Raulerson / Rita M. Cantor / Mete Civelek / Craig A. Glastonbury / Kerrin S. Small / Michael Boehnke / Aldons J. Lusis / Janet S. Sinsheimer / Karen L. Mohlke / Markku Laakso / Päivi Pajukanta / Arthur Ko

    Nature Communications, Vol 9, Iss 1, Pp 1-

    Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

    2018  Volume 1

    Abstract: In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is ... ...

    Abstract In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is available to download from the HTML version of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  10. Article ; Online: Author Correction

    David Z. Pan / Kristina M. Garske / Marcus Alvarez / Yash V. Bhagat / James Boocock / Elina Nikkola / Zong Miao / Chelsea K. Raulerson / Rita M. Cantor / Mete Civelek / Craig A. Glastonbury / Kerrin S. Small / Michael Boehnke / Aldons J. Lusis / Janet S. Sinsheimer / Karen L. Mohlke / Markku Laakso / Päivi Pajukanta / Arthur Ko

    Nature Communications, Vol 9, Iss 1, Pp 1-

    Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

    2018  Volume 1

    Abstract: In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is ... ...

    Abstract In the original version of this Article, Supplementary Table 10 contained incorrect primer sequences for the mobility shift assay for SNP rs4776984. These errors have now been fixed and the corrected version of the Supplementary Information PDF is available to download from the HTML version of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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