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  1. Article ; Online: Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics.

    Stewart, James Peter / Gazdova, Jana / Srivastava, Shambhavi / Revolta, Julia / Harewood, Louise / Maurya, Manisha / Darzentas, Nikos / Gonzalez, David

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2453, Page(s) 133–152

    Abstract: In the era of genomic medicine, targeted next generation sequencing strategies (NGS) are becoming increasingly adopted by clinical molecular diagnostic laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe ... ...

    Abstract In the era of genomic medicine, targeted next generation sequencing strategies (NGS) are becoming increasingly adopted by clinical molecular diagnostic laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe the EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay, which is designed to simultaneously detect B and T cell clonal rearrangements, translocations, copy number alterations, and sequence variants. The accompanying validated bioinformatics pipeline enables production of an integrated report. The combination of the laboratory protocol and bioinformatics pipeline in the EuroClonality-NDC minimizes the potential for human error, reduces economic costs compared to current molecular testing strategies, and should improve diagnostic outcomes.
    MeSH term(s) DNA Copy Number Variations ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunogenetics ; Immunoglobulins/genetics ; Receptors, Antigen, T-Cell/genetics
    Chemical Substances Immunoglobulins ; Receptors, Antigen, T-Cell
    Language English
    Publishing date 2022-05-27
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2115-8_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The impact of chromosomal rearrangements on regulation of gene expression.

    Harewood, Louise / Fraser, Peter

    Human molecular genetics

    2014  Volume 23, Issue R1, Page(s) R76–82

    Abstract: The effects that coding region single-nucleotide polymorphisms or mutations have on gene expression have been well documented, predominantly owing to their association with disease. The effects of structural chromosomal rearrangements are also receiving ... ...

    Abstract The effects that coding region single-nucleotide polymorphisms or mutations have on gene expression have been well documented, predominantly owing to their association with disease. The effects of structural chromosomal rearrangements are also receiving increasing attention with the development of new techniques that allow accurate, high-resolution data, whether genomic interaction or transcriptome data, to be generated right down to the single-cell level. Over the past 18 months, these advances in experimental techniques have been used to further confirm and delineate the substantial effects that chromosome rearrangements can have on the regulation of gene expression and provide evidence of direct links between the two.
    MeSH term(s) Chromosome Aberrations ; Gene Expression ; Gene Expression Regulation ; Gene Rearrangement ; Humans ; Mutation ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2014-06-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddu278
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  3. Article ; Online: The Potential of Digital Image Analysis to Determine Tumor Cell Content in Biobanked Formalin-Fixed, Paraffin-Embedded Tissue Samples.

    Greene, Christine / O'Doherty, Edwina / Abdullahi Sidi, Fatima / Bingham, Victoria / Fisher, Natalie C / Humphries, Matthew P / Craig, Stephanie G / Harewood, Louise / McQuaid, Stephen / Lewis, Claire / James, Jacqueline

    Biopreservation and biobanking

    2021  Volume 19, Issue 4, Page(s) 324–331

    Abstract: Introduction: ...

    Abstract Introduction:
    MeSH term(s) Formaldehyde ; Humans ; Neoplasms ; Paraffin Embedding ; Reproducibility of Results ; Software
    Chemical Substances Formaldehyde (1HG84L3525)
    Language English
    Publishing date 2021-03-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2593993-2
    ISSN 1947-5543 ; 1947-5535
    ISSN (online) 1947-5543
    ISSN 1947-5535
    DOI 10.1089/bio.2020.0105
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  4. Article ; Online: LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.

    Roller, Maša / Stamper, Ericca / Villar, Diego / Izuogu, Osagie / Martin, Fergal / Redmond, Aisling M / Ramachanderan, Raghavendra / Harewood, Louise / Odom, Duncan T / Flicek, Paul

    Genome biology

    2021  Volume 22, Issue 1, Page(s) 62

    Abstract: Background: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.: Results: The regulatory ... ...

    Abstract Background: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.
    Results: The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species.
    Conclusions: Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.
    MeSH term(s) Animals ; Chromosome Mapping ; Conserved Sequence ; Enhancer Elements, Genetic ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Long Interspersed Nucleotide Elements ; Mammals/genetics ; Organ Specificity/genetics ; Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Retroelements
    Chemical Substances Retroelements
    Language English
    Publishing date 2021-02-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02260-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

    Roller, Maša / Stamper, Ericca / Villar, Diego / Izuogu, Osagie / Martin, Fergal / Redmond, Aisling M / Ramachanderan, Raghavendra / Harewood, Louise / Odom, Duncan T / Flicek, Paul

    Genome biology. 2021 Dec., v. 22, no. 1

    2021  

    Abstract: BACKGROUND: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. RESULTS: The regulatory landscape ... ...

    Abstract BACKGROUND: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. RESULTS: The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. CONCLUSIONS: Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.
    Keywords brain ; evolution ; gene expression ; genomics ; liver ; mammals ; muscles ; retrotransposons ; testes
    Language English
    Dates of publication 2021-12
    Size p. 62.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02260-y
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  6. Article: Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing.

    Mc Connell, Lauren / Gazdova, Jana / Beck, Katja / Srivastava, Shambhavi / Harewood, Louise / Stewart, J P / Hübschmann, Daniel / Stenzinger, Albrecht / Glimm, Hanno / Heilig, Christoph E / Fröhling, Stefan / Gonzalez, David

    Cancers

    2020  Volume 12, Issue 12

    Abstract: Circulating tumour DNA (ctDNA) analysis using next generation sequencing (NGS) is being implemented in clinical practice for treatment stratification and disease monitoring. However, using ctDNA to detect structural variants, a common occurrence in ... ...

    Abstract Circulating tumour DNA (ctDNA) analysis using next generation sequencing (NGS) is being implemented in clinical practice for treatment stratification and disease monitoring. However, using ctDNA to detect structural variants, a common occurrence in sarcoma, can be challenging. Here, we use a sarcoma-specific targeted NGS panel to identify translocations and copy number variants in a cohort of 12 tissue specimens and matched circulating cell-free DNA (cfDNA) from soft tissue sarcoma patients, including alveolar rhabdomyosarcoma (
    Language English
    Publishing date 2020-12-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers12123627
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  7. Article ; Online: Structural variation and its effect on expression.

    Harewood, Louise / Chaignat, Evelyne / Reymond, Alexandre

    Methods in molecular biology (Clifton, N.J.)

    2012  Volume 838, Page(s) 173–186

    Abstract: Structural variation, whether it is caused by copy number variants or present in a balanced form, such as reciprocal translocations and inversions, can have a profound and dramatic effect on the expression of genes mapping within and close to the ... ...

    Abstract Structural variation, whether it is caused by copy number variants or present in a balanced form, such as reciprocal translocations and inversions, can have a profound and dramatic effect on the expression of genes mapping within and close to the rearrangement, as well as affecting others genome wide. These effects can be caused by altering the copy number of one or more genes or regulatory elements (dosage effect) or from physical disruption of links between regulatory elements and their associated gene or genes, resulting in perturbation of expression. Similarly, large-scale structural variants can result in genome-wide expression changes by altering the positions that chromosomes occupy within the nucleus, potentially disrupting not only local cis interactions, but also trans interactions that occur throughout the genome. Structural variation is, therefore, a significant factor in the study of gene expression and is discussed here in more detail.
    MeSH term(s) Chromosome Mapping ; DNA Copy Number Variations ; Gene Deletion ; Gene Dosage ; Gene Duplication ; Gene Expression ; Gene Rearrangement ; Genetic Variation ; Genome, Human ; Humans ; Phenotype ; Quantitative Trait Loci ; Regulatory Sequences, Nucleic Acid ; Translocation, Genetic
    Language English
    Publishing date 2012
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-61779-507-7_8
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  8. Article: Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

    Harewood, Louise / Collins, V. Peter / Eldridge, Matthew D / Fraser, Peter / Kishore, Kamal / Pearson, Danita / Schoenfelder, Stefan / Wingett, Steven

    Genome biology. 2017 Dec., v. 18, no. 1

    2017  

    Abstract: Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly ... ...

    Abstract Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.
    Keywords chromosome aberrations ; chromosomes ; humans ; neoplasms
    Language English
    Dates of publication 2017-12
    Size p. 125.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/s13059-017-1253-8
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  9. Article ; Online: LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

    Maša Roller / Ericca Stamper / Diego Villar / Osagie Izuogu / Fergal Martin / Aisling M. Redmond / Raghavendra Ramachanderan / Louise Harewood / Duncan T. Odom / Paul Flicek

    Genome Biology, Vol 22, Iss 1, Pp 1-

    2021  Volume 43

    Abstract: Abstract Background To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. Results The regulatory ... ...

    Abstract Abstract Background To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. Results The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. Conclusions Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.
    Keywords Regulatory evolution ; Gene regulation ; Promoters ; Enhancers ; Transposable elements ; Long Interspersed Nuclear Elements (LINEs) ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 616
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours.

    Harewood, Louise / Kishore, Kamal / Eldridge, Matthew D / Wingett, Steven / Pearson, Danita / Schoenfelder, Stefan / Collins, V Peter / Fraser, Peter

    Genome biology

    2017  Volume 18, Issue 1, Page(s) 125

    Abstract: Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly ... ...

    Abstract Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.
    Language English
    Publishing date 2017-06-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/s13059-017-1253-8
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