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  1. Article: Long-Read DNA and RNA Sequencing to Streamline Clinical Genetic Testing and Reduce Barriers to Comprehensive Genetic Testing.

    Damaraju, Nikhita / Miller, Angela L / Miller, Danny E

    The journal of applied laboratory medicine

    2024  Volume 9, Issue 1, Page(s) 138–150

    Abstract: Background: Obtaining a precise molecular diagnosis through clinical genetic testing provides information about disease prognosis or progression, allows accurate counseling about recurrence risk, and empowers individuals to benefit from precision ... ...

    Abstract Background: Obtaining a precise molecular diagnosis through clinical genetic testing provides information about disease prognosis or progression, allows accurate counseling about recurrence risk, and empowers individuals to benefit from precision therapies or take part in N-of-1 trials. Unfortunately, more than half of individuals with a suspected Mendelian condition remain undiagnosed after a comprehensive clinical evaluation, and the results of any individual clinical genetic test ordered during a typical evaluation may take weeks or months to return. Furthermore, commonly used technologies, such as short-read sequencing, are limited in the types of disease-causing variation they can identify. New technologies, such as long-read sequencing (LRS), are poised to solve these problems.
    Content: Recent technical advances have improved accuracy, increased throughput, and decreased the costs of commercially available LRS technologies. This has resolved many historical concerns about the use of LRS in the clinical environment and opened the door to widespread clinical adoption of LRS. Here, we review LRS technology, how it has been used in the research setting to clarify complex variants or identify disease-causing variation missed by prior clinical testing, and how it may be used clinically in the near future.
    Summary: LRS is unique in that, as a single data source, it has the potential to replace nearly every other clinical genetic test offered today. When analyzed in a stepwise fashion, LRS will simplify laboratory processes, reduce barriers to comprehensive genetic testing, increase the rate of genetic diagnoses, and shorten the amount of time required to make a molecular diagnosis.
    MeSH term(s) Humans ; Genetic Testing ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods ; Prognosis
    Language English
    Publishing date 2024-01-03
    Publishing country England
    Document type Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2576-9456
    ISSN 2576-9456
    DOI 10.1093/jalm/jfad107
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Synaptonemal Complex-Deficient

    Miller, Danny E

    G3 (Bethesda, Md.)

    2020  Volume 10, Issue 2, Page(s) 525–537

    Abstract: Genetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. ... ...

    Abstract Genetic stability depends on the maintenance of a variety of chromosome structures and the precise repair of DNA breaks. During meiosis, programmed double-strand breaks (DSBs) made in prophase I are normally repaired as gene conversions or crossovers. DSBs can also be made by other mechanisms, such as the movement of transposable elements (TEs), which must also be resolved. Incorrect repair of these DNA lesions can lead to mutations, copy-number changes, translocations, and/or aneuploid gametes. In
    MeSH term(s) Animals ; DNA Breaks, Double-Stranded ; DNA Copy Number Variations ; DNA Repair ; DNA Transposable Elements ; Drosophila melanogaster/genetics ; Female ; Male ; Synaptonemal Complex/genetics
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2020-02-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.119.400853
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The Interchromosomal Effect: Different Meanings for Different Organisms.

    Miller, Danny E

    Genetics

    2020  Volume 216, Issue 3, Page(s) 621–631

    Abstract: The term interchromosomal effect was originally used to describe a change in the distribution of exchange in the presence of an inversion. First characterized in the 1920s by ... ...

    Abstract The term interchromosomal effect was originally used to describe a change in the distribution of exchange in the presence of an inversion. First characterized in the 1920s by early
    MeSH term(s) Animals ; Chromosome Inversion ; Chromosomes/genetics ; Drosophila ; Humans ; Nondisjunction, Genetic ; Species Specificity ; Translocation, Genetic
    Language English
    Publishing date 2020-11-06
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.120.303656
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Applications of long-read sequencing to Mendelian genetics.

    Mastrorosa, Francesco Kumara / Miller, Danny E / Eichler, Evan E

    Genome medicine

    2023  Volume 15, Issue 1, Page(s) 42

    Abstract: Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder ... ...

    Abstract Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
    MeSH term(s) Humans ; Genetic Testing ; Sequence Analysis, DNA
    Language English
    Publishing date 2023-06-14
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-023-01194-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Panels, Exomes, Genomes, and More-Finding the Best Path Through the Diagnostic Odyssey.

    Lenahan, Arthur L / Squire, Audrey E / Miller, Danny E

    Pediatric clinics of North America

    2023  Volume 70, Issue 5, Page(s) 905–916

    Abstract: Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may ... ...

    Abstract Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may order testing in a stepwise fashion, and what to order after non-diagnostic testing can be challenging to determine. Here, we provide an overview of commonly used clinical genetic tests, guidance on when they are best used, and what they may miss. We conclude with a discussion of how new technologies might be used to identify challenging variants and simplify clinical testing in the future.
    MeSH term(s) Humans ; Exome ; Genetic Testing
    Language English
    Publishing date 2023-07-11
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 215711-1
    ISSN 1557-8240 ; 0031-3955
    ISSN (online) 1557-8240
    ISSN 0031-3955
    DOI 10.1016/j.pcl.2023.06.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Advances in the discovery and analyses of human tandem repeats.

    Chaisson, Mark J P / Sulovari, Arvis / Valdmanis, Paul N / Miller, Danny E / Eichler, Evan E

    Emerging topics in life sciences

    2023  Volume 7, Issue 3, Page(s) 361–381

    Abstract: Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human ... ...

    Abstract Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
    MeSH term(s) Humans ; Tandem Repeat Sequences/genetics ; DNA ; Epigenesis, Genetic
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-10-31
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20230074
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic.

    Greer, Stephanie U / Botello, Jacquelin / Hongo, Donna / Levy, Brynn / Shah, Premal / Rabinowitz, Matthew / Miller, Danny E / Im, Kate / Kumar, Akash

    Journal of translational medicine

    2023  Volume 21, Issue 1, Page(s) 378

    Abstract: Background: Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular ... ...

    Abstract Background: Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications.
    Methods: We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth.
    Results: Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis.
    Conclusions: We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.
    MeSH term(s) Humans ; Nanopore Sequencing ; DNA Copy Number Variations/genetics ; Workflow ; Genomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-06-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2118570-0
    ISSN 1479-5876 ; 1479-5876
    ISSN (online) 1479-5876
    ISSN 1479-5876
    DOI 10.1186/s12967-023-04243-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Correction to: Congenital pleuropulmonary blastoma in a newborn with a variant of uncertain significance in DICER1 evaluated by RNA-sequencing.

    Lyle, Allison N J / Ohlsen, Timothy J D / Miller, Danny E / Brown, Gabrielle / Waligorski, Natalie / Stark, Rebecca / Taylor, Mallory R / Puia-Dumitrescu, Mihai

    Maternal health, neonatology and perinatology

    2023  Volume 9, Issue 1, Page(s) 7

    Language English
    Publishing date 2023-05-25
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2809925-4
    ISSN 2054-958X
    ISSN 2054-958X
    DOI 10.1186/s40748-023-00161-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes.

    Li, Haosheng / Berent, Erica / Hadjipanteli, Savannah / Galey, Miranda / Muhammad-Lahbabi, Nigel / Miller, Danny E / Crown, K Nicole

    PLoS genetics

    2023  Volume 19, Issue 4, Page(s) e1010702

    Abstract: Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions ... ...

    Abstract Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.
    MeSH term(s) Animals ; Drosophila melanogaster/genetics ; Recombinational DNA Repair ; Chromosome Inversion/genetics ; DNA Repair/genetics ; Gene Conversion ; Crossing Over, Genetic ; Meiosis/genetics
    Language English
    Publishing date 2023-04-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1010702
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Meiotic Recombination: Taking the Path Less Traveled.

    Miller, Danny E / Hawley, R Scott

    Current biology : CB

    2017  Volume 27, Issue 1, Page(s) R26–R28

    Abstract: The proper distribution of crossovers during meiosis I ensures accurate chromosome segregation at the first meiotic division. A new study reveals both the consequences of improper crossover patterning in Drosophila and the role of Blm helicase in ... ...

    Abstract The proper distribution of crossovers during meiosis I ensures accurate chromosome segregation at the first meiotic division. A new study reveals both the consequences of improper crossover patterning in Drosophila and the role of Blm helicase in controlling this patterning.
    MeSH term(s) Animals ; Bloom Syndrome ; Chromosome Segregation ; Drosophila ; Homologous Recombination ; Meiosis
    Language English
    Publishing date 2017-01-07
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2016.11.002
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