Scott E. Devine
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View article: Structural and transduction patterns of human-specific polymorphic SVA insertions
Structural and transduction patterns of human-specific polymorphic SVA insertions Open
Background SINE variable number tandem repeat Alu elements (SVAs) are a unique group of hominid-specific composite retrotransposons with highly variable internal structure. They represent the youngest TE family in humans and contribute to …
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (13…
Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes Open
Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using severa…
Mutagenesis of human genomes by endogenous mobile elements on a population scale Open
Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of th…
View article: Mako: A Graph-Based Pattern Growth Approach to Detect Complex Structural Variants
Mako: A Graph-Based Pattern Growth Approach to Detect Complex Structural Variants Open
Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is…
Mako: a graph-based pattern growth approach to detect complex structural variants Open
Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is cha…
View article: Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Haplotype-resolved diverse human genomes and integrated analysis of structural variation Open
Resolving genomic structural variation Many human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among in…
View article: <i>De novo</i>assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation
<i>De novo</i>assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation Open
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent–child trio data. We present 64 assembled haplotypes from 32 diverse human genome…
Striking heterogeneity of somatic L1 retrotransposition in single normal and cancerous gastrointestinal cells Open
Significance Using a modified method, we analyzed single cells from adenocarcinomas of the colon, pancreas, and stomach and their paired normal tissues for somatic LINE-1 retrotransposition events. We found that somatic retrotransposition …
Pulmonary Nontuberculous Mycobacterial Infection. A Multisystem, Multigenic Disease Open
Rationale: The clinical features of patients infected with pulmonary nontuberculous mycobacteria (PNTM) are well described, but the genetic components of infection susceptibility are not.
Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly Open
Virtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and emerging clinical diagnostic approaches utilize short-reads (srWGS), which present constraints for genome-wide discovery of structura…
Aberrantly High Levels of Somatic LINE-1 Expression and Retrotransposition in Human Neurological Disorders Open
Retrotransposable elements (RTEs) have actively multiplied over the past 80 million years of primate evolution, and as a consequence, such elements collectively occupy ∼ 40% of the human genome. As RTE activity can have detrimental effects…
A fully phased accurate assembly of an individual human genome Open
The prevailing genome assembly paradigm is to produce consensus sequences that “collapse” parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand seque…
Multi-platform discovery of haplotype-resolved structural variation in human genomes Open
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing tec…
Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma Open
Glioma is a unique neoplastic disease that develops exclusively in the central nervous system (CNS) and rarely metastasizes to other tissues. This feature strongly implicates the tumor-host CNS microenvironment in gliomagenesis and tumor p…
View article: Multi-platform discovery of haplotype-resolved structural variation in human genomes
Multi-platform discovery of haplotype-resolved structural variation in human genomes Open
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing…
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology Open
Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms…
The Role of Somatic L1 Retrotransposition in Human Cancers Open
The human LINE-1 (or L1) element is a non-LTR retrotransposon that is mobilized through an RNA intermediate by an L1-encoded reverse transcriptase and other L1-encoded proteins. L1 elements remain actively mobile today and continue to muta…
A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer Open
Although human LINE-1 (L1) elements are actively mobilized in many cancers, a role for somatic L1 retrotransposition in tumor initiation has not been conclusively demonstrated. Here, we identify a novel somatic L1 insertion in the APC tumo…