Patrick Hasenfeld
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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: Origins of chromosome instability unveiled by coupled imaging and genomics
Origins of chromosome instability unveiled by coupled imaging and genomics Open
Somatic chromosome instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution 1–3 . Although CAs have been linked to mitotic errors resulting in the emergence of nuclear atypia 4–7 , …
View article: Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion Open
The most common genomic disorder, chromosome 22q11.2 microdeletion syndrome (22q11.2DS), is mediated by highly identical and polymorphic segmental duplications (SDs) known as low copy repeats (LCRs; regions A-D) that have been challenging …
View article: Structural variant and nucleosome occupancy dynamics postchemotherapy in a HER2+ breast cancer organoid model
Structural variant and nucleosome occupancy dynamics postchemotherapy in a HER2+ breast cancer organoid model Open
The most common chemotherapeutics induce DNA damage to eradicate cancer cells, yet defective DNA repair can propagate mutations, instigating therapy resistance and secondary malignancies. Structural variants (SVs), arising from copy-number…
View article: Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype
Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype Open
Chromosomal instability is a major driver of intratumoral heterogeneity (ITH), promoting tumor progression. In the present study, we combined structural variant discovery and nucleosome occupancy profiling with transcriptomic and immunophe…
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…
View article: Origins of<i>de novo</i>chromosome rearrangements unveiled by coupled imaging and genomics
Origins of<i>de novo</i>chromosome rearrangements unveiled by coupled imaging and genomics Open
Chromosomal instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution 1–3 . While CAs have been linked to mitotic errors resulting in the emergence of nuclear atypias 4–7 , the under…
View article: Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci Open
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genom…
View article: Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells Open
The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the hete…
View article: Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures
Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures Open
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often m…
View article: Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells Open
The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single cell genomes from 19 human donors of increasing age, revealing a heterogeneo…
View article: Gaps and complex structurally variant loci in phased genome assemblies
Gaps and complex structurally variant loci in phased genome assemblies Open
There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates mor…
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Additional file 2 of Inversion polymorphism in a complete human genome assembly
Additional file 2 of Inversion polymorphism in a complete human genome assembly Open
Additional file 2: Table S1. Nonredundant inversion callset reported in this study. Table S2. Putative novel inversions with respect to T2T-CHM13 reference. Table S3. Enrichment of inversions in pericentromeric regions. Table S4. List of m…
View article: Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Assembly of 43 human Y chromosomes reveals extensive complexity and variation Open
The uploaded file contains Supplementary Tables S1-S61 for the manuscript "Assembly of 43 human Y chromosomes reveals extensive complexity and variation"
View article: Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation
Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation Open
The prevalence of highly repetitive sequences within the human Y chromosome has led to its incomplete assembly and systematic omission from genomic analyses. Here, we present long-read de novo assemblies of 43 diverse Y chromosomes spannin…
View article: Semi-automated assembly of high-quality diploid human reference genomes
Semi-automated assembly of high-quality diploid human reference genomes Open
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still has many gaps and errors, and does not represent a biological genome a…
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
The completion of the human genome significantly improved our ability to discover and interpret genome copy number variation. In order to understand its impact on the characterization of inversion polymorphisms, we remapped data from 41 hu…
View article: A high-resolution map of small-scale inversions in the gibbon genome
A high-resolution map of small-scale inversions in the gibbon genome Open
Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, …
View article: Gaps and complex structurally variant loci in phased genome assemblies
Gaps and complex structurally variant loci in phased genome assemblies Open
There has been tremendous progress in the production of phased genome assemblies by combining long-read data with parental information or linking read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still gen…
View article: Gaps and complex structurally variant loci in phased genome assemblies
Gaps and complex structurally variant loci in phased genome assemblies Open
Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.
View article: Gaps and complex structurally variant loci in phased genome assemblies
Gaps and complex structurally variant loci in phased genome assemblies Open
Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.
View article: Gaps and complex structurally variant loci in phased genome assemblies
Gaps and complex structurally variant loci in phased genome assemblies Open
Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.