Allison Regier
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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: Mapping and characterization of structural variation in 17,795 human genomes
Mapping and characterization of structural variation in 17,795 human genomes Open
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and re…
View article: Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome Open
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer inde…
View article: Increased mutation and gene conversion within human segmental duplications
Increased mutation and gene conversion within human segmental duplications Open
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-ide…
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: Challenges in working with draft genomes
Challenges in working with draft genomes Open
As the cost of DNA sequencing falls, the relative cost of finishing steps (e.g., error correction and gap-closing) is increasing. As a result, many completed genome projects are only completed to draft stages and may not provide full infor…
View article: Automated assembly of high-quality diploid human reference genomes
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 greatly benefited society 1, 2 . However, it still has many gaps and errors, and does not represent a biological …
View article: A strategy for building and using a human reference pangenome
A strategy for building and using a human reference pangenome Open
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and sta…
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…
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
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…
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
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…
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: High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios Open
SUMMARY The 1000 Genomes Project (1kGP) is the largest fully open resource of whole genome sequencing (WGS) data consented for public distribution of raw sequence data without access or use restrictions. The final release of the 1kGP inclu…
View article: Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum Open
Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
View article: Additional file 2 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
Additional file 2 of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum Open
Additional file 2:SNPs between HB3 and Dd2(XLS 2 MB)
View article: Additional file 2 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Additional file 2 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
Additional file 2:. Excel format (.xlsx). Large Supplementary Tables. Contains Tables S1, S5-S8, and S10.
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…
View article: Association of Structural Variation with Cardiometabolic Traits in Finns
Association of Structural Variation with Cardiometabolic Traits in Finns Open
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometab…
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
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 combinatio…
View article: Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum Open
Additional file of High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
View article: A strategy for building and using a human reference pangenome
A strategy for building and using a human reference pangenome Open
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and sta…
View article: Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects
Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects Open
Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years to interrogate a broad range of traits, across diverse populations. These data are more valuable in aggregate: joint analysis o…