Harriet Dashnow
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View article: Long-read sequencing reveals extensive <i>FMR1</i> somatic mosaicism in Fragile-X associated tremor/ataxia syndrome in human brain
Long-read sequencing reveals extensive <i>FMR1</i> somatic mosaicism in Fragile-X associated tremor/ataxia syndrome in human brain Open
Fragile X–associated tremor/ataxia syndrome (FXTAS) is a progressive neurodegenerative disorder caused by a CGG repeat expansion in the 5’ untranslated region of the X-linked Fragile X messenger ribonucleoprotein 1 ( FMR1) . Although the C…
View article: The selective dynamics of interruptions at short tandem repeats
The selective dynamics of interruptions at short tandem repeats Open
Short tandem repeats (STRs) are hotspots of genomic instability that mutate at rates orders of magnitude greater than non-repetitive loci due to frequent replication slippage. Expansions at some STR loci cause Mendelian diseases, while var…
View article: STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci Open
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp motifs. TR variants contribute to several d…
View article: Mosaicism in Short Tandem Repeat Disorders: A Clinical Perspective
Mosaicism in Short Tandem Repeat Disorders: A Clinical Perspective Open
Fragile X, Huntington disease, and myotonic dystrophy type 1 are prototypical examples of human disorders caused by short tandem repeat variation, repetitive nucleotide stretches that are highly mutable both in the germline and somatic tis…
View article: Tandem repeat variation shapes immune cell type-specific gene expression
Tandem repeat variation shapes immune cell type-specific gene expression Open
Tandem repeats (TRs) - highly polymorphic, repetitive sequences across the human genome - are important regulators of gene expression but remain underexplored due to challenges in accurate genotyping and analysis. Here, we generate new who…
View article: Defining a tandem repeat catalog and variation clusters for genome-wide analyses
Defining a tandem repeat catalog and variation clusters for genome-wide analyses Open
Tandem repeat (TR) catalogs are important components of repeat genotyping studies as they define the genomic coordinates and expected motifs of all TR loci being analyzed. In recent years, genome-wide studies have used catalogs ranging in …
View article: The Platinum Pedigree: A long-read benchmark for genetic variants
The Platinum Pedigree: A long-read benchmark for genetic variants Open
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting com…
View article: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation Open
Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using l…
View article: A familial, telomere-to-telomere reference for human<i>de novo</i>mutation and recombination from a four-generation pedigree
A familial, telomere-to-telomere reference for human<i>de novo</i>mutation and recombination from a four-generation pedigree Open
Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNM…
View article: TRGT-denovo: accurate detection of<i>de novo</i>tandem repeat mutations
TRGT-denovo: accurate detection of<i>de novo</i>tandem repeat mutations Open
Motivation Identifying de novo tandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of th…
View article: STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci Open
Approximately 3% of the human genome consists of repetitive elements called tandem repeats (TRs), which include short tandem repeats (STRs) of 1–6bp motifs and variable number tandem repeats (VNTRs) of 7+bp motifs. TR variants contribute t…
View article: Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation Open
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read seque…
View article: Resolving the unsolved: Comprehensive assessment of tandem repeats at scale
Resolving the unsolved: Comprehensive assessment of tandem repeats at scale Open
Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare monogenic diseases. Recent advances in sequencing have enabled accurate, long reads that can characterize the full-length sequence and methylation pro…
View article: STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci
STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci Open
Expansions of short tandem repeats (STRs) cause dozens of rare Mendelian diseases. However, STR expansions, especially those arising from repeats not present in the reference genome, are challenging to detect from short-read sequencing dat…
View article: STRetch reference data
STRetch reference data Open
STRetch reference data
View article: STRetch reference data
STRetch reference data Open
STRetch reference data
View article: STRetch reference data - hg19
STRetch reference data - hg19 Open
hg19 reference genome with added STR decoysRequired to run STRling
View article: STRetch reference data - hg38
STRetch reference data - hg38 Open
STRling reference genome for hg38
View article: Effective variant filtering and expected candidate variant yield in studies of rare human disease
Effective variant filtering and expected candidate variant yield in studies of rare human disease Open
In studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence…
View article: Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software Open
Background Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, …
View article: datacarpentry/spreadsheet-ecology-lesson: Data Carpentry: Data Organization in Spreadsheets for Ecologists, June 2019
datacarpentry/spreadsheet-ecology-lesson: Data Carpentry: Data Organization in Spreadsheets for Ecologists, June 2019 Open
Data Carpentry lesson from Ecology curriculum to learn how to use spreadsheet to organize data.
View article: swcarpentry/r-novice-gapminder: Software Carpentry: R for Reproducible Scientific Analysis, June 2019
swcarpentry/r-novice-gapminder: Software Carpentry: R for Reproducible Scientific Analysis, June 2019 Open
This lesson in part of Software Carpentry workshop and teach novice programmers to write modular code and best practices for using R for data analysis.
View article: datacarpentry/R-ecology-lesson: Data Carpentry: Data Analysis and Visualization in R for Ecologists, June 2019
datacarpentry/R-ecology-lesson: Data Carpentry: Data Analysis and Visualization in R for Ecologists, June 2019 Open
Data Carpentry lesson from Ecology curriculum to learn how to analyse and visualise ecological data in R.
View article: Pooled-parent exome sequencing to prioritise <i>de novo</i> variants in genetic disease
Pooled-parent exome sequencing to prioritise <i>de novo</i> variants in genetic disease Open
In the clinical setting, exome sequencing has become standard-of-care in diagnosing rare genetic disorders, however many patients remain unsolved. Trio sequencing has been demonstrated to produce a higher diagnostic yield than singleton (p…