Haley Abel
A5061624565- Cancer Genomics and Diagnostics
- Lymphoma Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Sarcoma Diagnosis and Treatment
- Neurofibromatosis and Schwannoma Cases
- Neuroblastoma Research and Treatments
- Genomics and Phylogenetic Studies
- Acute Myeloid Leukemia Research
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Genomic variations and chromosomal abnormalities
- Lung Cancer Treatments and Mutations
- Chronic Lymphocytic Leukemia Research
- Epigenetics and DNA Methylation
- Genetic Mapping and Diversity in Plants and Animals
- Monoclonal and Polyclonal Antibodies Research
- Metabolomics and Mass Spectrometry Studies
- Hippo pathway signaling and YAP/TAZ
- CAR-T cell therapy research
- Cytokine Signaling Pathways and Interactions
- Chromosomal and Genetic Variations
- Mitochondrial Function and Pathology
- Cancer-related gene regulation
- Plant Disease Resistance and Genetics
- Gene expression and cancer classification
Washington University in St. Louis
2015-2024
James S. McDonnell Foundation
2016-2022
University of Colorado Boulder
2018
Medical College of Wisconsin
2015
Jackson Laboratory
2015
University of Utah
2010-2012
Cofactor Genomics (United States)
2010
University of Tennessee Health Science Center
2004
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. final, phase 3 release 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS resource, which now includes 602 complete trios, sequenced to depth 30X using Illumina. We performed single-nucleotide variant (SNV) short...
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
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 genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% genome: 26 million base pairs) integrate all forms genetic variation, even across complex loci. identified 107,590 structural variants (SVs), which 68% were not...
SUMMARY The 1000 Genomes Project (1kGP) is the largest fully open resource of whole genome sequencing (WGS) data consented for public distribution raw sequence without access or use restrictions. final release 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low coverage WGS. Here, we present a new, high 3,202-sample WGS resource, sequenced to targeted depth 30X using Illumina NovaSeq 6000 system, which now includes 602 complete trios. We performed...
Few studies have explored the impact of rare variants (minor allele frequency < 1%) on highly heritable plasma metabolites identified in metabolomic screens. The Finnish population provides an ideal opportunity for such explorations, given multiple bottlenecks and expansions that shaped its history, enrichment many otherwise alleles has resulted. Here, we report genetic associations 1391 6136 men from late-settlement region Finland. We identify 303 novel association signals, more than one...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. contains 47 phased, diploid assemblies from cohort of genetically diverse individuals. These cover more than 99% the expected sequence and are accurate at structural base-pair levels. Based on alignments assemblies, we generated that captures known variants haplotypes, reveals novel alleles structurally complex loci, adds 119 million base pairs euchromatic polymorphic 1,529 gene...
Abstract Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared pattern SNVs between unique duplicated regions 3,4 We find that are elevated 60% to estimate at least 23% this increase is due interlocus gene conversion (IGC) with up 4.3 megabase pairs SD sequence...
A recurrent somatic mutation frequently found in cytogenetically normal acute myeloid leukemia (AML) is internal tandem duplication (ITD) the fms-related tyrosine kinase 3 gene (FLT3). This generally detected clinical laboratory by PCR and electrophoresis-based product sizing. As number of clinically relevant mutations AML increases, it becomes increasingly attractive to incorporate FLT3 ITD testing into multiplex assays for many simultaneously, using next-generation sequencing (NGS)....
Allogeneic hematopoietic stem-cell transplantation is the only curative treatment for patients with myelodysplastic syndrome (MDS). The molecular predictors of disease progression after are unclear.We sequenced bone marrow and skin samples from 90 adults MDS who underwent allogeneic a myeloablative or reduced-intensity conditioning regimen. We detected mutations before using enhanced exome sequencing, we evaluated mutation clearance by error-corrected sequencing to genotype in obtained 30...
T-cell receptor (TCR) clonality assessment is a principal diagnostic test in the management of mycosis fungoides (MF). However, current polymerase chain reaction-based methods may produce ambiguous results, often because low abundance clonal T lymphocytes, resulting weak peaks that cannot be size-resolved by contemporary capillary electrophoresis (CE).We sought to determine if next-generation sequencing (NGS)-based detection has increased sensitivity for over CE-based MF.Clonality was...
The identification of recurrent gene rearrangements in the clinical laboratory is cornerstone for risk stratification and treatment decisions many malignant tumors. Studies have reported that targeted next-generation sequencing assays potential to identify such rearrangements; however, their utility unknown. We examine sensitivity specificity ALK KMT2A (MLL) rearrangement detection by laboratory. analyzed a series seven rearranged cancers, six leukemias, 77 ALK/KMT2A rearrangement-negative...
Abstract Summary Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals each SV manner that considers variant type, gene features and positional uncertainty. We show the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting they are under purifying selection, identifies deleterious variants...
Large-scale human genetics studies are now employing whole genome sequencing with the goal of conducting comprehensive trait mapping analyses all forms variation. However, methods for structural variation (SV) analysis have lagged far behind those smaller scale variants, and there is an urgent need to develop more efficient tools that size populations. Here, we present a fast highly scalable software toolkit (svtools) cloud-based pipeline assembling high quality SV maps-including deletions,...
Abstract TP53-mutated myeloid malignancies are associated with complex cytogenetics and extensive structural variants, which complicates detailed genomic analysis by conventional clinical techniques. We performed whole-genome sequencing (WGS) of 42 acute leukemia (AML)/myelodysplastic syndromes (MDS) cases paired normal tissue to better characterize the landscape AML/MDS. WGS accurately determines TP53 allele status, a key prognostic factor, resulting in reclassification 12% from monoallelic...