Biology subjects

Burchard, E.

Publications and source records attributed to Burchard, E..

8 recordsLinked to original sources

bioRxiv2025

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

Oxford Nanopore Technologies (ONT) sequencing platforms have enabled scientists to generate sequence reads of 20 kilobase or more, which has facilitated the assembly of complete genomes. Nanopore sequencing involves recording the change in electrical signals as the DNA molecule transverses the pore. Converting this signal information into bases - a process called basecalling - is challenging and require the implementation of machine learning. The models developed for ONT basecallers have continually improved. However, the mean quality of the reads generated fall below a Phred score of 20 (99% accuracy), the target quality for high-quality genome assembly, when used on challenging plant samples. These low-quality base calls limit the ability to conduct de novo genome assembly, accurate phasing of haplotypes, and long-read genotyping. To overcome these shortcomings, we fine-tuned ONTs high accuracy basecalling model using Bonito, an AI-based deep learning basecaller, to develop crop-specific models for five important species in the Rosaceae family. These species include highly valuable tree crops such as apple, peach, pear, plum, and sweet cherry. Through the development of an automated training pipeline, we were able to achieve [~]14% higher mean and median basecall quality, and a [~]20% increase in total reads with Phred scores >15. These results were achieved without significantly affecting the read length N50s and total reads called. As a result, these new crop-specific models will enable members of the Rosaceae genomics community to produce higher quality ONT sequencing data. Furthermore, we are releasing our automated pipeline to facilitate others to train their own organism or crop-specific models.

genomics↗

bioRxiv2023

Genome of the North American wild apple species Malus angustifolia

Apple (Malus x domestica Borkh.) production faces many challenges stemming from abiotic and biotic stresses. Abiotic stressors, such as extreme temperatures, droughts, and spring frosts, can lead to diminished yields and tree loss, while biotic stresses like fire blight and pest infestations further reduce tree health and fruit quality. To lessen the threat of these challenges, plant breeders aim to introduce resistance and resilience genes into cultivated varieties. However, high-relatedness among cultivated varieties and breeding lines, coupled with the long juvenility and generation times in apples, hinder the breeding process. The introduction of resistance traits from wild relatives is also constrained by these factors, as well as the lack of genomic resources that could assist in accelerating the introgression process. Herein, we report the assembly and annotation of Malus angustifolia, the Southern Crabapple, one of Eastern North Americas native species. Using a combination of Pacific Biosciences High Fidelity reads, Next-generation short read sequencing, as well as chromatin conformation capture sequencing, we achieve an extremely contiguous haplotype-resolved assembly. We perform comparative haplotypic analyses to identify SNPs and large structural variants, shedding light on the genomic landscape of M. angustifolia. Finally, we explore the phylogenetic and syntenic relationships between Eurasian Malus progenitors and the recently sequenced North American species, contributing valuable insights to the broader understanding of apple evolution and potential breeding strategies.

genomics↗

bioRxiv2023

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.

The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.

genomics↗

bioRxiv2023

Phenotypic subtyping via contrastive learning

Defining and accounting for subphenotypic structure has the potential to increase statistical power and provide a deeper understanding of the heterogeneity in the molecular basis of complex disease. Existing phenotype subtyping methods primarily rely on clinically observed heterogeneity or metadata clustering. However, they generally tend to capture the dominant sources of variation in the data, which often originate from variation that is not descriptive of the mechanistic heterogeneity of the phenotype of interest; in fact, such dominant sources of variation, such as population structure or technical variation, are, in general, expected to be independent of subphenotypic structure. We instead aim to find a subspace with signal that is unique to a group of samples for which we believe that subphenotypic variation exists (e.g., cases of a disease). To that end, we introduce Phenotype Aware Components Analysis (PACA), a contrastive learning approach leveraging canonical correlation analysis to robustly capture weak sources of subphenotypic variation. In the context of disease, PACA learns a gradient of variation unique to cases in a given dataset, while leveraging control samples for accounting for variation and imbalances of biological and technical confounders between cases and controls. We evaluated PACA using an extensive simulation study, as well as on various subtyping tasks using genotypes, transcriptomics, and DNA methylation data. Our results provide multiple strong evidence that PACA allows us to robustly capture weak unknown variation of interest while being calibrated and well-powered, far superseding the performance of alternative methods. This renders PACA as a state-of-the-art tool for defining de novo subtypes that are more likely to reflect molecular heterogeneity, especially in challenging cases where the phenotypic heterogeneity may be masked by a myriad of strong unrelated effects in the data. Code AvailabilityPACA is available as an open source R package on GitHub: https://github.com/Adigorla/PACA

genomics↗

bioRxiv2020

Population sequencing data reveal a compendium of mutational processes in human germline

Mechanistic processes underlying human germline mutations remain largely unknown. Variation in mutation rate and spectra along the genome is informative about the biological mechanisms. We statistically decompose this variation into separate processes using a blind source separation technique. The analysis of a large-scale whole genome sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. Seven of these processes lend themselves to a biological interpretation. One process is driven by bulky DNA lesions that resolve asymmetrically with respect to transcription and replication. Two processes independently track direction of replication fork and replication timing. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions. We also demonstrate that a recently discovered mutagenic process specific to oocytes can be localized solely from population sequencing data. This process is spread across all chromosomes and is highly asymmetric with respect to the direction of transcription, suggesting a major role of DNA damage.

genetics↗

bioRxiv2019

Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes

Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown.1 Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations was associated with both hematologic cancer incidence2-4 and coronary heart disease prevalence.5 Somatic mutations with leukemogenic potential may confer selective cellular advantages leading to clonal expansion, a phenomenon termed Clonal Hematopoiesis of Indeterminate Potential (CHIP).6 Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico-informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer. Aggregates of rare germline loss-of-function variants in CHEK2, a DNA damage repair gene, predisposed to CHIP acquisition. Overall, we observe that germline genetic variation altering hematopoietic stem cell function and the fidelity of DNA-damage repair increase the likelihood of somatic mutations leading to CHIP.

genomics↗

bioRxiv2018

Identification of Novel Common Breast Cancer Risk Variants in Latinas at the 6q25 Locus

Background: Breast cancer is a partially heritable trait and over 180 common genetic variants have been associated with breast cancer in genome wide association studies (GWAS). We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25 with the protective minor allele originating from Indigenous American ancestry. Here we report on additional GWAS and replication in Latinas.\n\nMethods: We performed GWAS in 2385 cases and 7342 controls who were either U.S. Latinas or Mexican women. We replicated 2412 cases and 1620 controls of U.S Latina, Mexican, and Colombian women. In addition, we replicated the top novel variants in study of African American and African women and in one study of Chinese women. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model based approach.\n\nResults: We identified 3 SNPs (p=1.9x10-8 - 2.8x10-8) at 6q25 locus not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.75 (0.68-0.83). In a replication in women of Latin American origin, we also observed a consistent effect (OR: 0.88; 95% CI: 0.78-0.99; p=0.037). Since the minor allele was common in East Asians and African American but not European ancestry populations, we replicated in a meta-analysis of those populations and also observed a consistent effect (OR 0.94; 95% CI: 0.91 - 0.97; p=0.013).\n\nConclusion: The effect size of this variant is relatively large compared to other common variants associated with breast cancer and adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.

genetics↗

bioRxiv2017

Exposure to Wood Smoke is Associated with Increased Risk of Asthma and Respiratory Symptoms in a Honduran Population

BackgroundExposure to environmental pollutants has been shown to be associated with asthma, but few studies have evaluated the effect of wood smoke on asthma and disease severity in a developing country, where use of stoves powered by solid fuels is a common practice.\n\nObjectiveIn a population in Olancho, Honduras, we evaluated the association between cooking fuel, stove type and asthma. We also evaluated the effects of these factors on asthma symptoms, lung function, and atopy.\n\nMethodsParticipants with physician-diagnosed asthma (n = 597) and controls without asthma (n = 429) were recruited from the Olancho province in Honduras. Participants were interviewed using a questionnaire and their baseline pulmonary function was measured using spirometry.\n\nResultsThe prevalence of use of wood as a cooking fuel was 66.9% in the study population, of which 42.1% of participants used wood as their only fuel. Use of wood as a cooking fuel was more prevalent among households with lower income, lower maternal education, and less urbanization. The prevalence of use of an open wood stove as the primary cooking stove among participants with asthma was 6.2% higher (95% CI 0.8 - 11.7%, p = .02) than among healthy controls. In a multiple logistic regression model, we identified a significant association between use of an open wood stove and asthma (OR = 1.80, 95% CI = 1.17 - 2.78, p = 0.007), compared to the referent (electric) stove category. Among participants with asthma, we identified a significant association between use of wood as cooking fuel and increased daytime respiratory symptoms (OR = 1.46, CI: 1.01 - 2.58, p = 0.046) and nocturnal symptoms (OR = 2.51, CI: 1.04 - 2.62, p = 0.04), though not with pulmonary function. Among control participants without asthma, use of wood as cooking fuel was associated with atopy (OR = 1.94, CI = 1.14 - 3.33, p = 0.015) and cough (OR = 2.22, CI = 1.09 - 4.88, p = 0.04).\n\nConclusionsUse of an open wood stove for cooking in a developing country appears to be a significant risk factor for asthma and respiratory symptoms. Exposure to wood smoke may play a role in atopic sensitization and respiratory symptoms, leading to the development of obstructive lung disease in susceptible individuals.

epidemiology↗