Biology subjects

Jorde, L. B.

Publications and source records attributed to Jorde, L. B..

9 recordsLinked to original sources

bioRxiv2025

Human acrocentric chromosome short arm de novo mutation and recombination

The extraordinary repetitive content of human acrocentric short arms has prevented detailed investigations into recombination and de novo mutation. Integrating multiple sequencing technologies, we created 156 phased short arms and assessed 107 intergenerational transmissions from 23 samples in a four-generation pedigree. We observed a significant depletion (P<0.0001) of p-arm allelic recombination but one ectopic chr13-chr21 recombination breakpoint mediated by a 630 kbp segmental duplication mapping 1.6 Mbp distal to the SST1 array. In contrast, 18 maternal-biased q-arm allelic recombinations are significantly enriched within 5 Mbp of the centromere. Compared to autosomal euchromatin, the overall p-arm de novo single-nucleotide variant rate (1.33x10- per base pair per generation) is 10-fold higher, with a significant reduction of C>T but increased C>G and A>C mutations. We hypothesize that acrocentric sequence composition biases and the dearth of allelic recombination contribute to an elevated mutation rate and unique mutational signatures suggestive of mismatch repair defects and oxidative stress-induced DNA lesions.

genomics↗

bioRxiv2024

The Platinum Pedigree: A long-read benchmark for genetic variants

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 completeness in difficult to analyze regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across Illumina, PacBio high-fidelity (HiFi), and Oxford Nanopore Technologies platforms. This generated a variant map with over 4.7 million single-nucleotide variants, 767,795 indels, 537,486 tandem repeats, and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds [~]200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878. As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by [~]34%.

genomics↗

bioRxiv2021

MFN2 Influences Amyotrophic Lateral Sclerosis Pathology

ObjectiveTo better understand the pathology of amyotrophic lateral sclerosis, we used sequence data from patients seen at the University of Utah to identify novel disease-associated loci. We utilized both in vitro and in vivo studies to determine the biological effect of patient mutations in MFN2. MethodSequence data for a total of 140 patients were run through VAAST and Phevor to determine genes that were more burdened with rare, nonsynonymous variants compared to control longevity cohort. Variants identified in MFN2 were expressed in Mfn2 knockout cells to determine if mutant MFN2 could rescue mitochondrial morphology defects. We identified additional rare, nonsynonymous variants in MFN2 in ALSdb that were expressed in knockout mouse embryonic fibroblasts (MEFs). Membrane potential was measured to quantify mitochondrial health upon mutant MFN2 expression. mfn2 knockout zebrafish were used to examine movement compared to wildtype and protein aggregation in brain. ResultsMFN2 mutations identified in ALS patients from our University of Utah cohort and ALSdb were defective in rescuing morphological defects in Mfn2 knockout MEFs. Selected mutants showed decreased membrane potential compared to wildtype MFN2 expression. Zebrafish heterozygous and homozygous for loss of mfn2 showed increased TDP-43 levels in their hindbrain and cerebellum. ConclusionIn total, 21 rare, deleterious mutations in MFN2 were tested in Mfn2 knockout MEFs. Mutant MFN2 expression was not able to rescue the knockout phenotype, though at differing degrees of severity. Decreased membrane potential also argues for inhibited mitochondrial function. Increased TDP-43 levels in mutant zebrafish illustrates MFN2s function in ALS pathology. MFN2 variants influence ALS pathology and highlight the importance of mitochondria in neurodegeneration.

genetics↗

bioRxiv2020

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. The germline mutation rate for single nucleotide variants and factors that significantly influence this rate, such as parental age, are now well established. However, far less is known about the frequency, distribution, and features that impact de novo structural mutations. We report a large, family-based study of germline mutations, excluding aneuploidy, that affect genome structure among 572 genomes from 33 families in a multigenerational CEPH-Utah cohort and 2,363 cases of non-familial autism spectrum disorder (ASD), 1,938 unaffected siblings, and both parents (9,599 genomes in total). We find that de novo structural mutations detected by alignment-based, short-read WGS occurred at an overall rate of at least 0.160 events per genome in unaffected individuals and was significantly higher (0.206 per genome) in ASD cases. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations, and that these mechanisms likely have markedly different rates and selective pressures than those leading to point mutations.

genomics↗

bioRxiv2020

Mobile Element Insertions and Associated Structural Variants in Longitudinal Breast Cancer Samples

While mobile elements are largely inactive in healthy somatic tissues, increased activity has been found in cancer tissues, with significant variation among different cancer types. In addition to insertion events, mobile elements have also been found to mediate many structural variation events in the genome. Here, to better understand the timing and impact of mobile element insertions and structural variants involving existing mobile elements in cancer, we examined their activity in longitudinal samples of four metastatic breast cancer patients. With whole-genome sequencing data from multiple timepoints through tumor progression, we used mobile element detection software followed by visual confirmation of the insertions. We identified 11 mobile element insertions or structural variants involving existing elements and found that the majority of these occurred early in tumor progression. Two of the identified insertions were SVA elements, which have rarely been found in previous cancer studies. Most of the variants appear to impact intergenic regions; however, we identified a translocation interrupting MAP2K4 involving Alu elements and a deletion in YTHDF2 involving mobile elements that likely inactivate reported tumor suppressor genes. The high variant allele fraction of the MAP2K4 translocation, the loss of the other copy of MAP2K4, the recurrent loss-of-function mutations found in this gene in other human cancers, and the important function of MAP2K4 indicate that this translocation is potentially a driver mutation. Overall, using a unique longitudinal dataset, we find that most variants are likely passenger mutations in the four patients we examined, but some variants impact tumor progression.

genomics↗

bioRxiv2019

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline -- TypeTE -- which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a gold standard set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.

bioinformatics↗

bioRxiv2019

Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation

The number of de novo mutations (DNMs) found in an offsprings genome is known to increase with both paternal and maternal age. But does the rate of mutation accumulation in parental gametes differ across families? To answer this question, we analyzed DNMs in 33 large, three-generation families collected in Utah by the Centre dEtude du Polymorphisme Humain (CEPH) consortium. We observed significant variability in parental age effects on DNM counts across families, ranging from 0.24 to 3.33 additional DNMs per year. Using up to 14 grandchildren in these families, we find that 3% of DNMs originated following primordial germ cell specification (PGCS) in a parent, and differ from non-mosaic germline DNMs in their mutational spectra. We also identify a median of 3 gonosomal mutations per sample in the F1 generation, which, along with post-PGCS DNMs, occur at equivalent frequencies on the paternal and maternal haplotypes. These results demonstrate that the rate of germline mutation accumulation varies among families with similar ancestry, and confirm that parental mosaicism is a substantial source of de novo mutations in children. Data and code availabilityCode used for statistical analysis and figure generation has been deposited on GitHub as a collection of annotated Jupyter Notebooks: https://github.com/quinlan-lab/ceph-dnm-manuscript. Data files containing germline de novo mutations, as well as the gonosomal and post-primordial germ cell specification (PGCS) mosaic mutations, are included with these Notebooks. To mitigate compatibility/version issues, we have also made all notebooks available in a Binder environment, accessible at the above GitHub repository.

genetics↗

bioRxiv2018

Pedigree-based estimation of human mobile element retrotransposition rates

Germline mutation rates in humans have been estimated for a variety of mutation types, including single nucleotide and large structural variants. Here we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We utilized three tools for calling Mobile Element Insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole genome sequence (WGS) data from 603 CEPH individuals, comprising 33 three-generation pedigrees. We identified 27 de novo MEIs in 440 births. The retrotransposition rate estimates for Alu elements, one in 40, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single nucleotide variants. The L1 retrotransposition rate is one in 62 births and is within range of previous estimates (1:20-1:200 births). The SVA retrotransposition rate, one in 55 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in Alu retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.

genetics↗

bioRxiv2018

Loss of TP73 function contributes to amyotrophic lateral sclerosis pathogenesis

Much remains unknown about the genetics and pathophysiology underlying the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We analyzed exome sequences from a cohort of 87 sporadic ALS (SALS) patients and 324 healthy individuals. TP73, a homolog of the TP53 tumor suppressor gene, had five rare deleterious protein-coding variants; in a separate collection of >2,900 ALS patients we identified an additional 19 rare deleterious variants in TP73. An in vitro C2C12 myoblast growth assay confirmed that these variants impair or alter TP73 function. In vivo mutagenesis of zebrafish tp73 using CRISPR led to impaired motor neuron development and abnormal axonal morphology, concordant with ALS pathology. Together, these results demonstrate that TP73 is a risk factor for ALS, and identifies a novel dysfunctional cellular process in the pathogenesis of ALS.

genetics↗