Germline mutations are the source of evolution and contribute substantially to many health-related processes. Here we use whole-genome deep sequencing data from 693 parents-offspring trios to examine ...the de novo point mutations (DNMs) in the offspring. Our estimate for the mutation rate per base pair per generation is 1.05 × 10(-8), well within the range of previous studies. We show that maternal age has a small but significant correlation with the total number of DNMs in the offspring after controlling for paternal age (0.51 additional mutations per year, 95% CI: 0.29, 0.73), which was not detectable in the smaller and younger parental cohorts of earlier studies. Furthermore, while the total number of DNMs increases at a constant rate for paternal age, the contribution from the mother increases at an accelerated rate with age.These observations have implications related to the incidence of de novo mutations relating to maternal age.
The space environment includes unique hazards like radiation and microgravity which can adversely affect biological systems. We assessed a multi-omics NASA GeneLab dataset where mice were hindlimb ...unloaded and/or gamma irradiated for 21 days followed by retinal analysis at 7 days, 1 month or 4 months post-exposure.
We compared time-matched epigenomic and transcriptomic retinal profiles resulting in a total of 4,178 differentially methylated loci or regions, and 457 differentially expressed genes. Highest correlation in methylation difference was seen across different conditions at the same time point. Nucleotide metabolism biological processes were enriched in all groups with activation at 1 month and suppression at 7 days and 4 months. Genes and processes related to Notch and Wnt signaling showed alterations 4 months post-exposure. A total of 23 genes showed significant changes in methylation and expression compared to unexposed controls, including genes involved in retinal function and inflammatory response.
This multi-omics analysis interrogates the epigenomic and transcriptomic impacts of radiation and hindlimb unloading on the retina in isolation and in combination and highlights important molecular mechanisms at different post-exposure stages.
Abstract NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning (ML) methods hold the promise to improve ...our ability to identify important signals within highly dimensional molecular data. However, the inherent limitation of study subject numbers within a spaceflight mission minimizes the utility of ML approaches. To overcome the sample power limitations, data from multiple spaceflight missions must be aggregated while appropriately addressing intra- and inter-study variabilities. Here we describe an approach to log transform, scale and normalize data from six heterogeneous, mouse liver-derived transcriptomics datasets ( n total = 137) which enabled ML-methods to classify spaceflown vs. ground control animals (AUC ≥ 0.87) while mitigating the variability from mission-of-origin. Concordance was found between liver-specific biological processes identified from harmonized ML-based analysis and study-by-study classical omics analysis. This work demonstrates the feasibility of applying ML methods on integrated, heterogeneous datasets of small sample size.
This study presents the annotated genomic sequence and exon–intron organization of the human and mouse epidermal growth factor receptor (EGFR) genes located on chromosomes 7p11.2 and 11, ...respectively. We report that the EGFR gene spans nearly 200 kb and that the full-length 170-kDa EGFR is encoded by 28 exons. In addition, we have identified two human and two mouse alternative EGFR transcripts of 2.4–3.0 kb using both computational and experimental methods. The human 3.0-kb and mouse 2.8-kb EGFR mRNAs are predominantly expressed in placenta and liver, respectively, and both transcripts encode 110-kDa truncated receptor isoforms containing only the extracellular ligand-binding domain. We also have demonstrated that the aberrant 2.8-kb EGFR transcript produced by the human A431 carcinoma cell line is generated by splicing to a recombinant 3′-terminal exon located in EGFR intron 16, which apparently was formed as a result of a chromosomal translocation. Finally, we have shown that the human, mouse, rat, and chicken 1.8- to 3.0-kb alternative EGFR transcripts are generated by distinct splicing mechanisms and that each of these mRNAs contains unique 3′ sequences that are not evolutionarily conserved. The presence of truncated receptor isoforms in diverse species suggests that these proteins may have important functional roles in regulating EGFR activity.
Genomic and molecular characterization of preterm birth Knijnenburg, Theo A.; Vockley, Joseph G.; Chambwe, Nyasha ...
Proceedings of the National Academy of Sciences - PNAS,
03/2019, Letnik:
116, Številka:
12
Journal Article
Recenzirano
Odprti dostop
Preterm birth (PTB) complications are the leading cause of long-term morbidity and mortality in children. By using whole blood samples, we integrated whole-genome sequencing (WGS), RNA sequencing ...(RNA-seq), and DNA methylation data for 270 PTB and 521 control families. We analyzed this combined dataset to identify genomic variants associated with PTB and secondary analyses to identify variants associated with very early PTB (VEPTB) as well as other subcategories of disease that may contribute to PTB. We identified differentially expressed genes (DEGs) and methylated genomic loci and performed expression and methylation quantitative trait loci analyses to link genomic variants to these expression and methylation changes. We performed enrichment tests to identify overlaps between new and known PTB candidate gene systems. We identified 160 significant genomic variants associated with PTB-related phenotypes. The most significant variants, DEGs, and differentially methylated loci were associated with VEPTB. Integration of all data types identified a set of 72 candidate biomarker genes for VEPTB, encompassing genes and those previously associated with PTB. Notably, PTB-associated genes RAB31 and RBPJ were identified by all three data types (WGS, RNA-seq, and methylation). Pathways associated with VEPTB include EGFR and prolactin signaling pathways, inflammation- and immunity-related pathways, chemokine signaling, IFN-γ signaling, and Notch1 signaling. Progress in identifying molecular components of a complex disease is aided by integrated analyses of multiple molecular data types and clinical data. With these data, and by stratifying PTB by subphenotype, we have identified associations between VEPTB and the underlying biology.
Cumulative information available about the organization of amplified chromosomal regions in human tumors suggests that the amplification repeat units, or amplicons, can be of a simple or complex ...nature. For the former, amplified regions generally retain their native chromosomal configuration and involve a single amplification target sequence. For complex amplicons, amplified DNAs usually undergo substantial reorganization relative to the normal chromosomal regions from which they evolve, and the regions subject to amplification may contain multiple target sequences. Previous efforts to characterize the 7p11.2 epidermal growth factor receptor ) amplicon in glioblastoma have relied primarily on the use of markers positioned by linkage analysis and/or radiation hybrid mapping, both of which are known to have the potential for being inaccurate when attempting to order loci over relatively short (<1 Mb) chromosomal regions. Due to the limited resolution of genetic maps that have been established through the use of these approaches, we have constructed a 2-Mb bacterial and P1-derived artificial chromosome (BAC-PAC) contig for the EGFR region and have applied markers positioned on its associated physical map to the analysis of 7p11.2 amplifications in a series of glioblastomas. Our data indicate that EGFR is the sole amplification target within the mapped region, although there are several additional 7p11.2 genes that can be coamplified and overexpressed with EGFR. Furthermore, these results are consistent with EGFR amplicons retaining the same organization as the native chromosome 7p11.2 region from which they are derived.
Several types of epidermal growth factor receptor (EGFR) gene mutations have been reported in glioblastomas, and in nearly all cases the alterations have been reported in tumors with EGFR ...amplification. The objectives of this study were to determine the frequency and diversity of EGFR mutations in glioblastomas and to determine whether gene mutation is inevitably associated with increased EGFR gene dosage. To accomplish these aims, we sequenced cDNA products representing the entire EGFR coding region in 44 glioblastomas, half of which had EGFR amplification. Coding sequence alterations were identified in 17 of the tumors, and each of these cases had amplified EGFR. No mutations were identified in the 22 tumors without EGFR amplification. An additional 26 glioblastomas with EGFR amplification were then examined to establish more reliable frequencies for each type of mutation identified in the tumors for which the entire gene was sequenced. Transcripts associated with the most common mutation lacked coding sequence for amino acids 6-273 (67%). This mutation has been described extensively in the literature. Transcripts encoding receptors that would truncate at amino acid 958 and transcripts encoding receptors that would lack amino acids 521-603 were the next most common types of alteration. Each of these were observed in 15% of the tumors with EGFR amplification. Other mutations were observed at lower frequencies, but among these were three cases with missense mutations. Sixteen of the 48 tumors with EGFR amplification showed multiple types of EGFR mutations (33%), and in one case it was determined that multiple alterations had occurred in the same transcript. In total, these data are consistent with EGFR mutation being exclusively and frequently associated with EGFR amplification. Furthermore, the determination of multiple EGFR mutations within individual tumors suggests that glioblastomas with EGFR amplification have the capacity to produce a variety of functionally distinct EGFRs.
Whole-genome sequencing (WGS) is fast evolving into a population genetics tool to estimate effect of sequence variants on human health and fitness. However, predicting the role of variants that ...confer protection remains challenging. Given this, we hypothesized that use of large population datasets and integrative-omics data could be used to delineate the role of protective variants in specific genes involved in Ebola viral pathogenesis. As a pilot study we performed trio-based WGS on 3060 ethnically diverse individuals derived from a study in which infants (and both parents) undergo WGS, as well as other omic analyses, at birth, and are then followed prospectively. Variants in genes (eg, NPC1, CTSB, VPS11, VPS33A, etc.) known to play key roles in Ebola viral entry into human cells were evaluated for overall variant burden and loss-of-function via protein truncation. An additional gene (NPC2) with overlapping biochemical role but no clear role in Ebola viral entry pathway was used as control. Additionally, RNASeq was performed on a subset of individuals. We screened WGS data for variants with predicted large functional effects in the gene set. We identified 69 novel variants (not in dbSNP v.144), of which 7 were missense and 4 protein truncating in NPC1 in heterozygous state, compared to 3 rare missense variants in control gene NPC2. Furthermore, we identified heterozygous protein truncating mutations in genes within the Ebola viral entry pathway (eg, CTSB = 7; VPS11 = 3; VPS41 = 3) compared to only 1 heterozygous variant in NPC1. Based on NPC1 variation spectrum in our cohort, and corresponding to results from previous biological models, we predicted that 0.11%-0.37% of our diverse population would have resistance to Ebola virus. RNASeq analysis of heterozygous NPC1 truncation variants showed skew in the allelic- distribution. We conclude that whole genome and transcriptome data can serve as a tool for predictive analysis of viral susceptibility and resistance.
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