Precise mass measurements of the neutron-rich 125−130 In isotopes have been performed with the TITAN Penning trap mass spectrometer. TITAN's electron beam ion trap was used to charge breed the ions to charge state q = 13+ thus providing the necessary resolving power to measure not only the ground states but also isomeric states at each mass number. In this paper, the properties of the ground states are investigated through a series of mass differentials, highlighting trends in the indium isotopic chain as compared to its proton-magic neighbor, tin (Z = 50). In addition, the energies of the indium isomers are presented. The (8 −) level in 128 In is found to be 78 keV lower than previously thought and the (21/2 −) isomer in 127 In is shown to be lower than the literature value by more than 150 keV.

BackgroundAlthough most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the genome. To ground this debate in data, it would be helpful to have a corpus of experimentally-verified cases of genes which have functionally distinct splice isoforms (FDSIs).ResultsWe established a curation framework for evaluating experimental evidence of FDSIs, and analyzed over 700 human and mouse genes, strongly biased towards genes that are prominent in the alternative splicing literature. Despite this bias, we found experimental evidence meeting the classical definition for functionally distinct isoforms for ~ 5% of the curated genes. If we relax our criteria for inclusion to include weaker forms of evidence, the fraction of genes with evidence of FDSIs remains low (~ 13%). We provide evidence that this picture will not change substantially with further curation and conclude there is a large gap between the presumed impact of splicing on gene function and the experimental evidence. Furthermore, many functionally distinct isoforms were not traceable to a specific isoform in Ensembl, a database that forms the basis for much computational research.ConclusionsWe conclude that the claim that alternative splicing vastly increases the functional repertoire of the genome is an extrapolation from a limited number of empirically supported cases. We also conclude that more work is needed to integrate experimental evidence and genome annotation databases. Our work should help shape research around the role of splicing on gene function from presuming large general effects to acknowledging the need for stronger experimental evidence.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5013-2) contains supplementary material, which is available to authorized users.

Recent years have seen a boom in the application of the next‐generation sequencing technology to the study of human disorders, including Autism Spectrum Disorder (ASD), where the focus has been on identifying rare, possibly causative genomic variants in ASD individuals. Because of the high genetic heterogeneity of ASD, a large number of subjects is needed to establish evidence for a variant or gene ASD‐association, thus aggregating data across cohorts and studies is necessary. However, methodological inconsistencies and subject overlap across studies complicate data aggregation. Here we present VariCarta, a web‐based database developed to address these challenges by collecting, reconciling, and consistently cataloging literature‐derived genomic variants found in ASD subjects using ongoing semi‐manual curation. The careful manual curation combined with a robust data import pipeline rectifies errors, converts variants into a standardized format, identifies and harmonizes cohort overlaps, and documents data provenance. The harmonization aspect is especially important since it prevents the potential double counting of variants, which can lead to inflation of gene‐based evidence for ASD‐association. The database currently contains 170,416 variant events from 10,893 subjects, collected across 61 publications, and reconciles 16,202 variants that have been reported in literature multiple times. VariCarta is freely accessible at http://varicarta.msl.ubc.ca. Autism Res 2019, 12: 1728–1736. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. Lay Summary The search for genetic factors underlying Autism Spectrum Disorder (ASD) yielded numerous studies reporting potentially causative genomic variants found in ASD individuals. However, methodological differences and subject overlap across studies complicate the assembly of these data, diminishing its utility and accessibility. We developed VariCarta, a web‐based database that aggregates carefully curated, annotated, and harmonized literature‐derived variants identified in individuals with ASD using ongoing semi‐manual curation.