Physics at the Large Hadron Collider (LHC) and the International e+e- Linear Collider (ILC) will be complementary in many respects, as has been demonstrated at previous generations of hadron and lepton colliders. This report addresses the possible interplay between the LHC and ILC in testing the Standard Model and in discovering and determining the origin of new physics. Mutual benefits for the physics programme at both machines can occur both at the level of a combined interpretation of Hadron Collider and Linear Collider data and at the level of combined analyses of the data, where results obtained at one machine can directly influence the way analyses are carried out at the other machine. Topics under study comprise the physics of weak and strong electroweak symmetry breaking, supersymmetric models, new gauge theories, models with extra dimensions, and electroweak and QCD precision physics. The status of the work that has been carried out within the LHC/ILC Study Group so far is summarized in this report. Possible topics for future studies are outlined. © 2006 Elsevier B.V. All rights reserved.

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals¹. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

The cross section of top quark-antiquark pair production in proton-proton collisions at [Formula: see text] is measured by the CMS experiment at the LHC, using data corresponding to an integrated luminosity of 2.2[Formula: see text]. The measurement is performed by analyzing events in which the final state includes one electron, one muon, and two or more jets, at least one of which is identified as originating from hadronization of a b quark. The measured cross section is [Formula: see text], in agreement with the expectation from the standard model.