Index selection of beef cattle for growth and milk production using computer simulation modelling

The Texas A&M University (TAMU) Beef Cattle Production model was expanded to include basic concepts of quantitative genetics. The traits simulated were birth weight, yearling weight, mature weight and milk production. The progeny inherited attributes from both the sire and the dam. The incorporation of genetic concepts into the model allowed for the introduction of variation between individuals and generations. This was achieved by interfacing the original model with stochastic genetic subroutines including a restricted selection index for desired genetic change. The index included birth weight and yearling weight. In addition, a function for estimating dystocia was also added. The model was used to simulate selection strategies for a small-to-moderate size breed of cattle and a large-size breed using a restricted selection index. There was an increase in both birth and yearling weight after 20 years of selection in the small-to-moderate size breed, and there was also an increase in dystocia. Antagonistic selection to decrease birth weight and increase yearling weight was simulated for the large breed. Birth weight and dystocia problems declined while yearling weight increased for all classes of animals. In both experiments correlated responses were recorded for mature size and milk production. It was concluded that the modified TAMU Beef Cattle Production model offers breeders an opportunity to compare different selection strategies and evaluate different breeding plans. (South African Journal of Animal Science, 2001, 31(2): 65-76

ASHLEYS: automated quality control for single-cell Strand-seq data

Single-cell DNA template strand sequencing (Strand-seq) enables chromosome length haplotype phasing, construction of phased assemblies, mapping sister-chromatid exchange events and structural variant discovery. The initial quality control of potentially thousands of single-cell libraries is still done manually by domain experts. ASHLEYS automates this tedious task, delivers near-expert performance and labels even large data sets in seconds. AVAILABILITY AND IMPLEMENTATION: github.com/friendsofstrandseq/ashleys-qc, MIT license

When is a growth-friendly strategy warranted? A matched comparison of growing rods versus primary posterior spinal fusion in juveniles with early-onset scoliosis

Background: In 7 to 11-year-old juveniles with severe early-onset scoliosis (EOS) the optimal surgical option remains uncertain. This study compares growing rods (GRs) followed by definitive posterior spinal fusion (PSF) versus primary PSF in this population. We hypothesized that the thoracic height afforded by GRs would be offset by increased rigidity, more complications, and more operations. Methods: This retrospective comparative study included EOS patients aged 7.0 to 11.9 years at index surgery treated with GR→PSF or primary PSF during 2013 to 2020. Primary outcomes were thoracic height gain (ΔT1-12H), major curve, complications, and total operations. Primary PSFs were matched with replacement 1-to-n to GR→PSFs by age at index, etiology, and major curve. Results: Twenty-eight GR→PSFs met criteria: 19 magnetically controlled GRs and 9 traditional GRs. Three magnetically controlled GRs were definitively explanted without PSF due to complications. The remaining 25 GR→PSFs were matched to 17 primary PSFs with 100% etiology match, mean Δ major curve 1 degree, and mean Δ age at index 0.5 years (PSFs older). Median ΔT1-12H pre-GR to post-PSF was 4.7 cm with median deformity correction of 37%. Median ΔT1-12H among primary PSFs was 1.9 cm with median deformity correction of 62%. GR→PSFs had mean 1.8 complications and 3.4 operations. Primary PSFs had mean 0.5 complications and 1.3 operations. Matched analysis showed adjusted mean differences of 2.3 cm greater ΔT1-12H among GR→PSFs than their matched primary PSFs, with 25% less overall coronal deformity correction, 1.2 additional complications, and 2.2 additional operations per patient. Conclusions: In juveniles aged 7 to 11 with EOS, on average GRs afford 2 cm of thoracic height over primary PSF at the cost of poorer deformity correction and additional complications and operations. Primary PSF affords an average of 2 cm of thoracic height gain; if an additional 2 cm will be impactful then GRs should be considered. However, in most juveniles the height gained may not warrant the iatrogenic stiffness, complications, and additional operations. Surgeons and families should weigh these benefits and harms when choosing a treatment plan. Level of Evidence: Level III - retrospective comparative study

Inversion polymorphism in a complete human genome assembly

The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2T reference genome and compared it to the GRCh38 reference. We find a ~ 21% increase in sensitivity improving mapping of 63 inversions on the T2T reference. We identify 26 misorientations within GRCh38 and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. Analysis of 10 additional samples reveals novel rare inversions at chromosomes 15q25.2, 16p11.2, 16q22.1-23.1, and 22q11.21

Gaps and complex structurally variant loci in phased genome assemblies

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

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution

Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species

A fully phased accurate assembly of an individual human genome

The prevailing genome assembly paradigm is to produce consensus sequences that "collapse" parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing (Strand-seq) and combine them with high-fidelity (HiFi) long sequencing reads, in a novel reference-free workflow for diploid de novo genome assembly. Employing this strategy, we produce completely phased de novo genome assemblies separately for each haplotype of a single individual of Puerto Rican origin (HG00733) in the absence of parental data. The assemblies are accurate (QV > 40), highly contiguous (contig N50 > 25 Mbp) with low switch error rates (0.4%) providing fully phased single-nucleotide variants (SNVs), indels, and structural variants (SVs). A comparison of Oxford Nanopore and PacBio phased assemblies identifies 150 regions that are preferential sites of contig breaks irrespective of sequencing technology or phasing algorithms

Functional analysis of structural variants in single cells using Strand-seq

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. The challenge to systematically discover SVs in single cells remains unsolved, with copy-neutral and complex variants typically escaping detection. We developed single cell tri-channel-processing (scTRIP), a computational framework that jointly integrates read depth, template strand and haplotype phase to comprehensively discover SVs in single cells. We surveyed SV landscapes of 565 single cell genomes, including transformed epithelial cells and patient-derived leukemic samples, and discovered abundant SV classes including inversions, translocations and large-scale genomic rearrangements mediating oncogenic dysregulation. We dissected the ‘molecular karyotype’ of the leukemic samples and examined their clonal structure. Different from prior methods, scTRIP also enabled direct detection and discrimination of SV mutational processes in individual cells, including breakage-fusion-bridge cycles. scTRIP will facilitate studies of clonal evolution, genetic mosaicism and somatic SV formation, and could improve disease classification for precision medicine