Scientific publications

In the FIRST ever peer-reviewed paper published on Onso and SBB technology, researchers demonstrate the superior accuracy and precision of Onso when compared with ILMN SBS technology.

In a recent preprint, researchers from Aligning Science Across Parkinson’s MD, Broad, Yale, Harvard, Banner Sun AZ, Genentech conducted a detailed of analysis of protocols for “allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level”. The study employed single-nucleus RNA-Seq (snRNA-Seq) as introns in pre-mRNA that were enriched for heterozygous variants, thus facilitating allelic assignments for ASE, concluding that allele-specific expression (ASE) analysis is better with HiFi – more accurate, cost-effective, and enabling isoform resolution vs. ILMN short-reads.

In a preprint led by UW and 18 additional institutions, researchers unlock the secrets of genetic inheritance across four generations using HiFi sequencing. This study marks “the most comprehensive, publicly available “truth set” of all classes of genomic variants”

a preprint led by UW in combination with 59 other institutions offers a major leap in our understanding of what it means to be human. Through this study, researchers walk away with “a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives”

In this preprint, researchers from JHU and Penn State conducted “first work to systematically analyze and report non-canonical recombination events in long-read datasets and assemblies”

In this preprint, researchers from PacBio, U UT, Radboud Netherlands, Mt. Sinai, Genomics England UK found that an expansion of TRGT identifies “all types of de novo TR mutations (including expansions, contractions, and compositional changes) within family trios”, allows detection of subtle variations often overlooked in vcf files, and “improves precision and specificity of de novo mutation (DNM) identification, reducing the number of de novo candidates by an order of magnitude compared to genotype-based approaches”

In this preprint, authors find that “targeted Fiber-seq enables the production of targeted long-read sequencing chromatin maps to resolve the heterogeneity of genetic and chromatin architectures with single-molecule precision”

In this study, researchers out of Denmark and Sweden provide a detailed comparison of HiFi vs. ONT for full-length 18S sequencing on “a precisely defined synthetic eukaryotic mock community”

In this preprint, scientists from Denmark, Australia, and Austria, conducted a study where HiFi sequencing was used for rRNA operon sequencing for 449 (multiplexed in pools of 92 samples) microbiome samples (14.9 million bacterial (median 4,528 bp, containing both 16S and 23S) and 13.4 million eukaryotic rRNA operon sequences (median 4,035 bp, containing both 18S and 28S)). “This dataset is an order of magnitude larger than the current most comprehensive database SILVA 138.1”, and provides “an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.”

Most human cells contain two non-identical genomes, and differences in their regulation underlie human development and disease. We demonstrate that Fiber-seq Inferred Regulatory Elements (FIREs) enable the accurate quantification of chromatin accessibility across the 6 Gbp diploid human genome with single-molecule and single-nucleotide precision. We find that cells can harbor >1,000 regulatory elements with haplotype-selective chromatin accessibility (HSCA) and show that these elements preferentially localize to genomic loci containing the most human genetic diversity, with the human leukocyte antigen (HLA) locus showing the largest amount of HSCA genome-wide in immune cells. Furthermore, we uncover HSCA elements with sequence non-deterministic chromatin accessibility, representing likely somatic epimutations, and show that productive transcription from the inactive X chromosome is buttressed by clustered promoter-proximal elements that escape X chromosome inactivation.

In this preprint, HiFi reveals segment duplications (SDs) unresolvable by short reads. This missing info is essential for understanding human disease, evolution and diversity. Researchers from HGSVC, UW, Altos Labs, JAX, CMKC conducted a study including a “population genetics survey of SDs by analyzing 170 [all HiFi] human genome assemblies where the majority of SDs are fully resolved using long-read sequence assembly.”

In this paper, researchers from China performed both PacBio Kinnex & ONT sequencing “with 10x genomics scRNA-seq and compared them to the benchmark NGS using exact the same cDNA libraries of different sample sizes”:

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of a gene family. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 families with exceptionally low within-family diversity, where extensive gene conversion and unequal-crossing over have resulted in highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 de novo SNVs and 4 de novo gene conversion events, 2 of which are non-allelic. Finally, we summarized extensive genetic diversity in 9 medically relevant genes previously considered challenging to genotype. Paraphase provides a framework for resolving gene paralogs, enabling accurate testing in medically relevant genes and population-wide studies of previously inaccessible genes.

RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform expression varies along one or more axes. Splicing, transcription start and polyadenylation sites vary strongly between cell types, influence protein architecture and associate with disease-linked variation. Additionally, neurotransmitter transport and synapse turnover genes harbor cell-type variability across anatomical regions. Regulation of cell-type-specific splicing is pronounced in the postnatal day 21-to-postnatal day 28 adolescent transition. Developmental isoform regulation is stronger than regional regulation for the same cell type. Cell-type-specific isoform regulation in mice is mostly maintained in the human hippocampus, allowing extrapolation to the human brain. Conversely, the human brain harbors additional cell-type specificity, suggesting gain-of-function isoforms. Together, this detailed single-cell atlas of full-length isoform regulation across development, anatomical regions and species reveals an unappreciated degree of isoform variability across multiple axes.