Cancer/metagenomics:  

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

(Fred Hutch, Italy, Korea, UW, Forsyth Inst MA, Dana Farber, Harvard)
“Using PacBio long-read single-molecule real-time sequencing, we generated complete and closed genomes, with corresponding epigenetic methylomes, for 146 unique Fusobacterium strains.”
 

Gene fusions/Kinnex: 

CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution

(Broad, ETH & SIB Switzerland) – “fusion detection from long isoform reads greatly outperformed short reads, with more fusion genes and fusion transcript splicing isoforms and greater numbers of tumor single cells expressing fusions detected.”

Cancer/single-cell/Kinnex:

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia

(U of UT, MD Anderson, UNC, OH State) – “Here, we utilized MAS-seq [including Revio], a long-read scRNAseq technology, to substantially increase transcript coverage across the entire length of the transcripts and expand the set of informative mutations to link cells to cancer subclones in six CLL patients who acquired BTKC481S mutations during BTK inhibitor treatment.”
 

Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids

(Switzerland) – using MAS-Seq to obtain the most comprehensive view of the alternative splicing landscape to date of clear-cell Renal Cell Carcinoma (ccRCC). 40% previously uncharacterized, of those 37% possess a complete protein-coding ORF. “many switching events were cell and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC”

De novo detection of somatic variants in long-read single-cell RNA sequencing data
(Switzerland) – presenting “LongSom, a computational workflow leveraging LR scRNA-seq data [early Kinnex version] to call de novo somatic single-nucleotide variants (SNVs), copy-number alterations (CNAs), and gene fusions to reconstruct the tumor clonal heterogeneity.”

Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines
(China) – “constructed complex models illustrating HPV integrated genome structures in SiHa and HeLa cells”, demonstrating “the valuable capabilities of long-read sequencing in detecting and characterizing HPV genomic integration structures within human cells.”

Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach
(Switzerland) -  same 10x Genomics 3' single-cell gene expression cDNA library compared on Illumina Novaseq 6000 and PacBio Sequel IIe.
 

Clinical: 
Applications of genome sequencing as a single platform for clinical constitutional genetic testing
(Stanford, U of Chicago, LetsGetChecked CA) – review centered “on evaluating the applications of genome sequencing as a single platform for clinical constitutional genetic testing”. Highlighting HiFi sequencing for improved interrogation of clinically significant genomic regions.