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Genome Research Papers Present Sequencing Method, Atlantic Herring Assembly, More

A University of Utah team outlines a sequencing strategy designed to assess the capped 5' ends of RNA in formalin-fixed, paraffin-embedded (FFPE) samples. The method — called FFPEcap-seq — includes template switching and an enzymatic enrichment step to boost the representation of 5' RNA ends, the researchers explain, noting that the strategy shares features with existing START-seq and nanoCAGE library construction methods. Based on their results, including analyses on archival FFPE blocks from two endometrial adenocarcinoma samples that were a decade or more old, the authors call FFPEcap-seq "a new method for accurately quantifying transcripts from FFPE-derived RNA." They note that since the approach "can be performed in less than a day with standard laboratory equipment and costs less than $15 to construct, we believe it is an attractive method for interrogating gene expression in FFPE samples."

Researchers from Sweden, the US, and elsewhere share findings from a new effort to sequence, assemble, and analyze the genome of the Atlantic herring, Clupea harengus. The team reasoned that a chromosome-level genome assembly could improve ecological adaptation analyses that use the fish as a model organism. Using Pacific Biosciences long reads, Hi-C long-range chromatin interaction-based scaffolds, SNP genotyping, and linkage map data, the investigators put together a 726 megabase hybrid assembly for the Atlantic herring, spanning 26 autosomal chromosomes. When they compared it with available chromosome-level assemblies for five other bony fish, the authors found that the herring genome has undergone more frequent rearrangements within rather than between chromosomes, including a large chromosome 12 inversion that differs between herring populations and may contribute to adaptations.

Finally, a team from Canada, the US, and Italy presents an algorithm aimed at retracing tumor phylogeny with a combination of single-cell and bulk sequence data. The researchers assessed computational strategies for bringing together the two sequence types, settling on an approach dubbed "phylogeny of tumors using integrated bulk and single-cell sequencing data," or PhISCs, that takes into account sources of allele dropout or variable coverage in single-cell sequence data. After applying PhISCs to simulated data and to real sequence datasets from colorectal and childhood acute lymphoblastic leukemia cases, the authors conclude that PhISCs "is not only very efficient but is also more accurate than the available alternatives."