Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.

The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While the detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification and annotation remain challenging.

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation.

Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer. To resolve genome dysregulation associated with HPV integration, we performed Oxford Nanopore Technologies long-read sequencing on 72 cervical cancer genomes from a Ugandan data set that was previously characterized using short-read sequencing. We find recurrent structural rearrangement patterns at HPV integration events, which we categorize as del(etion)-like, dup(lication)-like, translocation, multi-breakpoint, or repeat region integrations.

Prognostication with Thyroid GuidePx in the context of tall cell variants.

Background: The tall cell variant of papillary thyroid cancer generally has a worse prognosis compared with the classical variant. Thyroid GuidePx is a genomic classifier capable of classifying papillary thyroid cancer into 3 molecular subtypes using fine-needle aspirate. Type 1 and 2 have low recurrence rates, particularly in early tumors (1-4 cm and N0).

The benefit of a complete reference genome for cancer structural variant analysis.

The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification and annotation remains challenging.

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses.

Background: As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification (ie. determining the composition of a sample) in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg.

Risk Factors for Early-Onset Colorectal Cancer: A Systematic Review and Meta-analysis.

Background & Aims: Despite the widespread increase in the incidence of early-onset colorectal cancer (EoCRC), the reasons for this increase remain unclear. The objective of this study was to determine risk factors for the development of EoCRC.

Methods: We conducted a systematic literature review and meta-analysis of studies examining non-genetic risk factors for EoCRC, including demographic factors, comorbidities, and lifestyle factors.

A Systematic Review of the Effect of Lifestyle Interventions on Adipose Tissue Gene Expression: Implications for Carcinogenesis.

Objective: The mechanisms driving the associations between body weight and physical activity levels and multiple types of cancer are not yet well understood. The purpose of this review was to examine the effects of lifestyle interventions on proposed biomarkers of lifestyle and cancer risk at the level of adipose tissue in humans.

Methods: Embase, MEDLINE, and CINAHL were searched by using keywords relating to exercise or diet interventions, adipose tissue biology, and outcomes of interest.