UniVar: A variant interpretation platform enhancing rare disease diagnosis through robust filtering and unified analysis of SNV, INDEL, CNV and SV.

Background: Interpreting the pathogenicity of genetic variants associated with rare diseases is a laborious and time-consuming endeavour. To streamline the diagnostic process and lighten the burden of variant interpretation, it is crucial to automate variant annotation and prioritization. Unfortunately, currently available variant interpretation tools lack a unified and comprehensive workflow that can collectively assess the clinical significance of these types of variants together: small nucleotide variants (SNVs), small insertions/deletions (INDELs), copy number variants (CNVs) and structural variants (SVs).

SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads.

Deletions and tandem duplications (commonly called CNVs) represent the majority of structural variations in a human genome. They can be identified using short reads, but because they frequently occur in repetitive regions, existing methods fail to detect most of them. This is because CNVs in repetitive regions often do not produce the evidence needed by existing short reads-based callers (split reads, discordant pairs or read depth change).

Identifying barriers and opportunities to facilitate the uptake of whole genome sequencing in paediatric haematology and oncology practice.

Background: The clinical utility of whole genome sequencing (WGS) in paediatric cancer has been demonstrated in recent years. WGS has been routinely available in the National Health Service (NHS) England for all children with cancer in England since 2021, but its uptake has been variable geographically. To explore the underlying barriers to routine use of WGS in this population across England and more widely in the United Kingdom (UK) and the Republic of Ireland (ROI), a one-day workshop was held in Cambridge, United Kingdom in October 2022.

The Key Features of a Genetic Nondiscrimination Policy: A Delphi Consensus Statement.

Importance: Governments worldwide have become increasingly cognizant of the spread of genetic discrimination (negative treatment or harm on the basis of actual or presumed genetic characteristics). Despite efforts by a number of governments to establish regulations addressing this phenomenon, public concern about genetic discrimination persists.

Objective: To identify key elements of an optimal genetic nondiscrimination policy and inform policymakers as they seek to allay genetic nondiscrimination and related public anxieties.

variants cause a phenotypic spectrum from early-onset Parkinson's disease to perinatal lethality by disrupting mitochondrial pathways.

Dissecting biological pathways highlighted by Mendelian gene discovery has provided critical insights into the pathogenesis of Parkinson's disease (PD) and neurodegeneration. This approach ultimately catalyzes the identification of potential biomarkers and therapeutic targets. Here, we identify as a new gene implicated in PD and childhood neurodegeneration.

Revealing the role of SPP1 macrophages in glioma prognosis and therapeutic targeting by investigating tumor-associated macrophage landscape in grade 2 and 3 gliomas.

Background: Glioma is a highly heterogeneous brain tumor categorized into World Health Organization (WHO) grades 1-4 based on its malignancy. The suppressive immune microenvironment of glioma contributes significantly to unfavourable patient outcomes. However, the cellular composition and their complex interplays within the glioma environment remain poorly understood, and reliable prognostic markers remain elusive.

Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly.

Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue.

A review on trends in development and translation of omics signatures in cancer.

The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents.

The growing needs of genetic counselling-Feasibility in utilization of tele-genetic counselling in Asia and Hong Kong.

The need for the expansion of genomic services has been at a record time high in the past decade. As technological advancement continues to strengthen the entire genetic and genomic pipeline and clinical operational workflow, the major challenge remains to be the speed of workforce development to meet service growth. In particular, the international expansion of genetic counselling (GC) services has been a topic of interest for the past few years.

INSurVeyor: improving insertion calling from short read sequencing data.

Insertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold.

Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations.

Purpose: This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations.

Methods: A meta-analysis was conducted to identify studies from 2011 to 2021.

Results: One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations.

Distribution based MIL pooling filters: Experiments on a lymph node metastases dataset.

Histopathology is a crucial diagnostic tool in cancer and involves the analysis of gigapixel slides. Multiple instance learning (MIL) promises success in digital histopathology thanks to its ability to handle gigapixel slides and work with weak labels. MIL is a machine learning paradigm that learns the mapping between bags of instances and bag labels.

SVsearcher: A more accurate structural variation detection method in long read data.

Structural variations (SVs) represent genomic rearrangements (such as deletions, insertions, and inversions) whose sizes are larger than 50bp. They play important roles in genetic diseases and evolution mechanism. Due to the advance of long-read sequencing (i.

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

Motivation: Many studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear.

Results: We constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status.

Rare disease emerging as a global public health priority.

The genomics revolution over the past three decades has led to great strides in rare disease (RD) research, which presents a major shift in global policy landscape. While RDs are individually rare, there are common challenges and unmet medical and social needs experienced by the RD population globally. The various disabilities arising from RDs as well as diagnostic and treatment uncertainty were demonstrated to have detrimental influence on the health, psychosocial, and economic aspects of RD families.

HFE promotes mitotic cell division through recruitment of cytokinetic abscission machinery in hepatocellular carcinoma.

HFE (Hemochromatosis) is a conventional iron level regulator and its loss of function due to gene mutations increases the risk of cancers including hepatocellular carcinoma (HCC). Likewise, studies focusing on HFE overexpression in cancers are all limited to linking up these events as a consequence of iron level deregulation. No study has explored any iron unrelated role of HFE in cancers.