Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases.

The total burden of rare diseases is significant worldwide, with over 300 million people being affected. Many rare diseases have both well-defined clinical phenotypes and established genetic causes. However, a remarkable proportion of patients with high clinical suspicion of a rare disease remain genetically undiagnosed and stuck in the diagnostic odyssey after having a cascade of conventional genetic tests.

A roadmap for genome projects to foster psychosocial and economic evidence to further policy and practice.

Advances in genomic sequencing (GS) have transformed personalised treatment strategies for genetic diseases across a diverse array of clinical indications, resulting in notable public health progress. However, limited evidence on the broader psychosocial and economic impacts hinders its widespread adoption in healthcare systems. The launch of genome projects offers an opportunity to address the unmet needs of a wide range of genetic diseases.

Artificial intelligence-driven genotype-epigenotype-phenotype approaches to resolve challenges in syndrome diagnostics.

Background: Decisions to split two or more phenotypic manifestations related to genetic variations within the same gene can be challenging, especially during the early stages of syndrome discovery. Genotype-based diagnostics with artificial intelligence (AI)-driven approaches using next-generation phenotyping (NGP) and DNA methylation (DNAm) can be utilized to expedite syndrome delineation within a single gene.

Methods: We utilized an expanded cohort of 56 patients (22 previously unpublished individuals) with truncating variants in the MN1 gene and attempted different methods to assess plausible strategies to objectively delineate phenotypic differences between the C-Terminal Truncation (CTT) and N-Terminal Truncation (NTT) groups.

Accelerating genetic diagnostics in retinitis pigmentosa: implementation of a semi-automated bespoke cohort analysis workflow for Hong Kong Genome Project.

The study aims to enhance the efficiency of the genetic variant curation process at the Hong Kong Genome Institute by developing a Semi-Automated Bespoke Cohort Analysis Workflow (S-BCAW) for patients with, or suspected to have, retinitis pigmentosa (RP) in the Hong Kong Genome Project (HKGP), leveraging advances in next-generation sequencing (NGS). A comparative analysis involving 79 RP patients was conducted using both the conventional manual workflow and the novel S-BCAW, which integrates initial filtering and variant classification based on ACMG guidelines, followed by detailed manual review. The diagnostic yields from both methods were identical, but the bespoke workflow reduced analysis time by approximately 60% (1.

A step forward in genetic counselling: defining practice and ethics through the Genetic Counselling Practice Consortium in Hong Kong.

Genetic counselling plays a crucial role in the genomic era, assisting in disease risk determination, diagnosis and management. The lack of an accredited local training program for genetic counselling in Hong Kong has led to pragmatic on-the-job training and diverse practice models. In view of the needs for enhanced awareness in genomic counselling practices among healthcare professionals, a collaborative effort - the Hong Kong Genetic Counselling Practice Consortium - was initiated to develop genomic medicine in Hong Kong.

The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong genome project.

Background: Genome sequencing (GS) has revolutionised the diagnostic odyssey of patients with rare genetic diseases (RDs) and accelerated large-scale genome projects globally. However, the impact of GS on patients with RDs is yet to be investigated among genome projects in Asia. The Hong Kong Genome Project (HKGP) was implemented to benefit patients and families with RDs in Hong Kong, and to increase the inclusiveness of Chinese genomic data.

De novo and inherited variants in DDX39B cause a novel neurodevelopmental syndrome.

DDX39B is a conserved member of the DEAD-box family of ATP-dependent RNA helicases, critical in mRNA metabolism across eukaryotes. DDX39B is also a core component of the TRanscription-EXport (TREX) super protein complex, and recent studies have highlighted the important role of its subunits in neurodevelopmental disorders. Here, we describe six individuals from five families, four harbouring de novo missense variants in DDX39B and one with an inherited splicing variant, presenting with variable developmental delay, congenital hypotonia, epilepsy, short stature, skeletal abnormalities, dysmorphic features and microcephaly in three patients.

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.

Whole genome sequencing in paediatric channelopathy and cardiomyopathy.

Background: Precision medicine in paediatric cardiac channelopathy and cardiomyopathy has a rapid advancement over the past years. Compared to conventional gene panel and exome-based testing, whole genome sequencing (WGS) offers additional coverage at the promoter, intronic regions and the mitochondrial genome. However, the data on use of WGS to evaluate the genetic cause of these cardiovascular conditions in children and adolescents are limited.

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.

Simpson-Golabi-Behmel syndrome type 1 with normal birth parameters.

A newborn baby born at 34 weeks and 5 days gestation was admitted for prematurity, dysmorphic features and congenital heart defects. Antenatal scan at 21 weeks showed a large-for-gestational-age foetus with a large abdominal circumference and liver, ventricular septal defect, right prominent renal pelvis and echogenic bowel. Antenatal genetic tests for overgrowth syndromes were negative.

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.

Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong.

This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue.

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.

Socio-economic costs of rare diseases and the risk of financial hardship: a cross-sectional study.

Background: To achieve universal healthcare coverage (UHC), the rare disease (RD) population must also receive quality healthcare without financial hardship. This study evaluates the impact of RDs in Hong Kong (HK) by estimating cost from a societal perspective and investigating related risk of financial hardship.

Methods: A total of 284 RD patients and caregivers covering 106 RDs were recruited through HK's largest RD patient group, Rare Disease Hong Kong, in 2020.

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.

Fibrodysplasia ossificans progressiva in Hong Kong-A case report series.

Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare condition. The diagnosis could be challenging due to its rarity and non-specific presenting symptoms. However, early diagnosis and appropriate management help in preserving patients' function and quality of life.

Diazoxide-unresponsive Hyperinsulinemic Hypoglycaemia in a Preterm Infant with Heterozygous Insulin Receptor Gene Mutation.

Homozygous or compound heterozygous mutations in insulin receptor gene () lead to marked insulin resistance and hyperglycaemia in Donohue syndrome and Rabson-Mendenhall syndrome, conditions which are associated with significant morbidity early in life. In contrast, heterozygous variants result in a milder phenotype, known as type A insulin resistance syndrome. While presentation in adults with this condition is well reported, phenotypes in infant are less well-characterized.

Neuroimaging in Primary Coenzyme-Q-Deficiency Disorders.

Coenzyme Q (CoQ) is an endogenously synthesized lipid molecule. It is best known for its role as a cofactor within the mitochondrial respiratory chain where it functions in electron transfer and ATP synthesis. However, there are many other cellular pathways that also depend on the CoQ supply (redox homeostasis, ferroptosis and sulfide oxidation).

Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses.

Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants.

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases.

Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus.

Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept.

RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts.