Molecular and Genetic Medicine

Background: Galactosemia is a rare metabolic genetic disorder due to a deficiency of Galactose -1-Phosphate Uridyltransferase (GALT). The disorder usually affects many systems with acute as well as long-term consequences. Galactosemia is inherited as an autosomal recessive pattern. More than one hundred mutations have been identified, some associated with the severe clinical picture and others with benign or maybe asymptomatic. Here we presented a clinically normal infant with abnormal newborn screening and positive mutation most likely causing Duarte type of galactosemia. The prognosis of classical Galactosemia is poor with high morbidity and mortality rate while it is benign with Duarte type of galactosemia, which is related to complete or partial enzyme deficiency.

Material and methods: We report a female infant of Saudi origin product of consanguineous marriage (double consanguinity) With abnormal low (GALT) in repeated newborn screening tests through Dried Blood Spot (DBS) which is consistence with a genetics variant discovered by Whole Exome Sequence (WES).

Result: The constellation of clinical presentation and biochemical findings confirmed by Molecular genetics investigations showed a rare homozygous variant c.940A>G p.(Asn314Asp) in the GALT gene (OMIM:606999) which is consistence with Duarte galactosemia.

In this paper, we introduce a novel genome assembly optimization tool named LOCLA. It identifies reads aligned locally with high quality on gap flanks or scaffold boundaries, and assembles them into contigs for gap filling or scaffold connection. LOCLA enhances the quality of an assembly based on reads of diverse sequencing techniques, either 10x Genomics (10xG) Linked-Reads, PacBio HiFi reads or both. For example, with 10xG Linked-Reads, the long-range information provided by barcodes allows LOCLA to recruit additional reads belonging to the same gDNA molecule, resulting in accurate gap filling and increased sequence coverage.

In our experiments, we started by creating a preliminary draft assembly for each dataset using assembly tools such as Supernova and Canu assembler based on the type of sequencing reads. The preliminary draft assembly could either be a de novo assembly or a reference-based assembly. Then, we performed LOCLA on the assembly generally in the order of gap filling and then scaffolding. We validated LOCLA on four datasets, including three human samples and one non-model organism. For the first human sample (LLD0021C) and the non-model organism (B. sexangula), draft assemblies were generated with Supernova assembler using only 10xG Linked-Reads. We showed that LOCLA improved the draft assembly of LLD0021C by adding 23.3 million bases, which covered 28,746 protein coding regions, particularly in pericentromeric and telomeric regions. As for B. sexangula, LOCLA enhanced the assembly published by Pootakham W, et al. and by decreasing 41.4% of its gaps.

For the second human sample, the HG002 (NA24385) cell line, we mainly utilized PacBio HiFi reads. In contrast to the first human sample, we experimented on reference-based assemblies instead of de novo assemblies. We employed the RagTag reference-guided scaffolding tool to generate two draft assemblies and then filled gaps with LOCLA. The results indicated that LOCLA's candidate contig detection algorithm on gap flanks was robust, as it was able to recover a number of contigs that RagTag had not utilized, which were 27.9 million bases (22.26%) and 35.7 million bases (30.93%) for the two assemblies respectively. To evaluate the accuracy of the LOCLA-filled assemblies, we aligned them to the maternal haploid assembly of HG002 published by the Human Pan-genome Reference Consortium. We demonstrated that 95% of all sequences filled in by LOCLA have over 80% of similarity to the reference.

The third human dataset included 10x G Linked-Reads and PacBio HiFi reads of the CHM13 cell line. By utilizing reads of both sequencing techniques through gap filling and scaffolding modules of LOCLA, we added 46.2 million bases to the Supernova assembly. The additional content enabled us to identify genes linked to complex diseases (e.g., ARHGAP11A) and critical biological pathways.

Complex diseases, characterized by multifactorial inheritance patterns, are influenced by a combination of genetic and environmental factors. Genetic modifiers, secondary genetic variations that interact with primary disease-causing mutations, play a pivotal role in shaping the clinical manifestations and outcomes of complex diseases. This research article explores the concept of genetic modifiers, their mechanisms of action, and their implications in disease pathogenesis and treatment strategies. We delve into case studies across diverse disease domains, including cystic fibrosis, cardiovascular disorders, and neurodegenerative diseases, to elucidate how genetic modifiers contribute to phenotypic variability, disease severity, and response to therapeutic interventions. Additionally, we discuss emerging research methodologies, such as genome-wide association studies and functional genomics, that are advancing our understanding of genetic modifiers. Through comprehensive exploration, this article underscores the potential of genetic modifiers as therapeutic targets and diagnostic tools for personalized medicine, emphasizing the need for interdisciplinary collaborations and continued research in unraveling the intricate genetics of complex diseases.

Epigenetic modifications, crucial regulators of gene expression and cellular identity, have emerged as promising targets in molecular medicine for the treatment of diverse diseases. This research article explores the intricate world of epigenetic modifiers, elucidating their roles in shaping gene expression patterns and cellular functions. We delve into the mechanisms by which DNA methylation, histone modifications, and noncoding RNAs orchestrate epigenetic regulation. Through a comprehensive analysis, we highlight the dynamic role of epigenetic modifications in disease pathogenesis and progression, spanning cancer, neurodegenerative disorders, and cardiovascular diseases. The article underscores the potential of epigenetic modifiers as therapeutic interventions, discussing emerging strategies such as epigenome editing and targeted therapies. By examining clinical case studies and ongoing trials, we illustrate how harnessing epigenetic modifications can revolutionize disease treatment. Ethical considerations and challenges in epigenetic therapy are also addressed, emphasizing the importance of responsible innovation. In conclusion, this research article provides a comprehensive exploration of the transformative impact of epigenetic modifiers in advancing molecular medicine and paving the way for precision therapeutics.