Publications by authors named "Sonia Davila"

Article Synopsis
  • Structural variants (SVs) play a crucial role in genetic differences that relate to traits and diseases, but most research has focused on European populations.
  • This study compiles a catalogue of over 73,000 SVs from a diverse group of 8,392 Singaporeans, revealing that about 65% of these SVs are novel and specific to Asian ancestry groups.
  • The findings help identify clinically relevant SVs and improve genetic research by addressing biases related to ancestry, which is important for equity and diversity in the field.
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Rare genetic diseases affect 5-8% of the population but are often undiagnosed or misdiagnosed. Electronic health records (EHR) contain large amounts of data, which provide opportunities for analysing and mining. Data mining, in the form of cluster analysis and visualisation, was performed on a database containing deidentified health records of 1.

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Article Synopsis
  • * The research shows a significant genetic overlap between PCV and typical nAMD, with specific pathways related to collagen and fibrosis being more involved in PCV cases.
  • * In-depth genetic analysis of PCV patients revealed rare variants in the COL1A1 gene and highlighted the role of GATA5 and related genes in processes like retinal angiogenesis and fibrosis, thus contributing to understanding AMD in the Asian demographic.
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Genomic researchers increasingly utilize commercial cloud service providers (CSPs) to manage data and analytics needs. CSPs allow researchers to grow Information Technology (IT) infrastructure on demand to overcome bottlenecks when combining large datasets. However, without adequate security controls, the risk of unauthorized access may be higher for data stored on the cloud.

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Precision medicine promises to transform healthcare for groups and individuals through early disease detection, refining diagnoses and tailoring treatments. Analysis of large-scale genomic-phenotypic databases is a critical enabler of precision medicine. Although Asia is home to 60% of the world's population, many Asian ancestries are under-represented in existing databases, leading to missed opportunities for new discoveries, particularly for diseases most relevant for these populations.

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Asian populations are under-represented in human genomics research. Here, we characterize clinically significant genetic variation in 9051 genomes representing East Asian, South Asian, and severely under-represented Austronesian-speaking Southeast Asian ancestries. We observe disparate genetic risk burden attributable to ancestry-specific recurrent variants and identify individuals with variants specific to ancestries discordant to their self-reported ethnicity, mostly due to cryptic admixture.

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Background: Consumer-grade wearable devices enable detailed recordings of heart rate and step counts in free-living conditions. Recent studies have shown that summary statistics from these wearable recordings have potential uses for longitudinal monitoring of health and disease states. However, the relationship between higher resolution physiological dynamics from wearables and known markers of health and disease remains largely uncharacterized.

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Charcot-Marie-Tooth type 1A (CMT1A) is typically characterised as a childhood-onset, symmetrical, length-dependent polyneuropathy with a gradual progressive clinical course. Acute to subacute neurological deterioration in CMT1A is rare, and has been reported secondary to overlap pathologies including inflammatory neuropathy. We identified two patients with CMT1A who presented with acute to subacute, atraumatic, entrapment neuropathies as an initial symptom.

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Multinational studies have reported monogenic etiologies in 25%-30% of children with steroid-resistant nephrotic syndrome. Such large studies are lacking in Asia. We established Deciphering Diversities: Renal Asian Genetics Network (DRAGoN) and aimed to describe the genetic and clinical spectrums in Asians.

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Article Synopsis
  • - The study investigates the role of low-frequency genetic variants in telomere length (LTL) among 25,533 Singapore Chinese individuals, emphasizing their potential link to chronic diseases and mortality.
  • - Three specific variants near the POT1, TERF1, and STN1 genes were found to significantly affect LTL, with one variant (rs79314063) showing a notably strong effect independent of common variants.
  • - The research indicates that genetically determined LTL is particularly associated with lung adenocarcinoma, and one variant (rs79617270) is linked to increased cancer mortality and may influence colon cancer risk through its effect on LTL.
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  • Exfoliation syndrome is a systemic disorder characterized by the buildup of abnormal protein aggregates in the eye, leading to increased risk of glaucoma and potential blindness.
  • The study aimed to explore the association between exfoliation syndrome and rare genetic variants that could affect protein function, using whole-exome sequencing on participants from 14 countries over 20 years.
  • Results showed that individuals with exfoliation syndrome were more likely to have harmful genetic variants in the CYP39A1 gene compared to those without the condition, indicating a potential genetic factor in the disorder.
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Background: Family history has traditionally been an essential part of clinical care to assess health risks. However, declining sequencing costs have precipitated a shift towards genomics-first approaches in population screening programs rendering the value of family history unknown. We evaluated the utility of incorporating family history information for genomic sequencing selection.

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Information technology applications for patient-collection of family health history (FHH) increase identification of elevated-risk individuals compared to usual care. It is unknown if the method of collection impacts data collected or if simply going directly to the patient is what makes the difference. The objective of this study was to examine differences in data detail and risk identification rates between FHH collection directly from individuals using paper-based forms and an interactive web-based platform.

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Background: Cardiovascular disease (CVD) imposes much mortality and morbidity worldwide. The use of "deep learning", advancements in genomics, metabolomics, proteomics and devices like wearables have the potential to unearth new insights in the field of cardiology. Currently, in Asia, there are no studies that combine the use of conventional clinical information with these advanced technologies.

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Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, we found 98.3 million SNPs and small insertions or deletions, over half of which are novel.

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Sleep is associated with various health outcomes. Despite their growing adoption, the potential for consumer wearables to contribute sleep metrics to sleep-related biomedical research remains largely uncharacterized. Here we analyzed sleep tracking data, along with questionnaire responses and multi-modal phenotypic data generated from 482 normal volunteers.

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Background: Growing evidence suggests a role for cancer susceptibility genes such as and in young-onset colorectal cancers Using a cohort of young colorectal cancer patients, we sought to identify and provide functional evidence for germline pathogenic variants of DNA repair genes not typically associated with colorectal cancer.

Methods: We recruited 88 patients with young-onset colorectal cancers seen at a general oncology center. Whole-exome sequencing was performed to identify variants in DNA repair and colorectal cancer predisposition genes.

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Whilst the underlying principles of precision medicine are comparable across the globe, genomic references, health practices, costs and discrimination policies differ in Asian settings compared to the reported initiatives involving European-derived populations. We have addressed these variables by developing an evolving reference base of genomic and phenotypic data and a framework to return medically significant variants to consenting research participants applicable for the Asian context. Targeting 10,000 participants, over 2000 Singaporeans, with no known pre-existing health conditions, have consented to an extensive clinical health screen, family health history collection, genome sequencing and ongoing follow-up.

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Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells.

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Purpose: To identify the molecular cause in five unrelated families with a distinct autosomal dominant ocular systemic disorder we called ROSAH syndrome due to clinical features of retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and migraine headache.

Methods: Independent discovery exome and genome sequencing in families 1, 2, and 3, and confirmation in families 4 and 5. Expression of wild-type messenger RNA and protein in human and mouse tissues and cell lines.

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