Biology subjects

Underhill, H. R.

Publications and source records attributed to Underhill, H. R..

3 recordsLinked to original sources

bioRxiv2025

The insidious degeneration of white matter and cognitive decline in Fabry disease

Fabry disease is a rare X-linked deficiency of lysosomal alpha-galactosidase that causes glycolipid accumulation in tissues, including the brain. The most common neurologic sequelae of Fabry are cognitive decline and white matter lesions (WMLs) on brain magnetic resonance imaging (MRI). In the at-large population, however, WMLs are non-specific, highly prevalent, and most are clinically silent. Thus, we compared Fabry to typical brain aging to identify factors unique to Fabry-related cognitive decline. Twenty adult Fabry patients (75% female; median age 36.4 yrs, range: 19.8-63.2 yrs; 95% on enzyme replacement therapy) without a history of stroke or other neurologic diseases and 20 age/sex-matched healthy controls were enrolled in a case-control study. All participants underwent a neurocognitive assessment and a 3.0 T MRI study of the brain that used structural MRI (e.g., fluid-attenuated inversion recovery, FLAIR), semi-quantitative MRI (e.g., normalized FLAIR signal intensity), and quantitative MRI (diffusion tensor imaging, bound-pool fraction imaging). During a blinded review of structural MRIs, a neuroradiologists categorization of case-control status did not correspond to disease status (Fishers test, P>0.99) but rather to age (P=0.004), indicating qualitative changes associated with Fabry were similar to normal age-related brain alterations. Using quantitative MRI, however, we detected evidence of microstructural damage in the white matter of younger Fabry adults (<40 yrs). With age, WML severity increased and the corpus callosum atrophied in Fabry, phenomena absent in controls and consistent with progressive tissue damage. Neurocognitive assessments identified trends for lower verbal intelligence quotient and executive function in the younger Fabry participants, which became statistically significant in the older Fabry cohort. Our data indicate that the early onset of microstructural damage in Fabry drives the insidious degeneration of white matter, leading to reduced cognition. Aging Fabry patients may benefit from serial cognitive assessments to identify unmet therapeutic needs.

genetics↗

bioRxiv2019

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential yet more difficult than in studies of germline variation. In most genomic studies of tumors, genetic variation is frequently detected through pairwise comparisons of the tumor and a matched normal tissue from the sample donor, and in many cases, only somatic variants are reported. The disjoint genotype information that results hinders the use of existing tools that detect sample swaps solely based on genotypes of germline variants. To address this problem, we have developed somalier, which can operate directly on the alignments, so as not to require jointly-called germline variants. Instead, somalier extracts a small sketch of informative genetic variation for each sample. Sketches from hundreds of biopsies and normal tissues can then be compared in under a second. This speed also makes it useful for checking relatedness in large cohorts of germline samples. Somalier produces both text output and an interactive visual report that facilitates the detection and correction of sample swaps using multiple relatedness metrics. We introduce the tool and demonstrate its utility on a cohort of five glioma samples each with a normal, tumor, and cell-free DNA sample. Applying somalier to high-coverage sequence data from the 1000 Genomes Project also identifies several related samples. Somalier can be applied to diverse sequencing data types and genome builds, and is freely available for academic use at github.com/brentp/somalier.

bioinformatics↗

bioRxiv2016

Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

The interpretation of genetic variants identified during clinical sequencing has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC). Genuinely pathogenic variants, particularly in genes associated with severe autosomal dominant conditions, are assumed to be absent or extremely rare in these databases. Clinical exome sequencing of a six-year-old female patient with seizures, global developmental delay, dysmorphic features and failure to thrive identified an ASXL1 variant that was previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype matched the presentation of the patient, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Interrogation of the literature revealed that acquired somatic mosaicism of ASXL1 variants (including known pathogenic variants) during hematopoietic clonal expansion may be concomitant with aging in healthy individuals. We examined all high quality ASXL1 predicted truncating variant calls in the ExAC database and determined the majority could be attributed to this phenomenon. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like Bohring-Opitz syndrome have reduced penetrance, or the misclassification of potentially pathogenic variants.

genetics↗