Human Disease Ontology 2018 update: classification, content and workflow expansion

The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-inferred mechanistic disease classifications, thus providing novel perspectives on related diseases. Expansion of disease terms, alternative anatomy, cell type and genetic disease classifications and workflow automation highlight the updates for the DO since 2015. The enhanced breadth and depth of the DO’s knowledgebase has expanded the DO’s utility for exploring the multi-etiology of human disease, thus improving the capture and communication of health-related data across biomedical databases, bioinformatics tools, genomic and cancer resources and demonstrated by a 6.6× growth in DO’s user community since 2015. The DO’s continual integration of human disease knowledge, evidenced by the more than 200 SVN/GitHub releases/revisions, since previously reported in our DO 2015 NAR paper, includes the addition of 2650 new disease terms, a 30% increase of textual definitions, and an expanding suite of disease classification hierarchies constructed through defined logical axioms.

Molecular characterization of a novel, de novo, cryptic interstitial deletion on 19p13.3 in a child with a cutis aplasia and multiple congenital anomalies

We report on a de novo constitutional deletion within G-band region 19p13.3 in a girl with cutis aplasia of the scalp, facial anomalies, structural heart abnormalities, hypotonia, mild mental retardation and conductive hearing loss which we characterized with chromosomal microarray, fluorescence in situ hybridization (FISH), and SNP analyses. Initial microarray analysis revealed a 6-BAC-clone deletion covering an approximately 1.612 Mb region within 19p13.3. Subsequent BAC FISH studies delineated the proximal deletion breakpoint to within BAC clone RP11-125C3 and the distal deletion breakpoint to within BAC clone RP11-648B14. SNP analysis showed the deletion to be of paternal origin and further refined its distal breakpoint to within a 20 kb region between rs11666694 and novel SNP2 that we identified at g.2,924,845, and its proximal deletion breakpoint to within a 22 kb region between rs35280644 and rs262562. Accordingly, the size of the deletion was revised to 1.89-1.932 Mb in length. We identified many Alu, L1, and L2 repeats, as well as SINE and LINE sequences at both deletion breakpoints. We found the deletion to encompass 71 genes, two of which appear to be good candidates for the patient's observed craniofacial and cardiac anomalies: guanine nucleotide binding protein (G protein), alpha 11 (Gq class)(GNA11), and Transducin-like Enhancer of Split 2 (E(sp1) homolog, Drosophila)(TLE2).

Disruption at the PTCHD1 Locus on Xp22.11 in Autism spectrum disorder and intellectual disability

Autism is a common neurodevelopmental disorder with a complex mode of inheritance. It is one of the most highly heritable of the complex disorders, although the underlying genetic factors remain largely unknown. Here, we report mutations in the X-chromosome PTCHD1 (patched-related) gene in seven families with autism spectrum disorder (ASD) and in three families with intellectual disability. A 167-kilobase microdeletion spanning exon 1 was found in two brothers, one with ASD and the other with a learning disability and ASD features; a 90-kilobase microdeletion spanning the entire gene was found in three males with intellectual disability in a second family. In 900 probands with ASD and 208 male probands with intellectual disability, we identified seven different missense changes (in eight male probands) that were inherited from unaffected mothers and not found in controls. Two of the ASD individuals with missense changes also carried a de novo deletion at another ASD susceptibility locus (DPYD and DPP6), suggesting complex genetic contributions. In additional males with ASD, we identified deletions in the 5' flanking region of PTCHD1 that disrupted a complex noncoding RNA and potential regulatory elements; equivalent changes were not found in male control individuals. Thus, our systematic screen of PTCHD1 and its 5' flanking regions suggests that this locus is involved in ~1% of individuals with ASD and intellectual disability.

5HTTLPR predicts left fusiform gyrus activation to positive emotional stimuli

This study was designed to replicate and extend past research examining the impact of the serotonin transporter gene-linked polymorphic region (5HTTLPR) on neural activation during emotional processing. Six women with at least one short allele were compared to six age-matched women with long/long alleles of the 5HTTLPR. Participants were shown 36 positive and 36 negative slides from the International Affective Picture Set, while functional images were acquired using a 4-T magnetic resonance imaging scanner. Although we were unable to replicate past research demonstrating relatively increased amygdala activation among individuals with an "s" allele to negative stimuli, women with an s allele evidenced decreased left fusiform gyrus activation to positive emotional stimuli (as expected). We suggest that women with a short allele may be either less attentive or less "expert" with regard to positive emotional stimuli, and ideas for future research are presented.

Contraction of collagen gels seeded with tendon cells

Knowledge of the adaptation of the soft tissue to mechanical factors and biomolecules would be essential to better understand the mechanism of tendon injury and to improve the outcome of tendon repair. The responses to these factors could be different for the distinct types of cells in the tendon: cells from the tendon sheath, fibroblasts from the epitenon surface, or fibroblasts from the internal endotenon. In this study, we examined the mechanical and histological characteristics of the rate of contraction of the collagen gel seeded with epitenon and endotenon fibroblasts. The rate of contraction and the mechanical property of the contracted construct depend on the gel concentration and also the treatment of TGF-beta1.

Characterization of a familial balanced rec(13) in a child with mild MR and his half-sibling with two structurally rearranged chromosomes 13

In this report, we describe a 7-year-old child with mild mental retardation, developmental delay, and learning disabilities. His karyotype contained a rearrangement of chromosome 13, which appeared to include a duplication of 13q31-qter and a deletion of 13p12-pter regions. The chromosomal origin of the additional material was confirmed by fluorescence in situ hybridization (FISH) using a whole chromosome painting probe specific for chromosome 13. Family studies showed that his mother carried a balanced inversion of chromosome 13 and that his half-brother carried the balanced pericentric inversion of chromosome 13 from his mother as well as another structural rearrangement involving chromosome 13 presumably from his father. The findings from this study suggested that the proband's abnormal 13 resulted from an unbalanced crossing-over between the normal and maternal inverted chromosome 13.