Alex Geary

@alextremophile.bsky.social

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Postdoctoral Bioinformaticial in the Computational Rare Disease Genomics group (Nicky Whiffin). univ. Oxford 🧬💻 Loves Evolution, regulation, cheese and cats. She/Her

Photographs of Joris Veltman and Margot Wyrwoll smiling
Purple logo of the Institute of genetics and cancer
Photograph of Nicky Whiffin smiling in a snowy forest
Photograph of Computational Rare Disease Genomics group at a Christmas party.
Two panels showing the odds ratios of burden testing results for cases vs controls across regions and annotation types. It shows an increased number of variants in case vs control participants, however this is modest, and for the KOZAK and 3' intron groups the odds ratios are wide.
Figure with four panels, each showing the likely mechanism of disease for the four novel diagnostic variants in this paper. Panel A shows the gene SLC2A1 with a red striped bar representing an upstream open reading from that overlaps the grey striped box (the canonical coding sequence) and extends a short distance into the 5' UTR. Panel B shows the sequence of the NIPBL gene immediately prior to the CDS start site. A red A shows the introduction of an A, forming an AG dinucleotide in the AG exclusion zone, shortly after the predicted splice branch point which is shown in blue. Panel C shows methylation analysis for the SETD5 gene in positive controls (shown in green) and negative controls (shown in purple). The two individuals with the same SETD5 identified in this study are shown as overlapping black dots in the centre of the green positive control group. Panel D shows a sashimi plot of the RNA product for the individual with the GNAS variant (black) and two controls (purple). Higher numbers in the middle block (44 vs 7 and 6) indicate retention of this intron in the affected individual vs controls.
Image with two panels. One shows a schematic of the annotation pipeline used in the analysis, with de novo variant counts at each stage, and within each annotation group, resulting in a final set of 10 variants. The second shows the 10 variants highlighted in panel 1 with reference to their genes and annotations. One gold promoter region variant in gene ZBTB18 in the PhyloP annotation group, a star indicates that this was a novel diagnosis in this analysis. One dark red 5' UTR exon region variant in gene SLC40A1 in the PhyloP annotation group, the gene name for this gene is greyed out, indicating it having been excluded from the set of good diagnostic candidates. Two dark red 5' UTR exotic region variants in MEF2C (bold for known diagnosis) and SLC2A1, which is starred to show a new diagnosis. Three 5' Intronic variants in the spliceAI group are shown in teal, two are in the gene PAX6 (bold for known diagnoses) and one in NIPBL which is starred to indicate a novel diagnosis. Two 5' Intronic variants in the spliceAI plus CADD group is shown in teal, one is in RPL26 (bold for known diagnoses) and one in SETD5 which is starred to indicate a novel diagnosis. One 3' Intronic variant in the spliceAI group is shown in teal, this variant is in the gene GNAS and is starred to indicate a novel diagnosis. The final variant is in the 3'UTR exon group with a spliceAI annotation, in the gene MFRP, the gene name is greyed out to indicate it having been excluded as a good diagnostic candidate.
Photo of Nicky Whiffin, the principal investigator of the Rare Disease Genomics group at the university of Oxford. She is smiling in front of a lush green hedge, wearing an excellent teal dress. The caption reads “Nicky Whiffin, whose team at Oxford University discovered ReNU syndrome’