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Neural networks are a common machine learning architecture for predicting phenotype from genomic sequence. This analysis finds that they err in calling the variant direction of effect, with important implications for personalized predictions.
Loss-of-function mutations in primate-specific ZNF808 cause pancreatic agenesis. Mechanistically, the loss of ZNF808 leads to the activation of the MER11 family of transposable elements in a regulatory capacity that ultimately induces a liver-specific program of gene expression during pancreatic differentiation.
A multi-ancestry genome-wide association study of prostate cancer performed in 156,319 cases and 788,443 controls identifies 187 novel risk variants associated with the disease. Genetic risk scores associated with overall risk, and risk of aggressive disease in men of African ancestry.
The mitochondrial transcription factor A is excluded from the mitochondria in spermatozoa by virtue of phosphorylation of the mitochondrial presequence. This is associated with transport to the nucleus and loss of mitochondrial DNA (mtDNA) from the mitochondria, providing a mechanistic basis for uniparental inheritance of mtDNA in humans.
Somatic SLC30A1 mutations altering the zinc efflux transporter ZnT1 cause primary aldosteronism. These mutations result in membrane depolarization and opening of voltage-gated calcium channels, stimulating CYP11B2 expression and aldosterone production.
Meta-analysis of three large whole-exome sequencing datasets highlights protein-truncating and rare missense variants associated with breast cancer susceptibility.
A comparison of somatic mutations in skin from individuals from the UK and Singapore suggests that the difference in cancer incidence between the two countries is due to markedly different mutational spectra and patterns of selection.
The resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata, encodes an unusual tandem kinase fusion protein that confers wheat leaf rust resistance.
The resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum, encodes an unusual protein kinase fusion protein that confers wheat stem rust resistance.
Targeted sequencing finds a higher burden of rare protein-truncating variants in constrained genes among schizophrenia cases of diverse ancestries. Meta-analyses with existing datasets show that this excess burden is consistent across five ancestral populations.
High-quality multimodal single-cell, bulk and spatial genomics data are prepared from low-input, frozen needle biopsy specimens collected during routine clinical procedures.