† People involved in the organization of the challenge. ‡ People contributing data from their institutions.§ Equal senior authors.

Long non-coding RNAs (lncRNAs) can be important components in gene-regulatory networks 1 , but the exact nature and extent of their involvement in human Mendelian disease is largely unknown. Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27-63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventral nails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1 expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specific En1 activation in cis, thereby fine-tuning the gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud. Its loss results in the En1-related dorsal ventral limb phenotype, a subset of the full En1-associated phenotype. Our findings demonstrate that mutations involving lncRNA loci can result in human Mendelian disease. There has been enormous progress in exploring disease variants in the human genome. Yet, the interpretation of variants in the non-coding genome remains a challenge owing to the myriad mechanisms by which they can potentially cause disease. Besides disrupting cis-regulatory elements, non-coding variants may interfere with the function of non-coding transcripts. Indeed, a substantial fraction of the human genome is transcribed into RNA, although most transcripts lack protein-coding potential and are referred to as non-coding transcripts 2. Characterization of a small number of these RNA molecules has revealed that they may have roles as regulators of gene expression through diverse modes of action 3. However, the identification of functional non-coding transcript loci remains challenging. Thus, annotating non-coding transcript loci and unravelling their function will substantially improve our knowledge about gene regulation and the identification and interpretation of non-coding genetic variants with respect to disease pathogenesis. Non-coding deletions cause limb malformations We identified 27-63-kb non-coding deletions of chromosome 2 in three unrelated individuals (patients 1-3) with a type of limb malformation that, to our knowledge, remains undescribed. Affected individuals had a severe shortening and deformation of the legs and feet, 3/4 syndactyly of the hands, as well as the presence of nails on the palmar side of fingers IV and V (Fig. 1a, Extended Data Fig. 1a, b, Supplementary Note 1). Radiographs showed normal femora but severely shortened tibiae, triangular fibulae and malformed or absent bones in the feet (Fig. 1a, Extended Data Fig. 1a, Supplementary Note 1). Exome s...

Objective To evaluate the performance of contrast-enhanced mammography (CEM) compared to magnetic resonance imaging (MRI) for estimating residual tumor size after neoadjuvant chemotherapy (NAC) in women with newly diagnosed breast cancer. Methods The institutional review board approved this study. This prospective study included women with newly diagnosed breast cancer who underwent breast CEM and MRI at the end of the last cycle of NAC and before definitive surgery. Size of residual malignancy on post-NAC CEM and MRI was compared with surgical pathology. Agreements and correlations of CEM and MRI measurements with histological size were assessed. Results Thirty-three patients were included with a mean age of 45 years (range 22–76). The sensitivity, specificity, and positive and negative predictive value for detection of residual disease of CEM were 76%, 87.5%, 95%, and 86.4%, and those of MRI were 92%, 75%, 92%, and 75%. Comparing CEM to MRI, the mean difference was −0.8 cm, concordance coefficient was 0.7, and Pearson correlation was 0.7 (p = 0.0003). The concordance coefficient between measurements of each imaging modality and pathologic tumor size was 0.7 for CEM and 0.4 for MRI. Pearson correlation was 0.8 for CEM and 0.5 for MRI. Mean differences between CEM, MRI, and residual histopathological tumor size were 0.8 cm and 1.8 cm, respectively. Conclusions CEM has good correlation and agreement with histopathology for measuring residual disease after NAC. CEM was comparable to MRI, showing high positive predictive value and specificity for detecting residual disease.

Objective Brain metabolism, as studied by magnetic resonance spectroscopy (MRS), has been previously shown to be abnormal in Rett syndrome (RTT). However the relationship of MRS findings to age, disease severity and genotype is unknown. This study reports MRS findings in 40 RTT girls (1–14 years old) and 12 age-matched controls. Methods Single voxel, short echo time proton MRS of left frontal lobe white matter was performed. Levels of myo-inositol (mI), total choline (Cho), glutamate/glutamine (Glx), and N-acetyl aspartate (NAA) were expressed as ratios relative to creatine (Cr). Results NAA/Cr ratios decreased and mI/Cr ratios increased with age in RTT (both p<0.03) while these ratios were stable in controls. The mean Glx/Cr ratio was 36% higher in RTT than in controls (p=0.043). The mean NAA/Cr ratio was 12.6% lower in RTT patients with seizures compared to those without seizures (p=0.017). NAA/Cr ratios also decreased with increasing clinical severity score (p=0.031). Compared to patients with T158X, R255X, and R294X mutations, and C-terminal deletions, patients with the R168X mutation tended to have the highest severity score (0.01≤p≤0.11) and the lowest NAA/Cr ratio (0.029≤p<0.14). Interpretation Decreasing NAA/Cr and increasing mI/Cr with age are suggestive of progressive axonal damage and astrocytosis in RTT respectively, while increased Glx/Cr ratio may be secondary to increasing glutamate-glutamine cycling at the synaptic level. The relationships between NAA/Cr, presence or absence of seizures, and disease severity suggest that MRS provides a non-invasive measure of cerebral involvement in RTT, with greatest impairment in patients with the R168X mutation.

BACKGROUND AND PURPOSE:RTT, caused by mutations in the methyl CPG binding protein 2 (MeCP2) gene, is a disorder of neuronal maturation and connections. Our aim was to prospectively examine FA by DTI and correlate this with certain clinical features in patients with RTT.