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Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the ...

POGZ truncating alleles cause syndromic intellectual disability

Background Large-scale cohort-based whole exome sequencing of individuals with neurodevelopmental disorders (NDDs) has identified numerous novel candidate disease genes; however, detailed phenotypic information is often lacking in such studies. De novo mutations in pogo transposable element with zinc finger domain (POGZ) have been identified in six independent and diverse cohorts ...

Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3

Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu–Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region ...

Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination

Background Recurrent rearrangements of the human genome resulting in disease or variation are mainly mediated by non-allelic homologous recombination (NAHR) between low-copy repeats. However, other genomic structures, including AT-rich palindromes and retroviruses, have also been reported to underlie recurrent structural rearrangements. Notably, recurrent deletions of Yq12 ...

PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

Background Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Biosciences (PacBio) enable analysis of chromosomal structural variations (SVs), but the cost to achieve the required sequence coverage across the entire human genome ...

Curcumin facilitates a transitory cellular stress response in Trembler-J mice

We have previously shown that oral administration of curcumin significantly decreases the percentage of apoptotic Schwann cells and partially mitigates the severe neuropathy phenotype of the Trembler-J (Tr-J) mouse model in a dose-dependent manner. Here we compared the gene expression in sciatic nerves of 2-week-old pups and adult Tr-J with the same age groups of wild-type mice and ...

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication—inverted triplication—duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 ...

Assessing structural variation in a personal genome—towards a human reference diploid genome

Background Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental ...

Macrophage migration inhibitory factor acts as a neurotrophin in the developing inner ear

Lisa M. Bank Lynne M. Bianchi Fumi Ebisu Dov Lerman-Sinkoff Elizabeth C. Smiley Yu-chi Shen Poornapriya Ramamurthy Deborah L. Thompson Therese M. Roth Christine R. Beck Matthew Flynn Ryan S. Teller ... , Elizabeth C. Smiley, Yu-chi Shen, Poornapriya Ramamurthy, Deborah L. Thompson, Therese M. Roth, Christine R. Beck, Matthew Flynn, Ryan S. Teller, Luming Feng, G. Nicholas Llewellyn, Brandon Holmes, Cyrrene