Identification of an 85-kb Heterozygous 4p Microdeletion With Full Genome Analysis in Autosomal Dominant Charcot-Marie-Tooth Disease.

Background and Objectives: Charcot-Marie-Tooth disease (CMT) is a syndrome of a hereditary neurodegenerative condition affecting the peripheral nervous system and is a single gene disorder. Deep phenotyping coupled with advanced genetic techniques is critical in discovering new genetic defects of rare genetic disorders such as CMT. Methods: We applied multidisciplinary investigations to examine the neurophysiology and nerve pathology in a family that fulfilled the diagnosis of CMT2. When phenotype-guided first-tier genetic tests and whole-exome sequencing did not yield a molecular diagnosis, we conducted full genome analysis by examining phased whole-genome sequencing and whole-genome optical mapping data to search for the causal variation. We then performed a systematic review to compare the reported patients with interstitial microdeletion in the short arm of chromosome 4. Results: In this family with CMT2, we reported the discovery of a heterozygous 85-kb microdeletion in the short arm of chromosome 4 (4p16.3)[NC_000004.12:g.1733926_1819031del] spanning 3 genes [TACC3 (intron 6-exon 16), FGFR3 (total deletion), and LETM1 (intron 10-exon14)] that cosegregated with disease phenotypes in family members. The clinical features of peripheral nerve degeneration in our family are distinct from the well-known 4p microdeletion syndrome of Wolf-Hirschhorn syndrome, in which brain involvement is the major phenotype. Discussion: In summary, we used the full genome analysis approach to discover a new microdeletion in a family with CMT2. The deleted segment contains 3 genes (TACC3, FGFR3, and LETM1) that likely play a role in the pathogenesis of nerve degeneration.

Towards a reference genome that captures global genetic diversity.

The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity.

Chemical mechanism of surface-enhanced Raman scattering spectrum of pyridine adsorbed on Ag cluster: ab initio molecular dynamics approach.

The surface-enhanced Raman scattering (SERS) spectrum of pyridine adsorbed on Ag20 cluster (pyridine-Ag20 ) at room temperature is calculated by performing ab initio molecular dynamics simulations in connection with a Fourier transform of the polarizability autocorrelation function to investigate the static chemical enhancement behind the SERS spectrum. The five enhanced vibrational modes of pyridine, namely, υ6a, υ1, υ12, υ9a, and υ8a, can be assigned and identified by using a new analytical scheme, namely, single-frequency-pass filter, which is based on a Fourier transform filtering technique. To understand the factors evoking the enhancement in the SERS spectrum, the dynamic properties of molecular structures and charges for both of the free pyridine and adsorbed pyridine are analyzed. The calculated results indicate that the vibrational amplitudes of adsorbed pyridine are enhanced due to both of the electron transfer from pyridine to Ag20 cluster and the softening of pyridine bond. In addition, the N-Ag stretching within pyridine-Ag20 will couple with these five vibrational modes of pyridine. Consequently, the electron transfer between pyridine and Ag20 cluster induced by different molecular vibrational modes prompts the redistribution of electron density of pyridine. These factors collectively cause the noticeable change in polarizability during molecular vibrations and hence result in the enhancement of Raman peaks.