Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.

Balanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome and contribute substantial risk for developmental disorders (DDs). However, the rarity and lack of systematic screening for BCRs in the population has precluded unbiased analyses of the genomic features and mechanisms associated with risk for DDs versus normal developmental outcomes. Here, we sequenced and analyzed 1,420 BCR breakpoints across 710 individuals, including 406 DD cases and the first large-scale collection of 304 control BCR carriers. We found that BCRs were not more likely to disrupt genes in DD cases than controls, but were seven-fold more likely to disrupt genes associated with dominant DDs (21.3% of cases vs. 3.4% of controls; P = 1.60x10-12). Moreover, BCRs that did not disrupt a known DD gene were significantly enriched for breakpoints that altered topologically associated domains (TADs) containing dominant DD genes in cases compared to controls (odds ratio [OR] = 1.43, P = 0.036). We discovered six TADs enriched for noncoding BCRs (false discovery rate < 0.1) that contained known DD genes (MEF2C, FOXG1, SOX9, BCL11A, BCL11B, and SATB2) and represent candidate pathogenic long-range positional effect (LRPE) loci. These six TADs were collectively disrupted in 7.4% of the DD cohort. Phased Hi-C analyses of five cases with noncoding BCR breakpoints localized to one of these putative LRPEs, the 5q14.3 TAD encompassing MEF2C, confirmed extensive disruption to local 3D chromatin structures and reduced frequency of contact between the MEF2C promoter and annotated enhancers. We further identified six genomic features enriched in TADs preferentially disrupted by noncoding BCRs in DD cases versus controls and used these features to build a model to predict TADs at risk for LRPEs across the genome. These results emphasize the potential impact of noncoding structural variants to cause LRPEs in unsolved DD cases, as well as the complex interaction of features associated with predicting intolerance to alteration of three-dimensional chromatin topology.

Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) gene-editing system (CRISPR-Cas) is a valuable tool for fundamental and applied research applications. Significant improvements in editing efficacy have advanced genome editing strategies into phase 3 human clinical trials. However, recent studies suggest that our understanding of editing outcomes has lagged behind the developments made in generating the edits themselves. While many researchers have analyzed on- and off-target events through the lens of small insertions or deletions at predicted sites, screens for larger structural variants (SVs) and chromosomal abnormalities are not routinely performed. Full and comprehensive validation of on- and off-target effects is required to ensure reproducibility and to accurately assess the safety of future editing applications. Here we review SVs associated with CRISPR-editing in cells of human origin and highlight the methods used to detect and avoid them.

A digital receive beamformer implementing a "one sample per pixel" variable sampling technique is described. The sampling method reduces the required sampling rates by a factor of 3, and reduces the data capture rate by a factor of 2, in comparison with the previous systems based on variable sampling. The sampling method is capable of estimating broadband pulse envelopes accurate for bandwidths up to 83.0%. This beamforming method has been implemented on a field-programmable gate array with maximum transmit and receive delay errors measured to be less than ±1.0 ns. The beamformer was tested and verified on a previously described 45-MHz 64-element phased array. The system generates images with 128 lines, 512 pixels per RF line, and 2 transmit focal zones. The system generates images with approximately 55 dB of dynamic range and was tested by imaging wire targets submersed in a water bath, wire targets embedded in a tissue phantom, and real-time in vivo imaging of a human wrist.

We have developed a new, fast, and simple 3-D imaging approach referred to as Simultaneous Azimuth and Fresnel Elevation (SAFE) compounding using a bias-sensitive crossed-electrode array. The principle behind this technique is to perform conventional plane-wave compounding with a back set of electrodes, while implementing a reconfigurable Fresnel elevation lens with an orthogonal set of front electrodes. While a Fresnel lens would usually result in unacceptable secondary lobe levels, these lobes can be suppressed by compounding different Fresnel patterns. The azimuthal and elevational planes can be simultaneously compounded to increase the beam quality with no loss in frame rate. A 10-MHz, $64 \times 64$ element crossed-electrode relaxor array was fabricated on an electrostrictive one-to-three composite substrate to demonstrate the SAFE compounding approach. The electrostrictive composite array has a measured electromechanical coupling coefficient ( $k_{t}$ ) of 0.62 with a bias voltage of 90 V and a measured two-way pulse bandwidth of 60%. The electrical impedance magnitude of array elements on resonance was measured to be $90~\Omega$ with a phase angle of -35°. Radiation patterns were simulated showing a -6-dB beamwidth of $330~\mu \text{m}$ with secondary lobe levels suppressed more than -60 dB in the azimuth dimension, and a -6-dB beamwidth of $450~\mu \text{m}$ with secondary lobe levels suppressed to -50 dB in the elevation dimension after 64 compounds. Experimental radiation patterns were collected and found to be in good agreement with simulations. Experimental 3-D images of wire phantoms were collected using a Verasonics experimental ultrasound system.