Saliva samples as a source of DNA for high throughput genotyping: an acceptable and sufficient means in improvement of risk estimation throughout mammographic diagnostics

Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses

BACKGROUND

Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols.

METHODS

The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results.

RESULTS

The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol.

CONCLUSION

Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.

Case report: marfan syndrome (MFS) mimicking cutaneous vasculitis

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder caused by variants in the extracellular microfibril fibrillin (FBN1) gene. Here we report an FBN1 variant in a child with an unusual skin rash mimicking cutaneous vasculitis, and mild aortic root dilatation. The case was complicated by lack of typical skeletal MFS phenotype; and severe needle phobia preventing any blood testing for workup of suspected vasculitis. Therefore inflammatory markers, autoantibody profile and general hematology/biochemistry results were unknown. Diagnosis of MFS was made via genetic testing of a saliva sample alone using a next-generation sequencing (NGS) targeted gene panel designed to screen for monogenic forms of vasculitis and noninflammatory vasculopathic mimics. This revealed the patient was heterozygous for a pathogenic frameshift variant in FBN1; NM_000138, c.1211delC, p.(Pro404Hisfs*44), predicted to cause premature protein truncation leading to loss of function. The variant has not been detected in control populations and has previously been detected in individuals with MFS. This rapid diagnosis significantly impacted the patient management: avoidance of invasive investigations; avoidance of unnecessary immunosuppression; facilitating genetic counselling of the index case and family; and directly informing lifelong monitoring and ongoing treatment for aortic root involvement from MFS. This case further emphasizes the diagnostic utility of NGS early in the diagnostic workup of paediatric patients referred with suspected vasculitis, and we emphasize that MFS can present with cutaneous vasculitic-like features in the absence of the typical Marfanoid skeletal phenotype.

Shielding of viruses such as SARS-Cov-2 from ultraviolet radiation in particles generated by sneezing or coughing: Numerical simulations of survival fractions

SARS-CoV-2 and other microbes within aerosol particles can be partially shielded from UV radiation. The particles refract and absorb light, and thereby reduce the UV intensity at various locations within the particle. Previously, we demonstrated shielding in calculations of UV intensities within spherical approximations of SARS-CoV-2 virions within spherical particles approximating dried-to-equilibrium respiratory fluids. The purpose of this paper is to extend that work to survival fractions of virions (i.e., fractions of virions that can infect cells) within spherical particles approximating dried respiratory fluids, and to investigate the implications of these calculations for using UV light for disinfection. The particles may be on a surface or in air. Here, the survival fraction (S) of a set of individual virions illuminated with a UV fluence (F, in J/m²) is assumed described by S(kF) = exp(-kF), where k is the UV inactivation rate constant (m²/J). The average survival fraction (S_p) of the simulated virions in a group of particles is calculated using the energy absorbed by each virion in the particles. The results show that virions within particles of dried respiratory fluids can have larger S_p than do individual virions. For individual virions, and virions within 1-, 5-, and 9-µm particles illuminated (normal incidence) on a surface with 260-nm UV light, the S_p = 0.00005, 0.0155, 0.22, and 0.28, respectively, when kF = 10. The S_p decrease to <10^-7, <10^-7, 0.077, and 0.15, respectively, for kF = 100. Results also show that illuminating particles with UV beams from widely separated directions can strongly reduce the S_p. These results suggest that the size distributions and optical properties of the dried particles of virion-containing respiratory fluids are likely important to effectively designing and using UV germicidal irradiation systems for microbes in particles. The results suggest the use of reflective surfaces to increase the angles of illumination and decrease the S_p. The results suggest the need for measurements of the S_p of SARS-CoV-2 in particles having compositions and sizes relevant to the modes of disease transmission.

Viruses such as SARS-CoV-2 can be partially shielded from UV radiation when in particles generated by sneezing or coughing: Numerical simulations

UV radiation can inactivate viruses such as SARS-CoV-2. However, designing effective UV germicidal irradiation (UVGI) systems can be difficult because the effects of dried respiratory droplets and other fomites on UV light intensities are poorly understood. Numerical modeling of UV intensities inside virus-containing particles on surfaces can increase understanding of these possible reductions in UV intensity. We model UV intensities within spherical approximations of virions randomly positioned within spherical particles. The model virions and dried particles have sizes and optical properties to approximate SARS-CoV-2 and dried particles formed from respiratory droplets, respectively. In 1-, 5- and 9-µm diameter particles on a surface, illuminated by 260-nm UV light from a direction perpendicular to the surface, 0%, 10% and 18% (respectively) of simulated virions are exposed to intensities less than 1/100^th of intensities in individually exposed virions (i.e., they are partially shielded). Even for 302-nm light (simulating sunlight), where absorption is small, 0% and 11% of virions in 1- and 9-µm particles have exposures 1/100^th those of individually exposed virions. Shielding is small to negligible in sub-micron particles. Results show that shielding of virions in a particle can be reduced by illuminating a particle either from multiple widely separated incident directions, or by illuminating a particle rotating in air for a time sufficient to rotate through enough orientations. Because highly UV-reflective paints and surfaces can increase the angular ranges of illumination and the intensities within particles, they appear likely to be useful for reducing shielding of virions embedded within particles.

Mutations in the tail domain of MYH3 contributes to atrial septal defect

Atrial septal defect (ASD) is one of the most common congenital heart defects diagnosed in children. Sarcomeric genes has been attributed to ASD and knockdown of MYH3 functionally homologues gene in chick models indicated abnormal atrial septal development. Here, we report for the first time, a case-control study investigating the role of MYH3 among non-syndromic ASD patients in contributing to septal development. Four amplicons which will amplifies the 40 kb MYH3 were designed and amplified using long range-PCR. The amplicons were then sequenced using indexed paired-end libraries on the MiSeq platform. The STREGA guidelines were applied for planning and reporting. The non-synonymous c. 3574G>A (p.Ala1192Thr) [p = 0.001, OR = 2.30 (1.36-3.87)] located within the tail domain indicated a highly conserved protein region. The mutant model of c. 3574G>A (p.Ala1192Thr) showed high root mean square deviation (RMSD) values compared to the wild model. To our knowledge, this is the first study to provide compelling evidence on the pathogenesis of MYH3 variants towards ASD hence, suggesting the crucial role of non-synonymous variants in the tail domain of MYH3 towards atrial septal development. It is hoped that this gene can be used as panel for diagnosis of ASD in future.