The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change.

PURPOSE: Variants of uncertain significance (VUS) are a common result of diagnostic genetic testing and can be difficult to manage with potential misinterpretation and downstream costs, including time investment by clinicians. We investigated the rate of VUS reported on diagnostic testing via multi-gene panels (MGPs) and exome and genome sequencing (ES/GS) to measure the magnitude of uncertain results and explore ways to reduce their potentially detrimental impact. METHODS: Rates of inconclusive results due to VUS were collected from over 1.5 million sequencing test results from 19 clinical laboratories in North America from 2020 to 2021. RESULTS: We found a lower rate of inconclusive test results due to VUSs from ES/GS (22.5%) compared with MGPs (32.6%; P < .0001). For MGPs, the rate of inconclusive results correlated with panel size. The use of trios reduced inconclusive rates (18.9% vs 27.6%; P < .0001), whereas the use of GS compared with ES had no impact (22.2% vs 22.6%; P = ns). CONCLUSION: The high rate of VUS observed in diagnostic MGP testing warrants examining current variant reporting practices. We propose several approaches to reduce reported VUS rates, while directing clinician resources toward important VUS follow-up.

The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles.

Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.

Frequency of frontotemporal dementia gene variants in C9ORF72, MAPT, and GRN in academic versus commercial laboratory cohorts.

BACKGROUND: Frontotemporal lobar degeneration (FTLD) is a leading cause of dementia, and elucidating its genetic underpinnings is critical. FTLD research centers typically recruit patient cohorts that are limited by the center's specialty and the ways in which its geographic location affects the ethnic makeup of research participants. Novel sources of data are needed to get population estimates of the contribution of variants in known FTLD-associated genes. METHODS: We compared FLTD-associated genetic variants in microtubule-associated protein tau (MAPT), progranulin (GRN), and chromosome nine open reading frame 72 (C9ORF72) from an academic research cohort and a commercial clinical genetics laboratory. Pathogenicity was assessed using guidelines of the American College of Medical Genetics and Genomics and a rule-based DNA variant assessment system. We conducted chart reviews on patients with novel or rare disease-associated variants. RESULTS: A total of 387 cases with FTLD-associated variants from the commercial (n=2,082) and 78 cases from the academic cohort (n=2,089) were included for analysis. In the academic cohort, the most frequent pathogenic variants were C9ORF72 expansions (63%, n=49), followed by GRN (26%, n=20) and MAPT (11%, n=9). Each gene's contribution to disease was similarly ranked in the commercial laboratory but differed in magnitude: C9ORF72 (89%, n=345), GRN (6%, n=24), and MAPT (5%, n=19). Of the 37 unique GRN/MAPT variants identified, only six were found in both cohorts. Clinicopathological data from patients in the academic cohort strengthened classification of two novel GRN variant as pathogenic (p.Pro166Leufs*2, p.Gln406*) and one GRN variant of unknown significance as a possible rare risk variant (p.Cys139Arg). CONCLUSION: Differences in gene frequencies and identification of unique pathogenic alleles in each cohort demonstrate the importance of data sharing between academia and community laboratories. Using shared data sources with well-characterized clinical phenotypes for individual variants can enhance interpretation of variant pathogenicity and inform clinical management of at-risk patients and families.

The identification of serum biomarkers of high-let radiation exposure and biological sequelae.

In the event of a nuclear detonation, thousands of people will be exposed to non-lethal radiation doses. There are multiple long-term health concerns for exposed individuals who receive non-lethal radiation exposures. Low doses of radiation, especially of high linear energy transfer (LET) radiation, can lead to the development of neurocognitive defects. The identification of serum biomarkers that can be used to monitor the emergence of the long-term biological sequelae of radiation exposure, such as neurocognitive defects, would greatly help the post-exposure health monitoring of the affected population. The authors have determined the impact that cranial irradiation with 2 Gy of high LET (150 keV um) has on the ability of rats to perform spatial memory tasks, and identified serum protein changes that are biomarkers of radiation exposure and of radiation-induced neurocognitive impairment. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy (MALDI TOF-TOF) analysis of weak cation exchange (WCX) enriched serum protein preparations identified 23 proteins of interest: 10 were biomarkers of physical radiation dose, with six showing increased expression and four being undetectable in the irradiated rat serum. Four proteins were uniquely expressed in those rats that had good spatial memory and nine proteins were markers of bad spatial memory. This study provides proof of the concept that serum protein profiling can be used to identify biomarkers of radiation exposure and the emergence of radiation-sequelae in this rat model, and this approach could be easily applied to other systems to identify radiation biomarkers.

Proteomic expression profiling and identification of serum proteins using immobilized trypsin beads with MALDI-TOF/TOF.

MALDI-TOF mass spectrometry is a widely used technique for serum protein expression profiling and biomarker discovery. Many profiling strategies typically employ chemical affinity beads or surfaces to decrease sample complexity of dynamic fluids such as serum or plasma. However, many of the proteins captured on a particular surface or bead are not resolved in the lower mass ranges where time-of-flight mass spectrometers are most effective. Thus, a majority of reported protein expression profiling studies primarily interrogate the native low molecular mass constituents of the target sample. We report an expression profiling workflow that utilizes immobilized trypsin paramagnetic beads following an initial affinity bead fractionation step, thereby reducing large mass proteins to peptides that are better suited to analysis and sequencing determinations. Our bead-based trypsin approach resulted in more efficient digestion of complex serum protein extracts at short incubation times. This method was reproducible and readily adaptable to robotic sample handling and may be combined in tandem with other bead fractionation surfaces. When weak cationic and weak anionic bead surfaces were used, experimental conditions were optimized for tandem combinations of these beads with the immobilized trypsin step to produce an efficient serum fractionation strategy. A proof-of-concept pilot experiment using pooled human serum samples demonstrating reproducibility is presented, along with the sequence determination of selected tryptic peptides of serum proteins.

Serum proteomic biomarker discovery reflective of stage and obesity in breast cancer patients.

BACKGROUND: Currently no standardized blood test exists for breast cancer screening or staging purposes. The goals of this study were to use proteomic mass spectrometry approaches for profiling, fractionation, and identification of serum proteins from breast cancer patients for discovery of new biomarkers of stage and nodal status. STUDY DESIGN: Samples from 150 patients were collected preoperatively for patients undergoing breast biopsy. Serum was processed using weak cation exchange (WCX) fractionation and analyzed with matrix-assisted laser desorption ionization time of flight mass spectrometry. Spectra were processed and group profiles, peak statistics, and cross-validation scores were determined using a k-nearest neighbor genetic algorithm. Pools of subgroups based on stage, race, and obesity were processed with WCX fractionation followed by trypsin digestion. Differentially expressed proteins and peptides were identified by tandem mass spectrometry. RESULTS: Matrix-assisted laser desorption ionization time of flight proteomic profiling using WCX capture of serum proteins resulted in correct cancer stage classifications ranging from 72% to 84%. Nodal status was classified correctly with 88% cross-validation scores. Levels of endogenous low mass peptide fragments derived from kininogen, fibrinogen, plasminogen, and inter-alpha-trypsin inhibitor heavy chain 4 protein were increased in cancer stage III and stage IV samples. Adding trypsin digestions with WCX capture indicated increased levels of alpha-2-HS-glycoprotein, prothrombin, and serum amyloid A in stage IV samples. Obesity, but not race, was a factor in the relative levels of detected proteins/peptides. CONCLUSIONS: WCX fractionation alone or with trypsin digestion of serum suggest it can be possible to use a panel of proteins to predict breast cancer stage and nodal status. Additional study is required on the role of inflammatory molecules in breast cancer development.