Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.

Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.

Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis.

Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that scan-w and ccdc69-w are not essential for viability, female development, or fertility. Analysis of mesonephros+gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome, and identifies mostly non-overlapping sets of differentially expressed genes in separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.

Countermovement jump, handgrip, and balance performance change during euhydration, mild-dehydration, rehydration, and ad libitum drinking.

Objective: To examine the effects of euhydration, mild-dehydration, rehydration, and ad libitum drinking on countermovement jump (CMJ), handgrip strength, and performance of balance error scoring system test (BESS). Methods: Eighteen healthy male subjects (mean[M]±standard deviation[SD]; age, 23±3y; body mass, 80.1 ± 9.7 kg; height, 175.8 ± 5.7 cm) participated in this study. Participants reported to the laboratory to perform CMJ, handgrip strength, and BESS with different hydration statuses (euhydrated, EUH; when they initially sensed thirst, THIRST; dehydrated, DEH; following 30 minutes of rehydration, REH; and following 24-h ad libitum drinking, AD). Results: CMJ at EUH (M±SD; 54.6 ± 3.0 cm) was significantly higher than DEH (52.8 ± 3.0 cm, p = 0.027) and REH (52.6 ± 2.8 cm, p < 0.001). However, there was no difference between DEH and REH (p = 0.643). CMJ at THIRST (54.9 ± 3.0 cm, p = 0.004) was higher than REH. Also, AD (53.8 ± 2.8 cm, p = 0.027) was higher than REH. In left handgrip strength, THIRST (48.6 ± 9.5 kg) was higher than EUH (46.7 ± 10.1 kg, p = 0.018), DEH (45.8 ± 10.0 kg, p = 0.013), REH (46.1 ± 9.5 kg, p = 0.004), and AD (47.1 ± 9.7 kg, p = 0.05). Additionally, in the single-leg stance on a foam pad, more BESS errors were found at THIRST (6 ± 2) compared to EUH (5 ± 2, p = 0.007) and AD (5 ± 2, p = 0.002). Conclusion: The findings of this study were: ∼2% of mild dehydration induced by 24-h fluid restriction decreased lower body power measured by CMJ, acute rehydration did not restore the loss of lower body power induced by dehydration, and ∼0.5-0.9% of dehydration did not decrease lower body power.

Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group.

The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results. The Association for Molecular Pathology Electronic Health Record Working Group was convened to assess the challenges and opportunities and to recommend solutions on ways to resolve current problems associated with the display and use of genomic data in electronic health records.

A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome.

In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and even within-species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.

FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells.

Fragile-X mental retardation autosomal homologue-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and mis-splicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine- and arginine-rich intrinsically disordered domain; these domains are known to promote biomolecular condensation. Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNA-dependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease.

Low coverage of HPV vaccination in the national immunization programme in Brazil: Parental vaccine refusal or barriers in health-service based vaccine delivery?

BACKGROUND: The World Health Organization has recommended the introduction of HPV vaccines into national immunization programme (NIP), but vaccination coverage remains low worldwide. We assessed the coverage and the parental acceptance of female and male HPV vaccination in Brazil after its introduction into the NIP. METHODS: We conducted a random-digit-dial survey of parents in seven major Brazilian cities from July-2015 to October-2016. A knowledge, attitude and practices questionnaire was developed and validated by expert analysis, semantic analysis, and pre-testing. RESULTS: 826 out of 2,324 (35.5%) eligible parents completed the interview. Parental acceptance of the HPV vaccine for daughters and sons 18 years of age or less was high (92% and 86%, respectively). Parents refusing vaccination were less likely to know that: HPV is sexually transmitted and causes genital warts, HPV vaccination is more beneficial before sexual debut, and HPV vaccine reactions are minor, and they were more likely to believe HPV vaccination can cause severe adverse events. Parents accepting HPV vaccine for daughters but not forsons were more likely to ignore that the vaccine is recommended for boys. Attitudes associated with HPV vaccine acceptance included: general belief in vaccines, trust in the NIP and in the HPV vaccine efficacy. Among girls eligible for HPV vaccination through the NIP, 58.4% had received a two-dose scheme and 71.1% at least one dose. "No vaccination/missed vaccination at school" was the most common reason for missed HPV vaccination in theNIP. CONCLUSIONS: One year after introduction in the NIP, most parents surveyed in Brazil accepted HPV vaccination for their daughters and sons. Low coverage in the NIP seemed to be due to challenges in adolescent vaccine delivery and HPV vaccination barriers at health-care centers, rather than to vaccine refusal.