Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels.

Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count - both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders.

BACKGROUND: Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression. METHODS: We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance. RESULTS: We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs. CONCLUSION: Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.

High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders.

Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

Characterisation of gut microbiota composition in patients with axial spondyloarthritis and its modulation by TNF inhibitor treatment.

OBJECTIVE: To assess whether gut microbiota composition is associated with patient characteristics and may have predictive value on the response to TNF inhibitor (TNFi) treatment in axial spondyloarthritis (AxSpA). METHODS: The study involved 61 patients fulfilling the Assessment of SpondyloArthritis International Society classification criteria for AxSpA. All patients had active disease despite non-steroidal anti-inflammatory drugs intake and were eligible for treatment with a TNFi. At baseline, the mean Ankylosing Spondylitis Disease Activity Score was 2.9±1 and mean C reactive protein (CRP) level 9.7±11.4 mg/L. Bacterial 16S ribosomal RNA gene sequencing was performed on stool samples collected at baseline (month 0 (M0)) and 3 months after TNFi initiation (month 3 (M3)). Alpha and beta diversity metrics were calculated on the relative abundance of core operational taxonomic units (OTUs). RESULTS: The HLA-B27 status affected at least in part the global composition of faecal microbiota at M0 as well as the abundance/prevalence of several anaerobic bacteria in the families Oscillospiraceae, Lachnospiraceae and Bifidobacteriaceae. In contrast, smoking affected the global composition of faecal microbiota at both M0 and M3. The prevalence/abundance of seven bacterial OTUs at M0 was associated with response to TNFi treatment. One of the candidates, present only in non-responders, is the genus Sutterella, and the other six candidates are in the class Clostridia. CONCLUSIONS: Several SpA patients' characteristics modulate the composition of gut microbiota as did TNFi treatment. Moreover, the abundance/prevalence of seven OTUs at baseline may be used as a novel non-invasive index that predicts the response to TNFi with greater accuracy than HLA-B27 status, CRP level and measures of disease activity.

Delayed TME Surgery in a Watch-and-Wait Strategy After Neoadjuvant Chemoradiotherapy for Rectal Cancer: An Analysis of Hospital Costs and Surgical and Oncological Outcomes.

BACKGROUND: A watch-and-wait strategy for patients with rectal cancer with a clinical complete response after neoadjuvant chemoradiotherapy is a valuable alternative for rectal resection. However, there are patients who will have residual tumor or regrowth during watch and wait. OBJECTIVE: The aim of this study was to investigate safety and costs for patients who underwent delayed surgery after neoadjuvant chemoradiotherapy. DESIGN: This is a retrospective cohort study with prospectively collected data. SETTINGS: The study was conducted at a large teaching hospital. PATIENTS: Between January 2015 and May 2020, 622 new rectal cancer patients were seen, of whom 200 received neoadjuvant chemoradiotherapy. Ninety-four patients were included, 65 of whom underwent immediate surgery and 29 of whom required delayed surgery after an initial watch-and-wait approach. MAIN OUTCOME MEASURES: Outcome measures included 30-day postoperative morbidity rate, hospital costs. 2-year overall and disease-free survival. RESULTS: There was no difference in length of stay (9 vs 8; p = 0.83), readmissions (27.6% vs 10.0%; p = 0.10), surgical re-interventions (15.0% vs 3.4%; p = 0.16), or stoma-free rate (52.6% vs 31.0%; p = 0.09) between immediate and delayed surgery groups. Hospital costs were similar in the delayed group (€11,913 vs €13,769; p = 0.89). Two-year overall survival (93% vs 100%; p = 0.23) and disease-free survival (78% vs 81%; p = 0.47) rates were comparable. LIMITATIONS: Limitations included small sample size, follow-up time and retrospective design. CONCLUSION: Delayed surgery for regrowth in a watch-and-wait program or for persistent residual disease after a repeated assessment is not associated with an increased risk of postoperative morbidity or a significant rise in costs compared to immediate total mesorectal excision. There also appears to be no evident compromise in oncological outcome. Repeated response assessment in patients with a near complete clinical response after neoadjuvant chemoradiotherapy is a useful approach to identify more patients who can benefit from a watch-and-wait strategy. See Video Abstract at http://links.lww.com/DCR/B836 . CIRUGA DE TME RETRASADA EN UNA ESTRATEGIA DE WATCH AND WAIT DESPUS DE LA QUIMIORRADIOTERAPIA NEOADYUVANTE PARA CNCER DE RECTO UN ANLISIS DE COSTOS HOSPITALARIOS, Y DE RESULTADOS QUIRRGICOS Y ONCOLGICOS: ANTECEDENTES: Una estrategia de Watch and Wait para pacientes con cáncer de recto con una respuesta clínica completa después de quimiorradioterapia neoadyuvante es una alternativa valiosa en vez de resección rectal. Sin embargo, hay pacientes que tendrán tumor residual o un recrecimiento durante el Watch and Wait .OBJETIVO: El objetivo fue investigar la seguridad y los costos para los pacientes que se sometieron a una cirugía diferida después de la quimiorradioterapia neoadyuvante.DISEÑO: Este es un estudio de cohorte retrospectivo con datos recolectados prospectivamente.AJUSTE: El estudio se llevó a cabo en un gran hospital universitario.PACIENTES: Entre enero de 2015 y mayo de 2020, se atendieron 622 nuevos pacientes con cáncer de recto, de los cuales 200 recibieron quimiorradioterapia neoadyuvante. Se incluyeron 94 pacientes, de los cuales 65 se sometieron a cirugía inmediata y 29 pacientes requirieron cirugía diferida después de un enfoque inicial de observación y espera.PRINCIPALES MEDIDAS DE RESULTADO: se incluyeron la tasa de morbilidad posoperatoria a 30 días, los costos hospitalarios y las sobrevidas general y libre de enfermedad a dos años.RESULTADOS: No hubo diferencia en la duración de la estancia (9 vs 8, p = 0,83), reingresos (27,6% vs 10,0%, p = 0,10), reintervenciones quirúrgicas (15,0% vs 3,4%, p = 0,16) y tasa libre de estoma (52,6% vs 31,0%, p = 0,09) entre los grupos de cirugía inmediata y tardía. Los costos hospitalarios fueron similares en el grupo retrasado (11913 € frente a 13769 €, p = 0,89). Las tasas de sobrevida general a dos años (93% frente a 100%, p = 0,23) y sobrevida libre de enfermedad (78% frente a 81%, p = 0,47) fueron comparables.LIMITACIONES: Tamaño de muestra pequeño, tiempo de seguimiento y diseño retrospectivo.CONCLUSIÓN: La cirugía tardía para el recrecimiento en un programa de Watch and Wait o para la enfermedad residual persistente después de una evaluación repetida no se asocia con un riesgo mayor de morbilidad posoperatoria ni con un aumento significativo en los costos, en comparación con la escisión total de mesorrecto inmediata. Tampoco parece haber un compromiso evidente en el resultado oncológico. La evaluación repetida de la respuesta en pacientes con una respuesta clínica casi completa después de la quimiorradioterapia neoadyuvante es un enfoque útil para identificar más pacientes que pueden beneficiarse de una estrategia de Watch and Wait . Consulte Video Resumen en http://links.lww.com/DCR/B836 . (Traducción-Dr. Juan Carlos Reyes ).

Role of Local Excision for Suspected Regrowth in a Watch and Wait Strategy for Rectal Cancer.

Rectal cancer patients with a clinical complete response to neoadjuvant (chemo)radiation are eligible for Watch and Wait (W&W). For local regrowth, total mesorectal excision (TME) is considered the standard of care. This study evaluated local excision (LE) for suspected local regrowth. From 591 patients prospectively entered into a national W&W registry, 77 patients with LE for regrowth were included. Outcomes analyzed included histopathologic findings, locoregional recurrence, long-term organ preservation, and colostomy-free and overall survival. In total, 27/77 patients underwent early LE (<6 months after neoadjuvant radiotherapy) and 50/77 underwent late LE (≥6 months). Median follow-up was 53 (39−69) months. In 28/77 patients the LE specimen was histopathologically classified as ypT0 (including 9 adenomas); 11/77 were ypT1, and 38/77 were ypT2−3. After LE, 13/77 patients with ypT2−3 and/or irradical resection underwent completion TME. Subsequently, 14/64 patients without completion TME developed locoregional recurrence, and were successfully treated with salvage TME. Another 8/77 patients developed distant metastases. At 5 years, overall organ preservation was 63%, colostomy-free survival was 68%, and overall survival was 96%. There were no differences in outcomes between early or late LE. In W&W for rectal cancer, LE can be considered as an alternative to TME for suspected regrowth in selected patients who wish to preserve their rectum or avoid colostomy in distal rectal cancer.

A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples.

The COVID-19 pandemic caused by the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological monitoring and identification of new variants, which could represent a risk of increased transmissibility, virulence, or resistance to vaccines or treatment. Different next-generation sequencing approaches are used in SARS-CoV-2 sequencing, although with different ability to provide whole genome coverage without gaps and to reliably detect new variants. In this study, we compared the performance of three target enrichment methods (two multiplex amplification methods and one hybridization capture) using nasopharyngeal swabs from infected individuals. We applied these target enrichment methods to the same set of nasopharyngeal samples (N = 93) in high-throughput mode. SARS-CoV-2 genome was obtained using short-read next-generation sequencing. We observed that each method has some advantages, such as high mapping rate (CleanPlex and COVIDSeq) or absence of systematic variant calling error (SureSelect) as well as their limitations such as suboptimal uniformity of coverage (CleanPlex), high cost (SureSelect) or supply shortages (COVIDSeq). Nevertheless, each of the three target enrichment kits tested in this study yielded acceptable results of whole SARS-CoV-2 genome sequencing and either of them can therefore be used in prospective programs of genomic surveillance of SARS-CoV-2. Genomic surveillance will be crucial to overcoming the ongoing pandemic of COVID-19, despite its successive waves and continually emerging variants.

Genetic Analysis of Lung Cancer and the Germline Impact on Somatic Mutation Burden.

BACKGROUND: Germline genetic variation contributes to lung cancer (LC) susceptibility. Previous genome-wide association studies (GWAS) have implicated susceptibility loci involved in smoking behaviors and DNA repair genes, but further work is required to identify susceptibility variants. METHODS: To identify LC susceptibility loci, a family history-based genome-wide association by proxy (GWAx) of LC (48 843 European proxy LC patients, 195 387 controls) was combined with a previous LC GWAS (29 266 patients, 56 450 controls) by meta-analysis. Colocalization was used to explore candidate genes and overlap with existing traits at discovered susceptibility loci. Polygenic risk scores (PRS) were tested within an independent validation cohort (1 666 LC patients vs 6 664 controls) using variants selected from the LC susceptibility loci and a novel selection approach using published GWAS summary statistics. Finally, the effects of the LC PRS on somatic mutational burden were explored in patients whose tumor resections have been profiled by exome (n = 685) and genome sequencing (n = 61). Statistical tests were 2-sided. RESULTS: The GWAx-GWAS meta-analysis identified 8 novel LC loci. Colocalization implicated DNA repair genes (CHEK1), metabolic genes (CYP1A1), and smoking propensity genes (CHRNA4 and CHRNB2). PRS analysis demonstrated that these variants, as well as subgenome-wide significant variants related to expression quantitative trait loci and/or smoking propensity, assisted in LC genetic risk prediction (odds ratio = 1.37, 95% confidence interval = 1.29 to 1.45; P < .001). Patients with higher genetic PRS loads of smoking-related variants tended to have higher mutation burdens in their lung tumors. CONCLUSIONS: This study has expanded the number of LC susceptibility loci and provided insights into the molecular mechanisms by which these susceptibility variants contribute to LC development.

A postzygotic de novo NCDN mutation identified in a sporadic FTLD patient results in neurochondrin haploinsufficiency and altered FUS granule dynamics.

Frontotemporal dementia (FTD) is a heterogeneous clinical disorder characterized by progressive abnormalities in behavior, executive functions, personality, language and/or motricity. A neuropathological subtype of FTD, frontotemporal lobar degeneration (FTLD)-FET, is characterized by protein aggregates consisting of the RNA-binding protein fused in sarcoma (FUS). The cause of FTLD-FET is not well understood and there is a lack of genetic evidence to aid in the investigation of mechanisms of the disease. The goal of this study was to identify genetic variants contributing to FTLD-FET and to investigate their effects on FUS pathology. We performed whole-exome sequencing on a 50-year-old FTLD patient with ubiquitin and FUS-positive neuronal inclusions and unaffected parents, and identified a de novo postzygotic nonsense variant in the NCDN gene encoding Neurochondrin (NCDN), NM_014284.3:c.1206G > A, p.(Trp402*). The variant was associated with a ~ 31% reduction in full-length protein levels in the patient's brain, suggesting that this mutation leads to NCDN haploinsufficiency. We examined the effects of NCDN haploinsufficiency on FUS and found that depleting primary cortical neurons of NCDN causes a reduction in the total number of FUS-positive cytoplasmic granules. Moreover, we found that these granules were significantly larger and more highly enriched with FUS. We then examined the effects of a loss of FUS function on NCDN in neurons and found that depleting cells of FUS leads to a decrease in NCDN protein and mRNA levels. Our study identifies the NCDN protein as a likely contributor of FTLD-FET pathophysiology. Moreover, we provide evidence for a negative feedback loop of toxicity between NCDN and FUS, where loss of NCDN alters FUS cytoplasmic dynamics, which in turn has an impact on NCDN expression.

Global Overview of Response Rates in Patient and Health Care Professional Surveys in Surgery: A Systematic Review.

OBJECTIVE: Identify key demographic factors and modes of follow-up in surgical survey response. SUMMARY BACKGROUND DATA: Surveys are widely used in surgery to assess patient and procedural outcomes, but response rates vary widely which compromises study quality. Currently there is no consensus as to what the average response rate is and which factors are associated with higher response rates. METHODS: The National Library of Medicine (MEDLINE/PubMed) was systematically searched from Januray 1, 2007 until February 1, 2020 using the following strategy: (((questionnaire) OR survey) AND "response rate") AND (surgery OR surgical). Original survey studies from surgical(-related) fields reporting on response rate were included. Through one-way analysis of variance we present mean response rate per survey mode over time, number of additional contacts, country of origin, and type of interviewee. RESULTS: The average response is 70% over 811 studies in patients and 53% over 1746 doctor surveys. In-person surveys yield an average 76% response rate, followed by postal (65%) and online (46% web-based vs 51% email) surveys. Patients respond significantly more often than doctors to surveys by mail (P < 0.001), email (P = 0.003), web-based surveys (P < 0.001) and mixed mode surveys (P = 0.006). Additional contacts significantly improve response rate in email (P = 0.26) and web-based (P = 0.041) surveys in doctors. A wide variation in response rates was identified between countries. CONCLUSIONS: Every survey is unique, but the main commonality between studies is response rate. Response rates appear to be highly dependent on type of survey, follow-up, geography, and interviewee type.

Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul.

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.

Ecological Momentary Assessment: A Field Evaluation of Subjective Ratings of Speech in Noise.

PURPOSE: As hearing rehabilitation research evolves to include both retrospective and momentary assessment outcome measures, it is important to understand how in-the-moment contextual factors influence subjective ratings. We aimed to determine, over a 4-week period of participants responding to ecological momentary assessments (EMAs) in their own environments, whether: (1) participants will complete surveys in speech-in-noise listening situations; (2) ratings of speech in noise change in a predictable manner as the acoustic conditions change; and (3) EMAs provide patient insights beyond those provided from retrospective ratings. DESIGN: Fourteen adults aged 26 to 86 years with at least 6 months of hearing aid experience were recruited for an 8-week crossover field trial (4 weeks wearing hearing aids with no EMA; 4 weeks wearing hearing aids with EMA). Participants were fitted with hearing aids and provided with a streamer and a smartphone with an app that analyzed the acoustic signal from the hearing aids and alerted the participant to respond to a survey when predetermined acoustic conditions were detected. Participants were prompted to complete brief surveys up to 9 times/day that contained establishing questions, quality ratings, and items assessing perceived benefit, residual activity limitation, and satisfaction. Participants also completed retrospective questionnaires at intake and after each 4-week field trial. RESULTS: Participants completed an average of 4.4 surveys per day. The quality ratings changed as the acoustics changed: Ratings of intelligibility were lower for 10 dB signal-to-noise ratio (SNR) than 20 dB SNR (p = 0.006); ratings of noisiness were higher for 10 dB SNR than 20 dB SNR (p = 0.001) and higher for 65 dB SPL than 50 dB SPL (p < 0.001); ratings of effort were higher for 65 dB SPL than 50 dB SPL (p = 0.004); ratings of loudness were higher for 65 dB SPL than 50 dB SPL (p = 0.001). Descriptive analysis of satisfaction, benefit, and residual activity limitation responses showed that the momentary surveys provided more detail about individual variability across acoustic conditions than the retrospective questions. CONCLUSIONS: Participants completed more than 99% of the triggered surveys, demonstrating high compliance. Because the quality ratings generally changed in the hypothesized direction, it is concluded that the participants provided valid responses. The greater variability in responses with EMA than retrospective questionnaires demonstrates its potential utility as a clinical tool for exploring hearing aid outcomes in real-world environments.

Surveys in Surgical Education: A Systematic Review and Reporting Guideline.

OBJECTIVES: Survey studies are a commonly used method for data collection in surgical education research. Nevertheless, studies investigating survey design and response rates in surgical education research are lacking. The aim of this study was to gain an insight into survey response rates among surgical residents and medical students, and provide an initial reporting guideline for future survey studies in this field. DESIGN: PubMed (MEDLINE) was systematically searched for survey studies in surgical education from January 2007 until February 2020, according to the PRISMA statements checklist. Study selection was conducted by 2 authors, independently. Surveys directed at surgical residents and/or medical students were included if data on response rates was available. Studies reporting solely from nonsurgical fields of medicine, paramedicine, or nursing were excluded. Subgroup analyses were performed, comparing response rates for varying modes of survey, per country, and for the 10 journals with the most identified surveys. RESULTS: From the 5,693 records screened for a larger surgical survey database, a total of 312 surveys were included; 173 studies focused on surgical residents and 139 on medical students. The mean (SD) response rate was 55.7% (24.7%) for surgical residents and 69.0% (20.8%) for medical students. The number of published surveys increased yearly, mostly driven by an increase in surgical resident surveys. Although most surveys were Web-based (n = 166, 53.2%), this survey mode resulted in the lowest response rates (mean 52.6%). The highest response rates, with a mean of 79.8% (13.1%), were seen in in-person surveys (n = 89, 28.5%). Wide variations in response rates were seen between different countries and journals. CONCLUSIONS: Web-based surveys are gaining popularity for medical research in general and for surgical education specifically; however, this mode results in lower response rates than those of in-person surveys. The response rate of in-person surveys is especially high when focusing on medical students. To improve reporting of survey studies, we present the first step towards a reporting guideline.

Prognostic importance of lymph node count and ratio in rectal cancer after neoadjuvant chemoradiotherapy: Results from a cross-sectional study.

BACKGROUND: The aim of this study was to determine the prognostic value of lymph node count (LNC) and lymph node ratio (LNR) in rectal cancer after neoadjuvant chemoradiotherapy (CRT). METHODS: Patients who underwent neoadjuvant CRT and total mesorectal excision (TME) for Stage I-III rectal cancer were selected from a cross-sectional study including 71 Dutch centres. Primary outcome parameters were disease-free survival (DFS) and overall survival (OS). Prognostic significance of LNC and LNR (cut-off values 0.15, 0.20, 0.30) was tested for different (sub)groups. RESULTS: From 2095 registered patients, 458 were included, of which 240 patients with LNC < 12 and 218 patients with LNC ≥ 12. LNC was not significantly associated with DFS (p = 0.35) and OS (p = 0.59). In univariable analysis, LNR was significantly associated with DFS and OS in the whole cohort and LNC subgroups, but not in multivariable analysis. CONCLUSIONS: LNC was not associated with long-term oncological outcome in rectal cancer patients treated with CRT, nor was LNR when corrected for N-stage. However, LNR might be used to identify subgroups of node-positive patients with a favourable outcome.

Region-specific expression of young small-scale duplications in the human central nervous system.

BACKGROUND: The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. RESULTS: Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. The extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. CONCLUSIONS: Overall, our study suggests the involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level.

The lncRNA 44s2 Study Applicability to the Design of 45-55 Exon Skipping Therapeutic Strategy for DMD.

In skeletal muscle, long noncoding RNAs (lncRNAs) are involved in dystrophin protein stabilization but also in the regulation of myocytes proliferation and differentiation. Hence, they could represent promising therapeutic targets and/or biomarkers for Duchenne and Becker muscular dystrophy (DMD/BMD). DMD and BMD are X-linked myopathies characterized by a progressive muscular dystrophy with or without dilatative cardiomyopathy. Two-thirds of DMD gene mutations are represented by deletions, and 63% of patients carrying DMD deletions are eligible for 45 to 55 multi-exons skipping (MES), becoming BMD patients (BMDΔ45-55). We analyzed the genomic lncRNA presence in 38 BMDΔ45-55 patients and characterized the lncRNA localized in introns 44 and 55 of the DMD gene. We highlighted that all four lncRNA are differentially expressed during myogenesis in immortalized and primary human myoblasts. In addition, the lncRNA44s2 was pointed out as a possible accelerator of differentiation. Interestingly, lncRNA44s expression was associated with a favorable clinical phenotype. These findings suggest that lncRNA44s2 could be involved in muscle differentiation process and become a potential disease progression biomarker. Based on these results, we support MES45-55 therapy and propose that the design of the CRISPR/Cas9 MES45-55 assay consider the lncRNA sequences bordering the exonic 45 to 55 deletion.

Delayed Surgery after Neoadjuvant Treatment for Rectal Cancer Does Not Lead to Impaired Quality of Life, Worry for Cancer, or Regret.

Non operative management of complete clinical responders after neoadjuvant treatment for rectal cancer enjoys an increasing popularity because of the increased functional outcome results. Even a near complete response can evolve in a cCR, and therefore further delaying response assessment is accepted. However, up to 40% of patients will develop a regrowth and will eventually require delayed surgery. It is presently unknown if and to what extent quality of life of these patients is affected, compared to patients who undergo immediate surgery. Between January 2015-May 2020, 200 patients were treated with neoadjuvant therapy of whom 94 received TME surgery. Fifty-one (59%) of 87 alive patients returned the questionnaires: 33 patients who underwent immediate and 18 patients who underwent delayed surgery. Quality of life was measured through the QLQ-C30, QLQ-CR29, and Cancer Worry Scale questionnaires. Regret to participate in repeated response assessment protocol was assessed through the Decision Regret Scale. Exploratory factor analysis (EFA) and a 'known groups comparison' was performed to assess QLQ questionnaires validity in this sample. Higher mean physical function scores (89.2 vs. 77.6, p = 0.03) were observed in the immediate surgery group, which lost significance after correction for operation type (p = 0.25). Arousal for men was higher in the delayed surgery group (20.0 vs. 57.1, p = 0.02). There were no differences between surgical groups for the other questionnaire items. Worry for cancer was lower in the delayed surgery group (10.8 vs. 14.0, p = 0.21). Regret was very low (12-16%). EFA reproduced most QLQ C-30 and CR29 subscales with good internal consistency. Quality of life is not impaired in patients undergoing delayed TME surgery after neoadjuvant treatment for rectal cancer. Moreover, there is very low regret and no increase in worry for cancer. Therefore, from a quality of life perspective, this study supports a repeated response assessment strategy after CRTx for rectal carcinoma to identify all complete responders.

Impact of pre- and post-variant filtration strategies on imputation.

Quality control (QC) methods for genome-wide association studies and fine mapping are commonly used for imputation, however they result in loss of many single nucleotide polymorphisms (SNPs). To investigate the consequences of filtration on imputation, we studied the direct effects on the number of markers, their allele frequencies, imputation quality scores and post-filtration events. We pre-phrased 1031 genotyped individuals from diverse ethnicities and compared the imputed variants to 1089 NCBI recorded individuals for additional validation. Without QC-based variant pre-filtration, we observed no impairment in the imputation of SNPs that failed QC whereas with pre-filtration there was an overall loss of information. Significant differences between frequencies with and without pre-filtration were found only in the range of very rare (5E-04-1E-03) and rare variants (1E-03-5E-03) (p < 1E-04). Increasing the post-filtration imputation quality score from 0.3 to 0.8 reduced the number of single nucleotide variants (SNVs) < 0.001 2.5 fold with or without QC pre-filtration and halved the number of very rare variants (5E-04). Thus, to maintain confidence and enough SNVs, we propose here a two-step filtering procedure which allows less stringent filtering prior to imputation and post-imputation in order to increase the number of very rare and rare variants compared to conservative filtration methods.