Single pre-operative radiation therapy (SPORT-CK) trial for low-risk breast cancer: Early results of a phase 2 study.

BACKGROUND AND PURPOSE: Preoperative partial breast irradiation (PBI) is a novel technique that can be used in patients with early-stage breast cancer with the goal of limiting the irradiated breast volume, toxicity and number of fractions. The aim of this trial is to assess the toxicity, surgical, oncologic and cosmetic outcomes of preoperative PBI. MATERIALS AND METHODS: In this single-arm phase II trial, we enrolled women ≥ 60 years, with unifocal low-risk breast invasive ductal carcinoma (cT1N0, grade 1-2, ER+, Her2-). Patients were treated with a single fraction of 20 Gy of preoperative PBI using volumetric modulated arc therapy (VMAT). Patients then underwent breast-conserving surgery (BCS) +/- sentinel lymph node biopsy within 72 h of radiation. Primary outcomes were rate of surgical complications and early toxicity. Secondary outcomes were cosmesis at 12 months, chronic toxicity and ipsilateral breast tumor recurrence. RESULTS: Twenty-five patients were recruited with a median age of 67 years, and a median follow-up of 60 months. Sentinel biopsy was positive in 1 out of 24 patients (4 %). Two patients received adjuvant RT for close margins or positive lymph nodes. Within the first 90 days, none of the patients had surgical complications; almost all had grade 0 to 1 acute and late RTOG skin toxicity. The cosmetic outcome was rated between good and excellent in all cases by physicians and patients, except for one patient who self-rated her cosmesis as fair as of the third year. There were no recurrences. CONCLUSION: Preoperative single-fraction PBI is a safe and feasible treatment for elderly patients with low-risk early-stage breast cancer, with no surgical complications, very low rates of acute and late radiation toxicity, and excellent cosmetic outcomes. Randomized controlled trials are needed to compare preoperative to adjuvant PBI in this patient population.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree.

Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map (~3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.

Improved high quality sand fly assemblies enabled by ultra low input long read sequencing.

Phlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.

Closing the gap: Solving complex medically relevant genes at scale.

Comprehending the mechanism behind human diseases with an established heritable component represents the forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or the so-called 'dark regions' of the human genome. The advent of PacBio as a long-read platform has provided new insights, yet HiFi whole-genome sequencing (WGS) cost remains frequently prohibitive. We introduce a targeted sequencing and analysis framework, Twist Alliance Dark Genes Panel (TADGP), designed to offer phased variants across 389 medically important yet complex autosomal genes. We highlight TADGP accuracy across eleven control samples and compare it to WGS. This demonstrates that TADGP achieves variant calling accuracy comparable to HiFi-WGS data, but at a fraction of the cost. Thus, enabling scalability and broad applicability for studying rare diseases or complementing previously sequenced samples to gain insights into these complex genes. TADGP revealed several candidate variants across all cases and provided insight into LPA diversity when tested on samples from rare disease and cardiovascular disease cohorts. In both cohorts, we identified novel variants affecting individual disease-associated genes (e.g., IKZF1, KCNE1). Nevertheless, the annotation of the variants across these 389 medically important genes remains challenging due to their underrepresentation in ClinVar and gnomAD. Consequently, we also offer an annotation resource to enhance the evaluation and prioritization of these variants. Overall, we can demonstrate that TADGP offers a cost-efficient and scalable approach to routinely assess the dark regions of the human genome with clinical relevance.

Potentials and limitations of a food group-based algorithm to assess dietary nutrient intake of women in rural areas in Tanzania.

The aim of this study was to evaluate the accuracy of nutrient intake assessment with the food group-based algorithm "Calculator of Inadequate Micronutrient Intake" (CIMI) in comparison to the established nutrition software NutriSurvey. Using Food Frequency Questionnaires and 24-h dietary recalls of 1010 women from two rural districts in Tanzania, 23 relevant typical Tanzanian food groups were identified and subsequently the dietary protocols assessed via CIMI algorithm were compared by bivariate correlations and Bland-Altman analysis with the results of the NutriSurvey software (reference) and were set in relation to blood biomarkers of 666 participants. CIMI and NutriSurvey calculations regarding macro- and micronutrient intakes were similar. The Bland-Altman analyses and correlation coefficients of energy (0.931), protein (0.898), iron (0.775) and zinc (0.838) confirm the agreement of both calculations. The food group based CIMI algorithm is a practical tool to identify the inadequacy of macro- and micronutrient intake at population level.

Vitamin D fortification of selected edible insect species through UVB-treatment.

Edible insects are attracting increased interest worldwide, because they are arguably more sustainable than more established animal foods. Apart from being rich in protein and minerals, they can also form vitamin D3 after treatment with UVB light (290-315 nm). However, only limited research, which has almost exclusively been conducted on living insects, reared under UVB lamps, has been done in this regard. As research on mushrooms has shown, that vitamin D formation is much more effective and less time consuming, when a previously sliced or ground product is treated with UVB light, it would likely be more practical to treat powdered insects with UVB light, rather than rearing them under UVB lamps. Therefore, the aim of this work was to confirm the presence of vitamin D3 in powdered UVB-treated yellow mealworms (Tenebrio molitor), migratory locusts (Locusta migratoria) and two-spotted crickets (Gryllus bimaculatus) as well as to subsequently quantify potential vitamin D content. Samples were analyzed via HPLC, and presence of vitamin D3 was verified via standard addition and spectrum analysis. UVB-treated migratory locusts and two-spotted crickets did not contain quantifiable amounts of vitamin D3. However, UVB-treated mealworms showed substantial amounts of vitamin D3 (8.95-18.24 µg/g dry matter). Thus, the UVB-treatment of powdered mealworm is an effective approach via which to enhance their vitamin D3 content and even modest serving sizes can supply the recommended daily intake of vitamin D.

Long-read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development.

Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease-associated variants and understand the genetic basis of many rare diseases. Long-read genome sequencing provides improved sequencing in highly repetitive, homologous, and low-complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short-read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi-generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE-VNTR-Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss-of-function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss-of-expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long-read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short-read genomic testing.

Targeted Intraoperative Radiation Therapy during Breast-Conserving Surgery for Patients with Early Stage Breast Cancer: A Phase II Single Center Prospective Trial.

Purpose: Patients with early stage breast cancer (ESBC) are conventionally treated with breast-conserving surgery (BCS) followed by whole-breast external beam radiation therapy (EBRT). The emergence of targeted intraoperative radiation therapy (TARGIT) with Intrabeam has been used as a therapeutic alternative for patients with risk-adapted ESBC. Here we present our radiation therapy toxicities (RTT), postoperative complications (PC), and short-term outcomes of the prospective phase II trial at the McGill University Health Center. Methods and Materials: Patients aged ≥50 years with biopsy-proven hormone receptor-positive, grade 1 or 2, invasive ductal carcinoma of the breast, cT1N0, were eligible for the study. Enrolled patients underwent BCS followed by immediate TARGIT of 20 Gy in 1 fraction. Upon final pathology, patients with low-risk breast cancer (LRBC) received no further EBRT, and those with high-risk breast cancer (HRBC) received further 15 to 16 fractions of whole breast EBRT. HRBC criteria included pathologic tumor size >2 cm, grade 3, positive lympho-vascular invasion, multifocal disease, close margins (<2 mm), or positive nodal disease. Results: A total of 61 patients with ESBC were enrolled in the study; upon final pathology, 40 (65.6%) had LRBC, and 21 (34.4%) had HRBC. The median follow-up was 3.9 years. The most common HRBC criteria were close margins in 66.6% (n = 14) and lymphovascular invasion in 28.6% (n = 6). No grade 4 RTT were observed in either group. The most common PC were seroma and cellulitis for both groups. The rate of locoregional recurrence was 0% in both groups. The overall survival in LRBC was 97.5% and in HRBC 95.2% with no significant differences. Deaths were nonbreast cancer related. Conclusions: In patients with ESBC undergoing BCS, the use of TARGIT shows low rates of RTT and PC complications. Moreover, our short-term outcomes show no significant difference at 3.9 years median follow-up for locoregional recurrence or overall survival between groups of patients receiving TARGIT alone or TARGIT followed by EBRT. Of all patients, 34.4% required further EBRT, most commonly due to close margins.

Comprehensive de novo mutation discovery with HiFi long-read sequencing.

BACKGROUND: Long-read sequencing (LRS) techniques have been very successful in identifying structural variants (SVs). However, the high error rate of LRS made the detection of small variants (substitutions and short indels < 20 bp) more challenging. The introduction of PacBio HiFi sequencing makes LRS also suited for detecting small variation. Here we evaluate the ability of HiFi reads to detect de novo mutations (DNMs) of all types, which are technically challenging variant types and a major cause of sporadic, severe, early-onset disease. METHODS: We sequenced the genomes of eight parent-child trios using high coverage PacBio HiFi LRS (~ 30-fold coverage) and Illumina short-read sequencing (SRS) (~ 50-fold coverage). De novo substitutions, small indels, short tandem repeats (STRs) and SVs were called in both datasets and compared to each other to assess the accuracy of HiFi LRS. In addition, we determined the parent-of-origin of the small DNMs using phasing. RESULTS: We identified a total of 672 and 859 de novo substitutions/indels, 28 and 126 de novo STRs, and 24 and 1 de novo SVs in LRS and SRS respectively. For the small variants, there was a 92 and 85% concordance between the platforms. For the STRs and SVs, the concordance was 3.6 and 0.8%, and 4 and 100% respectively. We successfully validated 27/54 LRS-unique small variants, of which 11 (41%) were confirmed as true de novo events. For the SRS-unique small variants, we validated 42/133 DNMs and 8 (19%) were confirmed as true de novo event. Validation of 18 LRS-unique de novo STR calls confirmed none of the repeat expansions as true DNM. Confirmation of the 23 LRS-unique SVs was possible for 19 candidate SVs of which 10 (52.6%) were true de novo events. Furthermore, we were able to assign 96% of DNMs to their parental allele with LRS data, as opposed to just 20% with SRS data. CONCLUSIONS: HiFi LRS can now produce the most comprehensive variant dataset obtainable by a single technology in a single laboratory, allowing accurate calling of substitutions, indels, STRs and SVs. The accuracy even allows sensitive calling of DNMs on all variant levels, and also allows for phasing, which helps to distinguish true positive from false positive DNMs.

Cutaneous T-cell lymphoma developing in surgical scars post cardiac surgery: A case study.

Cutaneous T-cell lymphomas are a class of non-Hodgkin lymphomas characterized by the infiltration of malignant T cells into the skin. Their precise pathogenesis remains incompletely understood, but persistent and specific antigen stimulation of skin-homing CD4+ memory T cells by external or internal factors, combined with an inflammatory cytokine-rich tissue microenvironment, may be critical in the development of cutaneous T-cell lymphomas. We present herein a case of primary cutaneous T-cell lymphoma arising in two surgical scars that developed 6 months post-operatively and were successfully treated with external beam radiotherapy. This case highlights the notion that primary cutaneous T-cell lymphoma can develop locally at the site of injury/foreign body within a relatively short time post trauma/surgery. This work contributes to the literature of cutaneous T-cell lymphomas arising after a trauma, surgery, or a foreign body.

Calculator for inadequate micronutrient intake for Ethiopia (CIMI-Ethiopia): Validation of the software for lactating mothers and their children under 2 years.

Early identification of inadequate intake of nutrients from a person's diet is usually crucial to prevent the development of micronutrient malnutrition. However, there is no single dietary assessment tool for Ethiopia that can assess the nutrient intake of a person from the type of food she or he consumed with a given amount. Therefore, the Calculator for Inadequate Micronutrient Intake (CIMI) application was adapted in consideration of food and nutrition contexts in Ethiopia and validated for its suitability to compute nutrient intake and identify nutrient intake inadequacy. For this, a 24-h recall quantitative dietary data of children aged 12-23 months (n = 781) and lactating mothers (n = 1086) were collected between February 15 and 30, 2017, from rural Genta Afeshum district, Tigray region, Ethiopia. An individual nutrient intake was estimated by calculating using CIMI-Ethiopia and also by NutriSurvey (NS) software for comparison. The average (mean and median) intake of energy and most nutrients and the prevalence of inadequacy calculated by the two software for the children aged 12-23 months and lactating mothers were comparable, except that of the vitamin A. The correlation coefficients for the intake results calculated by CIMI-Ethiopia and NS were between 0.85 and 0.97 for the children and between 0.5 and 0.96 for the lactating mothers' group. Most of the mean intake differences calculated by the two methods were within the acceptable limits, except for the vitamins A, D, and B12 in the Bland-Altman plots. CIMI-Ethiopia is very sensitive to identifying energy, protein, and selected micronutrients inadequacy included in this study, both for the lactating mothers (84.1%-100%) and 12-23-month-old children (77.6%-100%) group. Our results showed that CIMI-Ethiopia estimates the energy and nutrient intake, and can be also used as a screening tool to identify energy, protein, and selected micronutrients inadequacy from an individual woman's and child's diet in rural Tigray, Ethiopia.

Approaches to long-read sequencing in a clinical setting to improve diagnostic rate.

Over the past decade, advances in genetic testing, particularly the advent of next-generation sequencing, have led to a paradigm shift in the diagnosis of molecular diseases and disorders. Despite our present collective ability to interrogate more than 90% of the human genome, portions of the genome have eluded us, resulting in stagnation of diagnostic yield with existing methodologies. Here we show how application of a new technology, long-read sequencing, has the potential to improve molecular diagnostic rates. Whole genome sequencing by long reads was able to cover 98% of next-generation sequencing dead zones, which are areas of the genome that are not interpretable by conventional industry-standard short-read sequencing. Through the ability of long-read sequencing to unambiguously call variants in these regions, we discovered an immunodeficiency due to a variant in IKBKG in a subject who had previously received a negative genome sequencing result. Additionally, we demonstrate the ability of long-read sequencing to detect small variants on par with short-read sequencing, its superior performance in identifying structural variants, and thirdly, its capacity to determine genomic methylation defects in native DNA. Though the latter technical abilities have been demonstrated, we demonstrate the clinical application of this technology to successfully identify multiple types of variants using a single test.

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes.

PURPOSE: This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS: Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS: Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION: Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.

Results from Two Countries on How Thwarted Interpersonal Needs Contribute to Understanding Self-Harm.

Self-harming behavior (SHB) represents an important public health issue and is one of the most critical predictors of completed death by suicide. The current study evaluated the incremental contribution of the Interpersonal Theory of Suicide constructs of thwarted belongingness and perceived burdensomeness for the prediction of SHB beyond that associated with having a psychiatric diagnosis. Community adults from two different countries included a Portuguese sample of 414 adults, aged between 18 and 65 years (M = 45.09, SD = 13.11), and predominantly female (79%), and an American sample of 290 adults (198 men, 91 women, 1 unreported) with a mean age of 37.76 years (SD = 10.84) ranging from 20 to 71, who participated online. Results demonstrated mediation effects for perceived burdensomeness in the association of thwarted belongingness with SHB, partial mediation in the Portuguese sample and full mediation in the American sample. Findings also indicated that the interaction between thwarted belongingness and perceived burdensomeness failed to make a statistically significant contribution to the prediction of SHB. The results are discussed within the Interpersonal Theory of Suicide and its relevance for clinical practice.

Extreme weekly locoregional hypofractionated radiation in elderly women with non-metastatic breast cancer.

BACKGROUND AND PURPOSE: Breast cancer locoregional (LR) radiation in the elderly requires careful consideration between the benefits of aggressive treatment and its potential toll on these patients. Extreme weekly LR hypofractionated radiation (HFRT), delivering >5 Gy per fraction, may be better suited in such a population. It represents a good compromise between RT omission and exhaustive daily radiation. This study aims to report the local and LR control rate as well as the acute and long-term side effects of the elderly patients treated with HFRT in our institution, and to compare these results to those from the literature. MATERIALS AND METHODS: We conducted a retrospective study by reviewing medical records of elderly patients with breast cancer treated with adjuvant once-weekly LR HFRT between 2011 and 2020. Fifty patients presenting with primary non-metastatic node-positive breast tumors were included. Treatment outcomes including local/LR control and overall survival were reported. Early and late toxicity profiles were also assessed. RESULTS: After a median follow-up of 4.8 years, only one local recurrence in the chest wall occurred and there was no regional recurrence. The distant metastatic rate was 6%. The long-term recurrence-free survival rate was 80% at 5 years. The cause specific survival rate was 90% at 5 years. The overall survival rate was 69.4% and 55.5% at 3 and 5 years, respectively. There were 44 (88%) patients with Grade 1 or 2 early toxicity. There was no Grade 3 or higher acute toxicity registered. Late toxicity was mainly Grade 1 or 2 subcutaneous fibrosis, lymphoedema, and neuropathy except for one patient with Grade 3 fibrosis. CONCLUSION: Extreme LR HFRT is well tolerated with good outcomes and is a good alternative for elderly and frail patients. Our results confirm the efficacy and safety of such a regimen. Further randomized trials assessing both oncologic outcome and toxicity profile are justified.

Dimensionality of Suicide Behaviors: Results within Two Samples from Two Different Countries.

Across two countries and two languages, this research examined the multidimensional associations of suicide behaviors (i.e., life-time attempts, life-time communication of intent to others, life-time self-harming, life-time suicide notes, and current suicide ideation) and empirically relevant psychological risk factors (i.e., different facets of mental pain, perceived burdensomeness, thwarted belongingness, and acquired capability), controlling for depressive symptoms. For the Portuguese sample, two underlying dimensions emerged: an ideation dimension and a behavioral dimension, and for the Canadian sample, three dimensions emerged: an ideation dimension and two behavioral dimensions that can be viewed as a splitting of the Portuguese second dimension. Results highlight possible cultural differences between the two countries and that suicide behaviors should be viewed as a multidimensional phenomenon not as a one-dimensional continuum.

Invalidating childhood environments and nonsuicidal self-injury in university students: Depression and mental pain as potential mediators.

OBJECTIVES: The aim of this study was to evaluate the potential mediating effects of depression and psychache (i.e., extreme mental pain) on the relationship between parental invalidation and nonsuicidal self-injury (NSSI) in young adults. METHOD: A sample of 2474 university students responded to previously validated measures of current NSSI, childhood parental invalidation, depression, and psychache. RESULTS: Using a parallel mediation model, path analysis using structural equation modeling demonstrated full mediation by depression and psychache of the link between parental invalidation and NSSI. CONCLUSIONS: Findings suggest that the association between invalidating childhood environments and NSSI has the potential to be mitigated by addressing issues of depression and psychache.

The multidimensionality of suicide risk factors and criteria in a nonclinical population: Replication across two countries and two languages.

Across two countries and two languages, this research examined the multidimensional associations between suicidality (e.g., past ideation/attempts, communication of intent) and empirically important psychological risk factors (e.g., mental pain, perceived burdensomeness, thwarted belongingness). For samples of 228 Canadian and 331 Portuguese university undergraduates, four dimensions emerged in each sample with two of these, intrapersonal and interpersonal, demonstrating strong replicability across countries and languages. It was concluded that suicidality is a phenomenon that demonstrates some multidimensional similarities across cultures.

Psychache Predicts Suicide Attempter Status Change in Students Starting University.

OBJECTIVES: Unlike many investigations that focus on suicide ideation rather than suicidal behavior, the present research evaluates the merit and relative efficacy of psychache (i.e., unbearable mental pain) for predicting self-reported suicide attempts among university students who are starting university. METHOD: A sample of 516 elevated-risk undergraduates was assessed during the first three weeks of starting university and, again, 10 weeks later. RESULTS: Psychache and depression, but not hopelessness, could predict change in suicide attempter status. When measures of psychache, depression, and hopelessness were considered simultaneously, only psychache provided significant, unique predictive power. CONCLUSIONS: Findings are interpreted as supporting Shneidman's model whereby psychache is seen as the cause of suicide.

Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing.

Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.